Recent Advances in Plant Genomics and Transcriptome Analysis

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 (31 March 2024) | Viewed by 19769

Special Issue Editor


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Guest Editor
Department of Molecular Bioscience, Kangwon National University, Chuncheon 24341, Republic of Korea
Interests: evolution; genetics; genomics; cytogenetics

Special Issue Information

Dear Colleagues,

Green plants (Viridiplantae) comprise about 450,000 ~ 500,000 species that are found in many environments from aquatic to arid deserts to alpine tundra ecosystems. During the 500 million years of plant evolution, genomes underwent highly dynamic turbulences such as whole genome duplications, polyploidization, transposable elements expansions/reductions; as a result, extant plant genome sizes are highly variable, for example,  2,340-fold in land plants and 4,680-fold in chlorophyte and streptophyte green algae. Nevertheless, the variation of number of genes encoded is not extensive among plant taxa because only small fraction of the genome sequences are transcribed to be translated into proteins. Thus, transcriptomics is one of the most important topics of research filed in modern genomics to obtain inferences of gene functions and species relationships. The technical innovations of DNA sequencing and computing techniques allowed genomics researchers to sequence the transcriptomes from diverse plant taxa. The topic of the Special Issue of Plants is “Recent Advances in Plant Genomics and Transcriptome Analysis”, which aims to combine recent progresses in whole genome sequences, transcriptomics, phylogenomics, and cytogenomics in plants.

Dr. Nam-Soo Kim
Guest Editor

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Keywords

  • whole genome sequencing
  • transcriptomics
  • chromosomes
  • phylogenomics

Published Papers (15 papers)

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Research

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40 pages, 3432 KiB  
Article
Decrypting Molecular Mechanisms Involved in Counteracting Copper and Nickel Toxicity in Jack Pine (Pinus banksiana) Based on Transcriptomic Analysis
by Alistar Moy and Kabwe Nkongolo
Plants 2024, 13(7), 1042; https://doi.org/10.3390/plants13071042 - 08 Apr 2024
Viewed by 346
Abstract
The remediation of copper and nickel-afflicted sites is challenged by the different physiological effects imposed by each metal on a given plant system. Pinus banksiana is resilient against copper and nickel, providing an opportunity to build a valuable resource to investigate the responding [...] Read more.
The remediation of copper and nickel-afflicted sites is challenged by the different physiological effects imposed by each metal on a given plant system. Pinus banksiana is resilient against copper and nickel, providing an opportunity to build a valuable resource to investigate the responding gene expression toward each metal. The objectives of this study were to (1) extend the analysis of the Pinus banksiana transcriptome exposed to nickel and copper, (2) assess the differential gene expression in nickel-resistant compared to copper-resistant genotypes, and (3) identify mechanisms specific to each metal. The Illumina platform was used to sequence RNA that was extracted from seedlings treated with each of the metals. There were 449 differentially expressed genes (DEGs) between copper-resistant genotypes (RGs) and nickel-resistant genotypes (RGs) at a high stringency cut-off, indicating a distinct pattern of gene expression toward each metal. For biological processes, 19.8% of DEGs were associated with the DNA metabolic process, followed by the response to stress (13.15%) and the response to chemicals (8.59%). For metabolic function, 27.9% of DEGs were associated with nuclease activity, followed by nucleotide binding (27.64%) and kinase activity (10.16%). Overall, 21.49% of DEGs were localized to the plasma membrane, followed by the cytosol (16.26%) and chloroplast (12.43%). Annotation of the top upregulated genes in copper RG compared to nickel RG identified genes and mechanisms that were specific to copper and not to nickel. NtPDR, AtHIPP10, and YSL1 were identified as genes associated with copper resistance. Various genes related to cell wall metabolism were identified, and they included genes encoding for HCT, CslE6, MPG, and polygalacturonase. Annotation of the top downregulated genes in copper RG compared to nickel RG revealed genes and mechanisms that were specific to nickel and not copper. Various regulatory and signaling-related genes associated with the stress response were identified. They included UGT, TIFY, ACC, dirigent protein, peroxidase, and glyoxyalase I. Additional research is needed to determine the specific functions of signaling and stress response mechanisms in nickel-resistant plants. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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18 pages, 6468 KiB  
Article
Transcriptome-Based Weighted Gene Co-Expression Network Analysis Reveals the Photosynthesis Pathway and Hub Genes Involved in Promoting Tiller Growth under Repeated Drought–Rewatering Cycles in Perennial Ryegrass
by Yunjia Ding, Xiaxiang Zhang, Jialei Li, Ruying Wang, Jie Chen, Lingna Kong, Xin Li, Zhimin Yang and Lili Zhuang
Plants 2024, 13(6), 854; https://doi.org/10.3390/plants13060854 - 15 Mar 2024
Viewed by 608
Abstract
Drought stress, which often occurs repeatedly across the world, can cause multiple and long-term effects on plant growth. However, the repeated drought–rewatering effects on plant growth remain uncertain. This study was conducted to determine the effects of drought–rewatering cycles on aboveground growth and [...] Read more.
Drought stress, which often occurs repeatedly across the world, can cause multiple and long-term effects on plant growth. However, the repeated drought–rewatering effects on plant growth remain uncertain. This study was conducted to determine the effects of drought–rewatering cycles on aboveground growth and explore the underlying mechanisms. Perennial ryegrass plants were subjected to three watering regimes: well-watered control (W), two cycles of drought–rewatering (D2R), and one cycle of drought–rewatering (D1R). The results indicated that the D2R treatment increased the tiller number by 40.9% and accumulated 28.3% more aboveground biomass compared with W; whereas the D1R treatment reduced the tiller number by 23.9% and biomass by 42.2% compared to the W treatment. A time-course transcriptome analysis was performed using crown tissues obtained from plants under D2R and W treatments at 14, 17, 30, and 33 days (d). A total number of 2272 differentially expressed genