Plant Molecular Phylogenetics and Evolutionary Genomics

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (1 October 2020) | Viewed by 95538

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Department of Evolutionary Biochemistry, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
Interests: plant molecular phylogeny and systematics; genome evolution; biodiversity; phytoplanktonic metagenome
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Dear Colleagues,

The primary aim of molecular phylogenetics is to determine the evolutionary interrelationships of living beings by comparing the structures of their information macromolecules or semantids. This approach to the ascertainment of phylogeny has undeniable advantages over the "classical" method based on the comparison of various phenotypic features, which is prone to parallel and convergent variability in different phyletic lines, especially in plants. At present, no phylogenetic study can be conducted without the use of molecular data. The progress that has now been achieved in reconstructing the phylogenetically grounded Tree of Life at different taxonomic levels has breathed life into the statement by the famous Theodosius Dobzhansky: "Nothing in biology makes sense except in the light of evolution". Now the phylogenetic approach serves as a blueprint for studies in almost all biological disciplines.

The use of the molecular genetic approach is not limited to phylogenic reconstruction and obtaining new data for systematics but is included in a wide range of studies on taxonomy, biodiversity and its conservation, biogeography, population genetics, molecular ecology, and agrobiology.

This Special Issue of Plants is open to research articles on all aspects of plant molecular evolution including molecular phylogenetics and systematics, phylogenomics, genomic biodiversity, barcoding and biogeography, molecular ecology, evo-devo, and phyloinformatics.

Prof. Dr. Alex Troitsky
Guest Editor

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Keywords

  • molecular phylogeny
  • phylogenomics
  • genomic biodiversity
  • taxonomy
  • evolutionary genomics

Published Papers (30 papers)

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18 pages, 4927 KiB  
Article
Genome-Wide Identification of the YABBY Gene Family in Seven Species of Magnoliids and Expression Analysis in Litsea
by Xuedie Liu, Xing-Yu Liao, Yu Zheng, Meng-Jia Zhu, Xia Yu, Yu-Ting Jiang, Di-Yang Zhang, Liang Ma, Xin-Yu Xu, Zhong-Jian Liu and Siren Lan
Plants 2021, 10(1), 21; https://doi.org/10.3390/plants10010021 - 24 Dec 2020
Cited by 10 | Viewed by 2630
Abstract
The YABBY gene family, specific to seed plants, encodes a class of transcription factors in the lamina maintenance and development of lateral organs. Magnoliids are sisters to the clade-containing eudicots and monocots, which have rapidly diversified among the common ancestors of these three [...] Read more.
The YABBY gene family, specific to seed plants, encodes a class of transcription factors in the lamina maintenance and development of lateral organs. Magnoliids are sisters to the clade-containing eudicots and monocots, which have rapidly diversified among the common ancestors of these three lineages. However, prior to this study, information on the function of the YABBY genes in magnoliids was extremely limited to the third major clades and the early diverging lineage of Mesangiospermae. In this study, the sum of 55 YABBY genes including five genes in INO, six in CRC, eight in YAB2, 22 in YAB5, and 14 in FIL clade were identified from seven magnoliid plants. Sequence analysis showed that all encoded YABBY protein sequences possess the highly conserved YABBY domain and C2C2 zinc-finger domain. Gene and protein structure analysis indicates that a certain number of exons were highly conserved and similar in the same class, and YABBY genes encode proteins of 71–392 amino acids and an open reading frame of 216–1179 bp in magnoliids. Additionally, the predicted molecular weight and isoelectric point of YABBY proteins in three species ranged from 7689.93 to 43578.13 and from 5.33 to 9.87, respectively. Meanwhile, the YABBY gene homolog expression of Litsea was detected at a temporal and spatial level during various developmental stages of leaf and reproductive tissues. This research could provide a brief overview of YABBY gene family evolution and its differential expression in magnoliids. Therefore, this comprehensive diversification analysis would provide a new insight into further understanding of the function of genes in seven magnoliids. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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29 pages, 3212 KiB  
Article
Molecular Phylogeny and Phylogeography of Potentilla multifida L. agg. (Rosaceae) in Northern Eurasia with Special Focus on Two Rare and Critically Endangered Endemic Species, P. volgarica and P. eversmanniana
by Ivan A. Schanzer, Alina V. Fedorova, Olga V. Shelepova and Guzyaliya F. Suleymanova
Plants 2020, 9(12), 1798; https://doi.org/10.3390/plants9121798 - 18 Dec 2020
Cited by 3 | Viewed by 2116
Abstract
The results of a molecular genetic study of Potentilla multifida agg. using two plastid markers (ndhC-trnV and psbA-trnH) and a nuclear ITS marker suggested that this group comprises a number of relatively young and incompletely differentiated species widely distributed in Northern [...] Read more.
The results of a molecular genetic study of Potentilla multifida agg. using two plastid markers (ndhC-trnV and psbA-trnH) and a nuclear ITS marker suggested that this group comprises a number of relatively young and incompletely differentiated species widely distributed in Northern Eurasia. The sequences were analyzed using tree-based (maximum likelihood) and network-based (statistical parsimony network) approaches. The plastid data suggested incomplete lineage sorting, characteristic of the group as a whole. The nuclear ITS results demonstrated quite a different pattern, with mostly conspecific accessions shaping monophyletic clades. The majority of the Potentilla sect. Multifidae species studied possess few, usually closely related plastid haplotypes, or are even monomorphic. In contrast, P. volgarica, a narrow endemic from the Volga River valley, presents plastid haplotypes belonging to two distantly related groups. Such a pattern of genetic diversity in P. volgarica may be explained by a long persistence of the species within an extremely small distribution range, on the right bank of the Volga River, most likely representing a contemporary refugium. The genealogy of plastid markers in P. volgarica suggests that this species is ancestral to P.eversmanniana, another narrow endemic from the S Urals. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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15 pages, 6847 KiB  
Article
Genome-Wide Identification of the Vacuolar H+-ATPase Gene Family in Five Rosaceae Species and Expression Analysis in Pear (Pyrus bretschneideri)
by Hongsheng Zhou, Wen Huang, Shufen Luo, Huali Hu, Yingtong Zhang, Leigang Zhang and Pengxia Li
Plants 2020, 9(12), 1661; https://doi.org/10.3390/plants9121661 - 27 Nov 2020
Cited by 4 | Viewed by 2334
Abstract
Vacuolar H+-ATPases (V-ATPase) are multi-subunit complexes that function as ATP hydrolysis-driven proton pumps. They play pivotal roles in physiological processes, such as development, metabolism, stress, and growth. However, there have been very few studies on the characterisation of V-ATPase (VHA) genes [...] Read more.
Vacuolar H+-ATPases (V-ATPase) are multi-subunit complexes that function as ATP hydrolysis-driven proton pumps. They play pivotal roles in physiological processes, such as development, metabolism, stress, and growth. However, there have been very few studies on the characterisation of V-ATPase (VHA) genes in Rosaceae species. Therefore, in the present study, we performed a genome-wide analysis and identified VHA gene family members in five Rosaceae species (Pyrus bretschneideri, Malus domestica, Prunus persica, Fragaria vesca, and Prunus mume). A total of 159 VHA genes were identified, and were classified into 13 subfamilies according to the phylogenetic analysis. The structure of VHA proteins revealed high similarity among different VHA genes within the same subgroup. Gene duplication event analysis revealed that whole-genome duplications represented the major pathway for expansion of the Pyrus bretschneideri VHA genes (PbrVHA genes). The tissue-specific expression analysis of the pear showed that 36 PbrVHA genes were expressed in major tissues. Seven PbrVHA genes were significantly downregulated when the pollen tube growth stopped. Moreover, many PbrVHA genes were differentially expressed during fruit development and storage, suggesting that VHA genes play specific roles in development and senescence. The present study provides fundamental information for further elucidating the potential roles of VHA genes during development and senescence. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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11 pages, 1349 KiB  
Article
Intragenomic Polymorphism of the ITS 1 Region of 35S rRNA Gene in the Group of Grasses with Two-Chromosome Species: Different Genome Composition in Closely Related Zingeria Species
by Alexander V. Rodionov, Alexander A. Gnutikov, Nikolai N. Nosov, Eduard M. Machs, Yulia V. Mikhaylova, Victoria S. Shneyer and Elizaveta O. Punina
Plants 2020, 9(12), 1647; https://doi.org/10.3390/plants9121647 - 25 Nov 2020
Cited by 8 | Viewed by 2291 | Correction
Abstract
Zingeria (Poaceae) is a small genus that includes Z. biebersteiniana, a diploid species with the lowest chromosome number known in plants (2n = 4) as well as hexaploid Z. kochii and tetraploid Z. pisidica, and/or Z. trichopoda species. The relationship between [...] Read more.
Zingeria (Poaceae) is a small genus that includes Z. biebersteiniana, a diploid species with the lowest chromosome number known in plants (2n = 4) as well as hexaploid Z. kochii and tetraploid Z. pisidica, and/or Z. trichopoda species. The relationship between these species and the other low-chromosomes species Colpodium versicolor are unclear. To explore the intragenomic polymorphism and genome composition of these species we examined the sequences of the internal transcribed spacer 1 of the 35S rRNA gene via NGS approach. Our study revealed six groups of ribotypes in Zingeria species. Their distribution confirmed the allopolyploid nature of Z. kochii, whose probable ancestors were Colpodium versicolor and Z. pisidica. Z. pisidica has 98% of rDNA characteristic only for this species, and about 0.3% of rDNA related to that of Z. biebersteiniana. We assume that hexaploid Z. kochii is either an old allopolyploid or a homodiploid that has lost most of the rRNA genes obtained from Z. biebersteiniana. In Z. trichopoda about 81% of rDNA is related to rDNA of Z. biebersteiniana and 19% of rDNA is derived from Poa diaphora sensu lato. The composition of the ribotypes of the two plants determined by a taxonomy specialist as Z. pisidica and Z. trichopoda is very different. Two singleton species are proposed on this base with ribotypes as discriminative characters. So, in all four studied Zingeria species, even if the morphological difference among the studied species was modest, the genomic constitution was significantly different, which suggests that these are allopolyploids that obtained genomes from different ancestors. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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17 pages, 4741 KiB  
Article
Complete Plastid Genome Sequencing of Eight Species from Hansenia, Haplosphaera and Sinodielsia (Apiaceae): Comparative Analyses and Phylogenetic Implications
by Wei Gou, Sheng-Bin Jia, Megan Price, Xian-Lin Guo, Song-Dong Zhou and Xing-Jin He
Plants 2020, 9(11), 1523; https://doi.org/10.3390/plants9111523 - 9 Nov 2020
Cited by 19 | Viewed by 2244
Abstract
Hansenia Turcz., Haplosphaera Hand.-Mazz. and Sinodielsia H.Wolff are three Apiaceae genera endemic to the Hengduan Mountains and the Himalayas, which usually inhabit elevations greater than 2000 m. The phylogenetic relationships between and within the genera were uncertain, especially the placement of Hap. himalayensis [...] Read more.
Hansenia Turcz., Haplosphaera Hand.-Mazz. and Sinodielsia H.Wolff are three Apiaceae genera endemic to the Hengduan Mountains and the Himalayas, which usually inhabit elevations greater than 2000 m. The phylogenetic relationships between and within the genera were uncertain, especially the placement of Hap. himalayensis and S. microloba. Therefore, we aimed to conduct comparative (simple sequence repeat (SSR) structure, codon usage bias, nucleotide diversity (Pi) and inverted repeat (IR) boundaries) and phylogenetic analyses of Hansenia, Haplosphaera and Sinodielsia (also compared with Chamaesium and Bupleurum) to reduce uncertainties in intergeneric and interspecific relationships. We newly assembled eight plastid genomes from Hansenia, Haplosphaera and Sinodielsia species, and analyzed them with two plastid genomes from GenBank of Hap. phaea,S. yunnanensis. Phylogenetic analyses used these ten genomes and another 22 plastid genome sequences of Apiaceae. We found that the newly assembled eight genomes ranged from 155,435 bp to 157,797 bp in length and all had a typical quadripartite structure. Fifty-five to 75 SSRs were found in Hansenia, Haplosphaera and Sinodielsia species, and the most abundant SSR was mononucleotide, which accounted for 58.47% of Hansenia, 60.21% of Haplosphaera and 48.01% of Sinodielsia. There was no evident divergence of codon usage frequency between the three genera, where codons ranged from 21,134 to 21,254. The Pi analysis showed that trnE(UUC)-trnT(GGU), trnH(GUG)-psbA and trnE(UUC)-trnT(GGU) spacer regions had the highest Pi values in the plastid genomes of Hansenia (0.01889), Haplosphaera (0.04333) and Sinodielsia (0.01222), respectively. The ndhG-ndhI spacer regions were found in all three genera to have higher diversity values (Pi values: 0.01028–0.2), and thus may provide potential DNA barcodes in phylogenetic analysis. IR boundary analysis showed that the length of rps19 and ycf1 genes entering IRs were usually stable in the same genus. Our phylogenetic tree demonstrated that Hap. himalayensis is sister to Han. weberbaueriana; meanwhile, Haplosphaera and Hansenia are nested together in the East Asia clade, and S. microloba is nested within individuals of S. yunnanensis in the Acronema clade. This study will enrich the complete plastid genome dataset of the Apiaceae genera and has provided a new insight into phylogeny reconstruction using complete plastid genomes of Hansenia, Haplosphaera and Sinodielsia. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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17 pages, 4249 KiB  
Article
Genetic Diversity of Aquatic Ranunculus (Batrachium, Ranunculaceae) in One River Basin Caused by Hybridization
by Jurgita Butkuvienė, Zofija Sinkevičienė, Donatas Naugžemys, Donatas Žvingila, Audrius Skridaila and Alexander A. Bobrov
Plants 2020, 9(11), 1455; https://doi.org/10.3390/plants9111455 - 28 Oct 2020
Cited by 8 | Viewed by 2236
Abstract
Aquatic Ranunculus (sect. Batrachium) include homophyllous and heterophyllous plants. The development of floating leaves may be induced by genetic mechanisms or/and environmental conditions and this fact complicates the morphologically based identification of species. DNA-based studies provide the opportunity to expand the knowledge [...] Read more.
Aquatic Ranunculus (sect. Batrachium) include homophyllous and heterophyllous plants. The development of floating leaves may be induced by genetic mechanisms or/and environmental conditions and this fact complicates the morphologically based identification of species. DNA-based studies provide the opportunity to expand the knowledge of this complicated group. We studied heterophyllous Ranunculus with well-developed capillary and intermediate leaves and visually homophyllous plants with capillary leaves from a single river basin, with the aim to evaluate their genetic polymorphism and taxonomic status—whether the plants with well-developed and weakly expressed intermediate leaves belong to different forms (taxa) or if they just express morphological variation of one or two taxa in a specific, very variable river environment. The studied heterophyllous and homophyllous plants from different rivers showed high genetic differentiation and a low level of genetic diversity within these groups. The molecular analysis did not reveal any inter simple sequence repeat (ISSR) polymorphism associated with the development of intermediate leaves. An analysis of nuclear ribosomal internal transcribed spacers ITS1–2 sequences revealed several ribotypes, which indicated the genetic heterogeneity of studied plants and indirectly confirmed the hybrid origin of some of them. Sterile plants originated from crossing of R. circinatus and R. penicillatus were discovered in the Skroblus River; however, identification of the parental species was impeded by the polymorphism detected. For this reason, cytological studies were performed and allowed confirmation of the hybrid origin of these plants. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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19 pages, 2494 KiB  
Article
Genome Wide Identification and Comparative Analysis of the Serpin Gene Family in Brachypodium and Barley
by Shazia Rehman, Bodil Jørgensen, Ejaz Aziz, Riffat Batool, Samar Naseer and Søren K. Rasmussen
Plants 2020, 9(11), 1439; https://doi.org/10.3390/plants9111439 - 26 Oct 2020
Cited by 9 | Viewed by 2694
Abstract
Serpins (serine protease inhibitors) constitute one of the largest and most widely distributed superfamilies of protease inhibitors and have been identified in nearly all organisms. To gain significant insights, a comprehensive in silico analysis of the serpin gene family was carried out in [...] Read more.
Serpins (serine protease inhibitors) constitute one of the largest and most widely distributed superfamilies of protease inhibitors and have been identified in nearly all organisms. To gain significant insights, a comprehensive in silico analysis of the serpin gene family was carried out in the model plant for temperate grasses Brachypodium distachyon and barley Hordeum vulgare using bioinformatic tools at the genome level for the first time. We identified a total of 27 BdSRPs and 25 HvSRP genes in Brachypodium and barley, respectively, showing an unexpectedly high gene number in these model plants. Gene structure, conserved motifs and phylogenetic comparisons of serpin genes supported the role of duplication events in the expansion and evolution of serpin gene family. Further, purifying selection pressure was found to be a main driving force in the evolution of serpin genes. Genome synteny analysis indicated that BdSRP genes were present in syntenic regions of barley, rice, sorghum and maize, suggesting that they evolved before the divergence of these species from common ancestor. The distinct expression pattern in specific tissues further suggested a specialization of functions during development and in plant defense. These results suggest that the LR serpins (serpins with Leu-Arg residues at P2–P1′) identified here can be utilized as candidates for exploitation in disease resistance, pest control and preventing stress-induced cell death. Additionally, serpins were identified that could lead to further research aimed at validating and functionally characterizing the role of potential serpin genes from other plants. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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16 pages, 5435 KiB  
Article
Identification, Evolutionary and Expression Analysis of PYL-PP2C-SnRK2s Gene Families in Soybean
by Zhaohan Zhang, Shahid Ali, Tianxu Zhang, Wanpeng Wang and Linan Xie
Plants 2020, 9(10), 1356; https://doi.org/10.3390/plants9101356 - 14 Oct 2020
Cited by 29 | Viewed by 3372
Abstract
Abscisic acid (ABA) plays a crucial role in various aspects of plant growth and development, including fruit development and ripening, seed dormancy, and involvement in response to various environmental stresses. In almost all higher plants, ABA signal transduction requires three core components; namely, [...] Read more.
Abscisic acid (ABA) plays a crucial role in various aspects of plant growth and development, including fruit development and ripening, seed dormancy, and involvement in response to various environmental stresses. In almost all higher plants, ABA signal transduction requires three core components; namely, PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs), and class III SNF-1-related protein kinase 2 (SnRK2s). The exploration of these three core components is not comprehensive in soybean. This study identified the GmPYL-PP2C-SnRK2s gene family members by using the JGI Phytozome and NCBI database. The gene family composition, conservation, gene structure, evolutionary relationship, cis-acting elements of promoter regions, and its coding protein domains were analyzed. In the entire genome of the soybean, there are 21 PYLs, 36 PP2Cs, and 21 SnRK2s genes; further, by phylogenetic and conservation analysis, 21 PYLs genes are classified into 3 groups, 36 PP2Cs genes are classified into seven groups, and 21 SnRK2s genes are classified into 3 groups. The conserved motifs and domain analysis showed that all the GmPYLs gene family members contain START-like domains, the GmPP2Cs gene family contains PP2Cc domains, and the GmSnRK2s gene family contains S_TK domains, respectively. Furthermore, based on the high-throughput transcriptome sequencing data, the results showed differences in the expression patterns of GmPYL-PP2C-SnRK2s gene families in different tissue parts of the same variety, and the same tissue part of different varieties. Our study provides a basis for further elucidation of the identification of GmPYL-PP2C-SnRK2s gene family members and analysis of their evolution and expression patterns, which helps to understand the molecular mechanism of soybean response to abiotic stress. In addition, this provides a conceptual basis for future studies of the soybean ABA core signal pathway. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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15 pages, 4524 KiB  
Article
Complete Chloroplast Genome of Argania spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae
by Slimane Khayi, Fatima Gaboun, Stacy Pirro, Tatiana Tatusova, Abdelhamid El Mousadik, Hassan Ghazal and Rachid Mentag
Plants 2020, 9(10), 1354; https://doi.org/10.3390/plants9101354 - 13 Oct 2020
Cited by 19 | Viewed by 3320
Abstract
Argania spinosa (Sapotaceae), an important endemic Moroccan oil tree, is a primary source of argan oil, which has numerous dietary and medicinal proprieties. The plant species occupies the mid-western part of Morocco and provides great environmental and socioeconomic benefits. The complete chloroplast (cp) [...] Read more.
Argania spinosa (Sapotaceae), an important endemic Moroccan oil tree, is a primary source of argan oil, which has numerous dietary and medicinal proprieties. The plant species occupies the mid-western part of Morocco and provides great environmental and socioeconomic benefits. The complete chloroplast (cp) genome of A. spinosa was sequenced, assembled, and analyzed in comparison with those of two Sapotaceae members. The A. spinosa cp genome is 158,848 bp long, with an average GC content of 36.8%. The cp genome exhibits a typical quadripartite and circular structure consisting of a pair of inverted regions (IR) of 25,945 bp in length separating small single-copy (SSC) and large single-copy (LSC) regions of 18,591 and 88,367 bp, respectively. The annotation of A. spinosa cp genome predicted 130 genes, including 85 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. A total of 44 long repeats and 88 simple sequence repeats (SSR) divided into mononucleotides (76), dinucleotides (7), trinucleotides (3), tetranucleotides (1), and hexanucleotides (1) were identified in the A. spinosa cp genome. Phylogenetic analyses using the maximum likelihood (ML) method were performed based on 69 protein-coding genes from 11 species of Ericales. The results confirmed the close position of A. spinosa to the Sideroxylon genus, supporting the revisiting of its taxonomic status. The complete chloroplast genome sequence will be valuable for further studies on the conservation and breeding of this medicinally and culinary important species and also contribute to clarifying the phylogenetic position of the species within Sapotaceae. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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18 pages, 6977 KiB  
Article
Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade
by Zhihua Wu, Hong Liu, Wen Huang, Lisha Yi, Erdai Qin, Tiange Yang, Jing Wang and Rui Qin
Plants 2020, 9(9), 1178; https://doi.org/10.3390/plants9091178 - 11 Sep 2020
Cited by 9 | Viewed by 3226
Abstract
RWP-RK is a plant-specific family of transcription factors, involved in nitrate response, gametogenesis, and nodulation. However, genome-wide characterization, phylogeny, and the regulation of RWP-RK genes in the nodulating and non-nodulating plant species of nitrogen-fixing clade (NFC) are widely unknown. Therefore, we identified a [...] Read more.
RWP-RK is a plant-specific family of transcription factors, involved in nitrate response, gametogenesis, and nodulation. However, genome-wide characterization, phylogeny, and the regulation of RWP-RK genes in the nodulating and non-nodulating plant species of nitrogen-fixing clade (NFC) are widely unknown. Therefore, we identified a total of 292 RWP-RKs, including 278 RWP-RKs from 25 NFC species and 14 RWP-RKs from the outgroup, Arabidopsis thaliana. We classified the 292 RWP-RKs in two subfamilies: the NIN-like proteins (NLPs) and the RWP-RK domain proteins (RKDs). The transcriptome and phylogenetic analysis of RWP-RKs suggested that, compared to RKD genes, the NLP genes were just upregulated in nitrate response and nodulation. Moreover, nodule-specific NLP genes of some nodulating NFC species may have a common ancestor (OG0002084) with AtNLP genes in A. thaliana. Further, co-expression networks of A.thaliana under N-starvation and N-supplementation conditions revealed that there is a higher correlation between expression of AtNLP genes and symbiotic genes during N-starvation. In P. vulgaris, we confirmed that N-starvation stimulated nodulation by regulating expression of PvNLP2, closely related to AtNLP6 and AtNLP7 with another common origin (OG0004041). Taken together, we concluded that different origins of the NLP genes involved in both N-starvation response and specific expression of nodulation would contribute to the evolution of nodulation in NFC plant species. Our results shed light on the phylogenetic relationships of NLP genes and their differential regulation in nitrate response of A. thaliana and nodulation of NFC. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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21 pages, 3708 KiB  
Article
The East Asian Winter Monsoon Acts as a Major Selective Factor in the Intraspecific Differentiation of Drought-Tolerant Nitraria tangutorum in Northwest China
by Hengxia Yin, Lirong Wang, Yong Shi, Chaoju Qian, Huakun Zhou, Wenying Wang, Xiao-Fei Ma, Lam-Son Phan Tran and Benyin Zhang
Plants 2020, 9(9), 1100; https://doi.org/10.3390/plants9091100 - 27 Aug 2020
Cited by 9 | Viewed by 2641
Abstract
The influence of Quaternary climate fluctuation on the geographical structure and genetic diversity of species distributed in the regions of the Qinghai–Tibet Plateau (QTP) has been well established. However, the underlying role of the East Asian monsoon system (EAMS) in shaping the genetic [...] Read more.
The influence of Quaternary climate fluctuation on the geographical structure and genetic diversity of species distributed in the regions of the Qinghai–Tibet Plateau (QTP) has been well established. However, the underlying role of the East Asian monsoon system (EAMS) in shaping the genetic structure of the population and the demography of plants located in the arid northwest of China has not been explored. In the present study, Nitraria tangutorum, a drought-tolerant desert shrub that is distributed in the EAMS zone and has substantial ecological and economic value, was profiled to better understand the influence of EAMS evolution on its biogeographical patterns and demographic history. Thus, the phylogeographical structure and historical dynamics of this plant species were elucidated using its five chloroplast DNA (cpDNA) fragments. Hierarchical structure analysis revealed three distinct, divergent lineages: West, East-A, and East-B. The molecular dating was carried out using a Bayesian approach to estimate the time of intraspecies divergence. Notably, the eastern region, which included East-A and East-B lineages, was revealed to be the original center of distribution and was characterized by a high level of genetic diversity, with the intraspecific divergence time dated to be around 2.53 million years ago (Ma). These findings, combined with the data obtained by ecological niche modeling analysis, indicated that the East lineages have undergone population expansion and differentiation, which were closely correlated with the development of the EAMS, especially the East Asian winter monsoon (EAWM). The West lineage appears to have originated from the migration of N. tangutorum across the Hexi corridor at around 1.85 Ma, and subsequent colonization of the western region. These results suggest that the EAWM accelerated the population expansion of N. tangutorum and subsequent intraspecific differentiation. These findings collectively provide new information on the impact of the evolution of the EAMS on intraspecific diversification and population demography of drought-tolerant plant species in northwest China. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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22 pages, 2333 KiB  
Article
The Phylogeny of Class B Flavoprotein Monooxygenases and the Origin of the YUCCA Protein Family
by Igor I. Turnaev, Konstantin V. Gunbin, Valentin V. Suslov, Ilya R. Akberdin, Nikolay A. Kolchanov and Dmitry A. Afonnikov
Plants 2020, 9(9), 1092; https://doi.org/10.3390/plants9091092 - 25 Aug 2020
Cited by 5 | Viewed by 3279
Abstract
YUCCA (YUCCA flavin-dependent monooxygenase) is one of the two enzymes of the main auxin biosynthesis pathway (tryptophan aminotransferase enzyme (TAA)/YUCCA) in land plants. The evolutionary origin of the YUCCA family is currently controversial: YUCCAs are assumed to have emerged via a horizontal gene [...] Read more.
YUCCA (YUCCA flavin-dependent monooxygenase) is one of the two enzymes of the main auxin biosynthesis pathway (tryptophan aminotransferase enzyme (TAA)/YUCCA) in land plants. The evolutionary origin of the YUCCA family is currently controversial: YUCCAs are assumed to have emerged via a horizontal gene transfer (HGT) from bacteria to the most recent common ancestor (MRCA) of land plants or to have inherited it from their ancestor, the charophyte algae. To refine YUCCA origin, we performed a phylogenetic analysis of the class B flavoprotein monooxygenases and comparative analysis of the sequences belonging to different families of this protein class. We distinguished a new protein family, named type IIb flavin-containing monooxygenases (FMOs), which comprises homologs of YUCCA from Rhodophyta, Chlorophyta, and Charophyta, land plant proteins, and FMO-E, -F, and -G of the bacterium Rhodococcus jostii RHA1. The type IIb FMOs differ considerably in the sites and domain composition from the other families of class B flavoprotein monooxygenases, YUCCAs included. The phylogenetic analysis also demonstrated that the type IIb FMO clade is not a sibling clade of YUCCAs. We have also identified the bacterial protein group named YUC-like FMOs as the closest to YUCCA homologs. Our results support the hypothesis of the emergence of YUCCA via HGT from bacteria to MRCA of land plants. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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20 pages, 2149 KiB  
Article
Framework Phylogeny, Evolution and Complex Diversification of Chinese Oaks
by Jia Yang, Yu-Fan Guo, Xiao-Dan Chen, Xiao Zhang, Miao-Miao Ju, Guo-Qing Bai, Zhan-Lin Liu and Gui-Fang Zhao
Plants 2020, 9(8), 1024; https://doi.org/10.3390/plants9081024 - 13 Aug 2020
Cited by 7 | Viewed by 3120
Abstract
Oaks (Quercus L.) are ideal models to assess patterns of plant diversity. We integrated the sequence data of five chloroplast and two nuclear loci from 50 Chinese oaks to explore the phylogenetic framework, evolution and diversification patterns of the Chinese oak’s lineage. [...] Read more.
Oaks (Quercus L.) are ideal models to assess patterns of plant diversity. We integrated the sequence data of five chloroplast and two nuclear loci from 50 Chinese oaks to explore the phylogenetic framework, evolution and diversification patterns of the Chinese oak’s lineage. The framework phylogeny strongly supports two subgenera Quercus and Cerris comprising four infrageneric sections Quercus, Cerris, Ilex and Cyclobalanopsis for the Chinese oaks. An evolutionary analysis suggests that the two subgenera probably split during the mid-Eocene, followed by intergroup divergence within the subgenus Cerris around the late Eocene. The initial diversification of sections in the subgenus Cerris was dated between the mid-Oligocene and the Oligocene–Miocene boundary, while a rapid species radiation in section Quercus started in the late Miocene. Diversification simulations indicate a potential evolutionary shift on section Quercus, while several phenotypic shifts likely occur among all sections. We found significant negative correlations between rates of the lineage diversification and phenotypic turnover, suggesting a complex interaction between the species evolution and morphological divergence in Chinese oaks. Our infrageneric phylogeny of Chinese oaks accords with the recently proposed classification of the genus Quercus. The results point to tectonic activity and climatic change during the Tertiary as possible drivers of evolution and diversification in the Chinese oak’s lineage. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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13 pages, 3319 KiB  
Article
The First Genetic Map for a Psoraleoid Legume (Bituminaria bituminosa) Reveals Highly Conserved Synteny with Phaseoloid Legumes
by Matthew N. Nelson, Jafar S. Jabbari, Rust Turakulov, Aneeta Pradhan, Maria Pazos-Navarro, Jacob S. Stai, Steven B. Cannon and Daniel Real
Plants 2020, 9(8), 973; https://doi.org/10.3390/plants9080973 - 31 Jul 2020
Cited by 3 | Viewed by 2714
Abstract
We present the first genetic map of tedera (Bituminaria bituminosa (L.) C.H. Stirton), a drought-tolerant forage legume from the Canary Islands with useful pharmaceutical properties. It is also the first genetic map for any species in the tribe Psoraleeae (Fabaceae). The map [...] Read more.
We present the first genetic map of tedera (Bituminaria bituminosa (L.) C.H. Stirton), a drought-tolerant forage legume from the Canary Islands with useful pharmaceutical properties. It is also the first genetic map for any species in the tribe Psoraleeae (Fabaceae). The map comprises 2042 genotyping-by-sequencing (GBS) markers distributed across 10 linkage groups, consistent with the haploid chromosome count for this species (n = 10). Sequence tags from the markers were used to find homologous matches in the genome sequences of the closely related species in the Phaseoleae tribe: soybean, common bean, and cowpea. No tedera linkage groups align in their entirety to chromosomes in any of these phaseoloid species, but there are long stretches of collinearity that could be used in tedera research for gene discovery purposes using the better-resourced phaseoloid species. Using Ks analysis of a tedera transcriptome against five legume genomes provides an estimated divergence time of 17.4 million years between tedera and soybean. Genomic information and resources developed here will be invaluable for breeding tedera varieties for forage and pharmaceutical purposes. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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14 pages, 4475 KiB  
Article
Phylogeny and Comparative Analysis of Chinese Chamaesium Species Revealed by the Complete Plastid Genome
by Xian-Lin Guo, Hong-Yi Zheng, Megan Price, Song-Dong Zhou and Xing-Jin He
Plants 2020, 9(8), 965; https://doi.org/10.3390/plants9080965 - 30 Jul 2020
Cited by 15 | Viewed by 3020
Abstract
Chamaesium H. Wolff (Apiaceae, Apioideae) is a small genus mainly distributed in the Hengduan Mountains and the Himalayas. Ten species of Chamaesium have been described and nine species are distributed in China. Recent advances in molecular phylogenetics have revolutionized our understanding of Chinese [...] Read more.
Chamaesium H. Wolff (Apiaceae, Apioideae) is a small genus mainly distributed in the Hengduan Mountains and the Himalayas. Ten species of Chamaesium have been described and nine species are distributed in China. Recent advances in molecular phylogenetics have revolutionized our understanding of Chinese Chamaesium taxonomy and evolution. However, an accurate phylogenetic relationship in Chamaesium based on the second-generation sequencing technology remains poorly understood. Here, we newly assembled nine plastid genomes from the nine Chinese Chamaesium species and combined these genomes with eight other species from five genera to perform a phylogenic analysis by maximum likelihood (ML) using the complete plastid genome and analyzed genome structure, GC content, species pairwise Ka/Ks ratios and the simple sequence repeat (SSR) component. We found that the nine species’ plastid genomes ranged from 152,703 bp (C. thalictrifolium) to 155,712 bp (C. mallaeanum), and contained 133 genes, 34 SSR types and 585 SSR loci. We also found 20,953–21,115 codons from 53 coding sequence (CDS) regions, 38.4–38.7% GC content of the total genome and low Ka/Ks (0.27–0.43) ratios of 53 aligned CDS. These results will facilitate our further understanding of the evolution of the genus Chamaesium. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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20 pages, 13329 KiB  
Article
Genome-Wide Identification and Expression Profile Analysis of the Phospholipase C Gene Family in Wheat (Triticum aestivum L.)
by Xianguo Wang, Yang Liu, Zheng Li, Xiang Gao, Jian Dong, Jiacheng Zhang, Longlong Zhang, Linda S. Thomashow, David M. Weller and Mingming Yang
Plants 2020, 9(7), 885; https://doi.org/10.3390/plants9070885 - 13 Jul 2020
Cited by 16 | Viewed by 3780
Abstract
Phospholipid-hydrolyzing enzymes include members of the phospholipase C (PLC) family that play important roles in regulating plant growth and responding to stress. In the present study, a systematic in silico analysis of the wheat PLC gene family revealed a total of 26 wheat [...] Read more.
Phospholipid-hydrolyzing enzymes include members of the phospholipase C (PLC) family that play important roles in regulating plant growth and responding to stress. In the present study, a systematic in silico analysis of the wheat PLC gene family revealed a total of 26 wheat PLC genes (TaPLCs). Phylogenetic and sequence alignment analyses divided the wheat PLC genes into 2 subfamilies, TaPI-PLC (containing the typical X, Y, and C2 domains) and TaNPC (containing a phosphatase domain). TaPLC expression patterns differed among tissues, organs, and under abiotic stress conditions. The transcript levels of 8 TaPLC genes were validated through qPCR analyses. Most of the TaPLC genes were sensitive to salt stress and were up-regulated rapidly, and some were sensitive to low temperatures and drought. Overexpression of TaPI-PLC1-2B significantly improved resistance to salt and drought stress in Arabidopsis, and the primary root of P1-OE was significantly longer than that of the wild type under stress conditions. Our results not only provide comprehensive information for understanding the PLC gene family in wheat, but can also provide a solid foundation for functional characterization of the wheat PLC gene family. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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18 pages, 4064 KiB  
Article
The Complete Chloroplast Genome Sequencing and Comparative Analysis of Reed Canary Grass (Phalaris arundinacea) and Hardinggrass (P. aquatica)
by Yi Xiong, Yanli Xiong, Shangang Jia and Xiao Ma
Plants 2020, 9(6), 748; https://doi.org/10.3390/plants9060748 - 14 Jun 2020
Cited by 10 | Viewed by 3000
Abstract
There are 22 species in the Phalaris genera that distribute almost all over the temperate regions of the world. Among them, reed canary grass (Phalaris arundinacea, tetraploid and hexaploid) and hardinggrass (P. aquatica, tetraploid) have been long cultivated as [...] Read more.
There are 22 species in the Phalaris genera that distribute almost all over the temperate regions of the world. Among them, reed canary grass (Phalaris arundinacea, tetraploid and hexaploid) and hardinggrass (P. aquatica, tetraploid) have been long cultivated as forage grass and have received attention as bio-energy materials in recent years. We aimed to facilitate inter-species/ploidies comparisons, and to illuminate the degree of sequence variation within existing gene pools, chloroplast (cp) genomes of three Phalaris cytotypes (P. aquatica/4x, P. arundinacea/4x and P. arundinacea/6x) were sequenced and assembled. The result indicated that certain sequence variations existed between the cp genomes of P. arundinacea and P. aquatica. Several hotspot regions (atpI~atpH, trnT-UGU~ndhJ, rbcL~psaI, and ndhF~rpl32) were found, and variable genes (infA, psaI, psbK, etc.) were detected. SNPs (single nucleotide polymorphisms) and/or indels (insertions and deletions) were confirmed by the high Ka/Ks and Pi value. Furthermore, distribution and presence of cp simple sequence repeats (cpSSRs) were identified in the three Phalaris cp genomes, although little difference was found between hexaploid and tetraploid P. arundinacea, and no rearrangement was detected among the three Phalaris cp genomes. The evolutionary relationship and divergent time among these species were discussed. The RNA-seq revealed several differentially expressed genes (DEGs), among which psaA, psaB, and psbB related to leaf color were further verified by leaf color differences. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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23 pages, 3559 KiB  
Article
Transcriptome Analysis of Jojoba (Simmondsia chinensis) during Seed Development and Liquid Wax Ester Biosynthesis
by Saqer S. Alotaibi, Mona M. Elseehy, Bandar S. Aljuaid and Ahmed M. El-Shehawi
Plants 2020, 9(5), 588; https://doi.org/10.3390/plants9050588 - 4 May 2020
Cited by 17 | Viewed by 3337
Abstract
Jojoba is one of the main two known plant source of natural liquid wax ester for use in various applications, including cosmetics, pharmaceuticals, and biofuel. Due to the lack of transcriptomic and genomic data on lipid biosynthesis and accumulation, molecular marker breeding has [...] Read more.
Jojoba is one of the main two known plant source of natural liquid wax ester for use in various applications, including cosmetics, pharmaceuticals, and biofuel. Due to the lack of transcriptomic and genomic data on lipid biosynthesis and accumulation, molecular marker breeding has been used to improve jojoba oil production and quality. In the current study, the transcriptome of developing jojoba seeds was investigated using the Illunina NovaSeq 6000 system, 100 × 106 paired end reads, an average length of 100 bp, and a sequence depth of 12 Gb per sample. A total of 176,106 unigenes were detected with an average contig length of 201 bp. Gene Ontology (GO) showed that the detected unigenes were distributed in the three GO groups biological processes (BP, 5.53%), cellular component (CC, 6.06%), and molecular functions (MF, 5.88%) and distributed in 67 functional groups. The lipid biosynthesis pathway was established based on the expression of lipid biosynthesis genes, fatty acid (FA) biosynthesis, FA desaturation, FA elongation, fatty alcohol biosynthesis, triacylglycerol (TAG) biosynthesis, phospholipid metabolism, wax ester biosynthesis, and lipid transfer and storage genes. The detection of these categories of genes confirms the presence of an efficient lipid biosynthesis and accumulation system in developing jojoba seeds. The results of this study will significantly enhance the current understanding of wax ester biology in jojoba seeds and open new routes for the improvement of jojoba oil production and quality through biotechnology applications. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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20 pages, 5344 KiB  
Article
Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship
by Jun Li, Deng-Feng Xie, Xian-Lin Guo, Zhen-Ying Zheng, Xing-Jin He and Song-Dong Zhou
Plants 2020, 9(4), 543; https://doi.org/10.3390/plants9040543 - 22 Apr 2020
Cited by 28 | Viewed by 3714
Abstract
Bupleurum L. (Apiaceae) is a perennial and herbal genus, most species of which have high medicinal value. However, few studies have been performed using plastome data in this genus, and the phylogenetic relationships have always been controversial. In this study, the plastid genomes [...] Read more.
Bupleurum L. (Apiaceae) is a perennial and herbal genus, most species of which have high medicinal value. However, few studies have been performed using plastome data in this genus, and the phylogenetic relationships have always been controversial. In this study, the plastid genomes of Bupleurum chinense and Bupleurum commelynoideum were sequenced, and their gene content, order, and structure were counted and analyzed. The only three published Bupleurum species (B. boissieuanum, B. falcatum, and B. latissimum) and other fifteen allied species were selected to conduct a series of comparative and phylogenetic analyses. The genomes of B. chinense and B. commelynoideum were 155,869 and 155,629 bp in length, respectively, both of which had a typical quadripartite structure. The genome length, structure, guanine and cytosine (GC) content, and gene distribution were highly similar to the other three Bupleurum species. The five Bupleurum species had nearly the same codon usages, and eight regions (petN-psbM, rbcL-accD, ccsA-ndhD, trnK(UUU)-rps16, rpl32-trnL(UAG)-ccsA, petA-psbJ, ndhF-rpl32, and trnP(UGG)-psaJ-rpl33) were found to possess relatively higher nucleotide diversity, which may be the promising DNA barcodes in Bupleurum. Phylogenetic analysis revealed that all Bupleurum species clustered into a monophyletic clade with high bootstrap support and diverged after the Chamaesium clade. Overall, our study provides new insights into DNA barcoding and phylogenetic relationship between Bupleurum and its related genera, and will facilitate the population genomics, conservation genetics, and phylogenetics of Bupleurum in Apiaceae. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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19 pages, 3817 KiB  
Article
The Complete Chloroplast Genome of Two Important Annual Clover Species, Trifolium alexandrinum and T. resupinatum: Genome Structure, Comparative Analyses and Phylogenetic Relationships with Relatives in Leguminosae
by Yanli Xiong, Yi Xiong, Jun He, Qingqing Yu, Junming Zhao, Xiong Lei, Zhixiao Dong, Jian Yang, Yan Peng, Xinquan Zhang and Xiao Ma
Plants 2020, 9(4), 478; https://doi.org/10.3390/plants9040478 - 9 Apr 2020
Cited by 22 | Viewed by 3504
Abstract
Trifolium L., which belongs to the IR lacking clade (IRLC), is one of the largest genera in the Leguminosae and contains several economically important fodder species. Here, we present whole chloroplast (cp) genome sequencing and annotation of two important annual grasses, Trifolium alexandrinum [...] Read more.
Trifolium L., which belongs to the IR lacking clade (IRLC), is one of the largest genera in the Leguminosae and contains several economically important fodder species. Here, we present whole chloroplast (cp) genome sequencing and annotation of two important annual grasses, Trifolium alexandrinum (Egyptian clover) and T. resupinatum (Persian clover). Abundant single nucleotide polymorphisms (SNPs) and insertions/deletions (In/Dels) were discovered between those two species. Global alignment of T. alexandrinum and T. resupinatum to a further thirteen Trifolium species revealed a large amount of rearrangement and repetitive events in these fifteen species. As hypothetical cp open reading frame (ORF) and RNA polymerase subunits, ycf1 and rpoC2 in the cp genomes both contain vast repetitive sequences and observed high Pi values (0.7008, 0.3982) between T. alexandrinum and T. resupinatum. Thus they could be considered as the candidate genes for phylogenetic analysis of Trifolium species. In addition, the divergence time of those IR lacking Trifolium species ranged from 84.8505 Mya to 4.7720 Mya. This study will provide insight into the evolution of Trifolium species. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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18 pages, 3439 KiB  
Article
The First Glimpse of Streptocarpus ionanthus (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes
by Cornelius M. Kyalo, Zhi-Zhong Li, Elijah M. Mkala, Itambo Malombe, Guang-Wan Hu and Qing-Feng Wang
Plants 2020, 9(4), 456; https://doi.org/10.3390/plants9040456 - 4 Apr 2020
Cited by 13 | Viewed by 3753
Abstract
Streptocarpus ionanthus (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of Str. ionanthus is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to understand the molecular variation within Str. ionanthus using a phylogenomic [...] Read more.
Streptocarpus ionanthus (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of Str. ionanthus is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to understand the molecular variation within Str. ionanthus using a phylogenomic approach. We sequence the chloroplast genomes of five subspecies of Str. ionanthus, compare their structural features and identify divergent regions. The five genomes are identical, with a conserved structure, a narrow size range (170 base pairs (bp)) and 115 unique genes (80 protein-coding, 31 tRNAs and 4 rRNAs). Genome alignment exhibits high synteny while the number of Simple Sequence Repeats (SSRs) are observed to be low (varying from 37 to 41), indicating high similarity. We identify ten divergent regions, including five variable regions (psbM, rps3, atpF-atpH, psbC-psbZ and psaA-ycf3) and five genes with a high number of polymorphic sites (rps16, rpoC2, rpoB, ycf1 and ndhA) which could be investigated further for phylogenetic utility in Str. ionanthus. Phylogenomic analyses here exhibit low polymorphism within Str. ionanthus and poor phylogenetic separation, which might be attributed to recent divergence. The complete chloroplast genome sequence data concerning the five subspecies provides genomic resources which can be expanded for future elucidation of Str. ionanthus phylogenetic relationships. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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17 pages, 17618 KiB  
Article
New Insights into Evolution of Plant Heat Shock Factors (Hsfs) and Expression Analysis of Tea Genes in Response to Abiotic Stresses
by Ping Xu, Qinwei Guo, Xin Pang, Peng Zhang, Dejuan Kong and Jia Liu
Plants 2020, 9(3), 311; https://doi.org/10.3390/plants9030311 - 2 Mar 2020
Cited by 11 | Viewed by 3341
Abstract
Heat shock transcription factor (Hsf) is one of key regulators in plant abotic stress response. Although the Hsf gene family has been identified from several plant species, original and evolution relationship have been fragmented. In addition, tea, an important crop, genome sequences have [...] Read more.
Heat shock transcription factor (Hsf) is one of key regulators in plant abotic stress response. Although the Hsf gene family has been identified from several plant species, original and evolution relationship have been fragmented. In addition, tea, an important crop, genome sequences have been completed and function of the Hsf family genes in response to abiotic stresses was not illuminated. In this study, a total of 4208 Hsf proteins were identified within 163 plant species from green algae (Gonium pectorale) to angiosperm (monocots and dicots), which were distributed unevenly into each of plant species tested. The result indicated that Hsf originated during the early evolutionary history of chlorophytae algae and genome-wide genetic varies had occurred during the course of evolution in plant species. Phylogenetic classification of Hsf genes from the representative nine plant species into ten subfamilies, each of which contained members from different plant species, imply that gene duplication had occurred during the course of evolution. In addition, based on RNA-seq data, the member of the Hsfs showed different expression levels in the different organs and at the different developmental stages in tea. Expression patterns also showed clear differences among Camellia species, indicating that regulation of Hsf genes expression varied between organs in a species-specific manner. Furthermore, expression of most Hsfs in response to drought, cold and salt stresses, imply a possible positive regulatory role under abiotic stresses. Expression profiles of nineteen Hsf genes in response to heat stress were also analyzed by quantitative real-time RT-PCR. Several stress-responsive Hsf genes were highly regulated by heat stress treatment. In conclusion, these results lay a solid foundation for us to elucidate the evolutionary origin of plant Hsfs and Hsf functions in tea response to abiotic stresses in the future. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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18 pages, 6265 KiB  
Article
Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis
by Jacinta N. Munyao, Xiang Dong, Jia-Xin Yang, Elijah M. Mbandi, Vincent O. Wanga, Millicent A. Oulo, Josphat K. Saina, Paul M. Musili and Guang-Wan Hu
Plants 2020, 9(3), 296; https://doi.org/10.3390/plants9030296 - 1 Mar 2020
Cited by 35 | Viewed by 4932
Abstract
The genus Chlorophytum includes many economically important species well-known for medicinal, ornamental, and horticultural values. However, to date, few molecular genomic resources have been reported for this genus. Therefore, there is limited knowledge of phylogenetic studies, and the available chloroplast (cp) genome of [...] Read more.
The genus Chlorophytum includes many economically important species well-known for medicinal, ornamental, and horticultural values. However, to date, few molecular genomic resources have been reported for this genus. Therefore, there is limited knowledge of phylogenetic studies, and the available chloroplast (cp) genome of Chlorophytum (C. rhizopendulum) does not provide enough information on this genus. In this study, we present genomic resources for C. comosum and C. gallabatense, which had lengths of 154,248 and 154,154 base pairs (bp), respectively. They had a pair of inverted repeats (IRa and IRb) of 26,114 and 26,254 bp each in size, separating the large single-copy (LSC) region of 84,004 and 83,686 bp from the small single-copy (SSC) region of 18,016 and 17,960 bp in C. comosum and C. gallabatense, respectively. There were 112 distinct genes in each cp genome, which were comprised of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The comparative analysis with five other selected species displayed a generally high level of sequence resemblance in structural organization, gene content, and arrangement. Additionally, the phylogenetic analysis confirmed the previous phylogeny and produced a phylogenetic tree with similar topology. It showed that the Chlorophytum species (C. comosum, C. gallabatense and C. rhizopendulum) were clustered together in the same clade with a closer relationship than other plants to the Anthericum ramosum. This research, therefore, presents valuable records for further molecular evolutionary and phylogenetic studies which help to fill the gap in genomic resources and resolve the taxonomic complexes of the genus. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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18 pages, 4095 KiB  
Article
Transcriptome-Wide Identification, Evolutionary Analysis, and GA Stress Response of the GRAS Gene Family in Panax ginseng C. A. Meyer
by Nan Wang, Kangyu Wang, Shaokun Li, Yang Jiang, Li Li, Mingzhu Zhao, Yue Jiang, Lei Zhu, Yanfang Wang, Yingjie Su, Yi Wang and Meiping Zhang
Plants 2020, 9(2), 190; https://doi.org/10.3390/plants9020190 - 4 Feb 2020
Cited by 18 | Viewed by 3007
Abstract
GRAS transcription factors are a kind of plant-specific transcription factor that have been found in a variety of plants. According to previous studies, GRAS proteins are widely involved in the physiological processes of plant signal transduction, stress, growth and development. The Jilin ginseng [...] Read more.
GRAS transcription factors are a kind of plant-specific transcription factor that have been found in a variety of plants. According to previous studies, GRAS proteins are widely involved in the physiological processes of plant signal transduction, stress, growth and development. The Jilin ginseng (Panax ginseng C.A. Meyer) is a heterogeneous tetraploid perennial herb of the Araliaceae family, ginseng genus. Important information regarding the GRAS transcription factors has not been reported in ginseng. In this study, 59 Panax ginseng GRAS (PgGRAS) genes were obtained from the Jilin ginseng transcriptome data and divided into 13 sub-families according to the classification of Arabidopsis thaliana. Through systematic evolution, structural variation, function and gene expression analysis, we further reveal GRAS’s potential function in plant growth processes and its stress response. The expression of PgGRAS genes responding to gibberellin acids (GAs) suggests that these genes could be activated after application concentration of GA. The qPCR analysis result shows that four PgGRAS genes belonging to the DELLA sub-family potentially have important roles in the GA stress response of ginseng hairy roots. This study provides not only a preliminary exploration of the potential functions of the GRAS genes in ginseng, but also valuable data for further exploration of the candidate PgGRAS genes of GA signaling in Jilin ginseng, especially their roles in ginseng hairy root development and GA stress response. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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13 pages, 3072 KiB  
Article
Comparative Analysis of Actaea Chloroplast Genomes and Molecular Marker Development for the Identification of Authentic Cimicifugae Rhizoma
by Inkyu Park, Jun-Ho Song, Sungyu Yang and Byeong Cheol Moon
Plants 2020, 9(2), 157; https://doi.org/10.3390/plants9020157 - 27 Jan 2020
Cited by 5 | Viewed by 2725
Abstract
Actaea (Ranunculaceae; syn. Cimicifuga) is a controversial and complex genus. Dried rhizomes of Actaea species are used as Korean traditional herbal medicine. Although Actaea species are valuable, given their taxonomic classification and medicinal properties, sequence information of Actaea species is limited. In [...] Read more.
Actaea (Ranunculaceae; syn. Cimicifuga) is a controversial and complex genus. Dried rhizomes of Actaea species are used as Korean traditional herbal medicine. Although Actaea species are valuable, given their taxonomic classification and medicinal properties, sequence information of Actaea species is limited. In this study, we determined the complete chloroplast (cp) genome sequences of three Actaea species, including A. simplex, A. dahurica, and A. biternata. The cp genomes of these species varied in length from 159,523 to 159,789 bp and contained 112 unique functional genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene order, orientation, and content were well conserved in the three cp genomes. Comparative sequence analysis revealed the presence of hotspots, including ndhC-trnV-UAC, in Actaea cp genomes. High-resolution phylogenetic relationships were established among Actaea species based on cp genome sequences. Actaea species were clustered into each Actaea section, consistent with the Angiosperm Phylogeny Group (APG) IV system of classification. We also developed a novel indel marker, based on copy number variation of tandem repeats, to facilitate the authentication of the herbal medicine Cimicifugae Rhizoma. The availability Actaea cp genomes will provide abundant information for the taxonomic and phylogenetic analyses of Actaea species, and the Actaea (ACT) indel marker will be useful for the authentication of the herbal medicine. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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15 pages, 2473 KiB  
Article
Comparative Chloroplast Genomics of Fritillaria (Liliaceae), Inferences for Phylogenetic Relationships between Fritillaria and Lilium and Plastome Evolution
by Jiao Huang, Yan Yu, Yan-Mei Liu, Deng-Feng Xie, Xing-Jin He and Song-Dong Zhou
Plants 2020, 9(2), 133; https://doi.org/10.3390/plants9020133 - 21 Jan 2020
Cited by 26 | Viewed by 3689
Abstract
Fritillaria is a genus that has important medicinal and horticultural values. The study involved the most comprehensive chloroplast genome samples referring to Old and New World clades of Fritillaria for marker selection and phylogenetic studies. We reported and compared eleven newly sequenced whole-plastome [...] Read more.
Fritillaria is a genus that has important medicinal and horticultural values. The study involved the most comprehensive chloroplast genome samples referring to Old and New World clades of Fritillaria for marker selection and phylogenetic studies. We reported and compared eleven newly sequenced whole-plastome sequences of Fritillaria which proved highly similar in overall size (151,652–152,434 bp), genome structure, gene content, and order. Comparing them with other species of Liliales (6 out of 10 families) indicated the same similarity but showed some structural variations due to the contraction or expansion of the inverted repeat (IR) regions. A/T mononucleotides, palindromic, and forward repeats were the most common types. Six hypervariable regions (rps16-trnQ, rbcL-accD, accD-psaI, psaJ-rpl33, petD-rpoA, and rpl32-trnL) were discovered based on 26 Fritillaria whole-plastomes to be potential molecular markers. Based on the plastome data that were collected from 26 Fritillaria and 21 Lilium species, a phylogenomic study was carried out with three Cardiocrinum species as outgroups. Fritillaria was sister to Lilium with a high support value, and the interspecies relationships within subgenus Fritillaria were resolved very well. The six hypervariable regions can be used as candidate DNA barcodes of Fritillaria and the phylogenomic framework can guide extensive genomic sampling for further phylogenetic analyses. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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15 pages, 3800 KiB  
Article
Comparative Analysis between Wild and Cultivated Cucumbers Reveals Transcriptional Changes during Domestication Process
by Eslam M. Abdel-Salam, Mohammad Faisal, Abdulrahman A. Alatar, Quaiser Saquib and Hend A. Alwathnani
Plants 2020, 9(1), 63; https://doi.org/10.3390/plants9010063 - 3 Jan 2020
Cited by 6 | Viewed by 3619
Abstract
The cultivated cucumber (Cucumis sativus L.) was reported to have been developed from a wild cucumber (Cucumis hystrix Chakrav.), nevertheless, these two organisms exhibit noteworthy differences. For example, the wild cucumber is known for its high resistance to different biotic and [...] Read more.
The cultivated cucumber (Cucumis sativus L.) was reported to have been developed from a wild cucumber (Cucumis hystrix Chakrav.), nevertheless, these two organisms exhibit noteworthy differences. For example, the wild cucumber is known for its high resistance to different biotic and abiotic stresses. Moreover, the leaves and fruits of the wild cucumber have a bitter taste compared to the cultivated cucumber. These differences could be attributed mainly to the differences in gene expression levels. In the present investigation, we analyzed the RNA-sequencing data to show the differentially expressed genes (DEGs) between the wild and cultivated cucumbers. The identified DEGs were further utilized for Gene Ontology (GO) and pathway enrichment analysis and for identification of transcription factors and regulators. In the results, several enriched GO terms in the biological process, cellular component, and molecular functions categories were identified and various enriched pathways, especially the biosynthesis pathways of secondary products were recognized. Plant-specific transcription factor families were differentially expressed between the wild and cultivated cucumbers. The results obtained provide preliminary evidence for the transcriptional differences between the wild and cultivated cucumbers which developed during the domestication process as a result of natural and/or artificial selection, and they formulate the basis for future genetic research and improvement of the cultivated cucumber. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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17 pages, 5719 KiB  
Article
Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae
by Huyen-Trang Vu, Ngan Tran, Thanh-Diem Nguyen, Quoc-Luan Vu, My-Huyen Bui, Minh-Tri Le and Ly Le
Plants 2020, 9(1), 61; https://doi.org/10.3390/plants9010061 - 2 Jan 2020
Cited by 18 | Viewed by 5675
Abstract
Paphiopedilum delenatii is a native orchid of Vietnam with highly attractive floral traits. Unfortunately, it is now listed as a critically endangered species with a few hundred individuals remaining in nature. In this study, we performed next-generation sequencing of P. delenatii and assembled [...] Read more.
Paphiopedilum delenatii is a native orchid of Vietnam with highly attractive floral traits. Unfortunately, it is now listed as a critically endangered species with a few hundred individuals remaining in nature. In this study, we performed next-generation sequencing of P. delenatii and assembled its complete chloroplast genome. The whole chloroplast genome of P. delenatii was 160,955 bp in size, 35.6% of which was GC content, and exhibited typical quadripartite structure of plastid genomes with four distinct regions, including the large and small single-copy regions and a pair of inverted repeat regions. There were, in total, 130 genes annotated in the genome: 77 coding genes, 39 tRNA genes, 8 rRNA genes, and 6 pseudogenes. The loss of ndh genes and variation in inverted repeat (IR) boundaries as well as data of simple sequence repeats (SSRs) and divergent hotspots provided useful information for identification applications and phylogenetic studies of Paphiopedilum species. Whole chloroplast genomes could be used as an effective super barcode for species identification or for developing other identification markers, which subsequently serves the conservation of Paphiopedilum species. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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14 pages, 3737 KiB  
Article
Evolutionary Analysis of Calcium-Dependent Protein Kinase in Five Asteraceae Species
by Liping Zhu, Bowen Zheng, Wangyang Song, Hongbin Li and Xiang Jin
Plants 2020, 9(1), 32; https://doi.org/10.3390/plants9010032 - 24 Dec 2019
Cited by 3 | Viewed by 2975
Abstract
Calcium-dependent protein kinase (CPK) is crucial in Ca2+ signal transduction, and is a large gene family in plants. In our previous work, we reported Hevea brasiliensis CPKs were important for natural rubber biosynthesis. However, this CPK gene family in other rubber producing [...] Read more.
Calcium-dependent protein kinase (CPK) is crucial in Ca2+ signal transduction, and is a large gene family in plants. In our previous work, we reported Hevea brasiliensis CPKs were important for natural rubber biosynthesis. However, this CPK gene family in other rubber producing plants has not been investigated. Here, we report the CPKs in five representative Asteraceae species, including three rubber-producing and two non-rubber species. A total of 34, 34, 40, 34 and 30 CPKs were identified from Taraxacum koksaghyz, Lactuca sativa, Helianthus annuus, Chrysanthemum nankingense and Cynara cardunculus, respectively. All CPKs were classified into four individual groups (group I to IV). In addition, 10 TkCPKs, 11 LsCPKs, 20 HaCPKs, 13 CnCPKs and 7 CcCPKs duplicated paralogs were identified. Further evolutionary analysis showed that, compared to other subfamilies, the group III had been expanded in the Asteraceae species, especially in the rubber-producing species. Meanwhile, the CPKs in group III from Asteraceae species tend to expand with low calcium binding capacity. This study provides a systematical evolutionary investigation of the CPKs in five representative Asteraceae species, suggesting that the sub-family specific expansion of CPKs might be related to natural rubber producing. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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1 pages, 165 KiB  
Correction
Correction: Rodionov, A.V., et al. Intragenomic Polymorphism of the ITS 1 Region of 35S rRNA Gene in the Group of Grasses with Two-Chromosome Species: Different Genome Composition in Closely Related Zingeria Species. Plants 2020, 9, 1647
by Alexander V. Rodionov, Alexander A. Gnutikov, Nikolai N. Nosov, Eduard M. Machs, Yulia V. Mikhaylova, Victoria S. Shneyer and Elizaveta O. Punina
Plants 2021, 10(3), 463; https://doi.org/10.3390/plants10030463 - 1 Mar 2021
Cited by 1 | Viewed by 1395
Abstract
The authors wish to make the following corrections to their paper [...] Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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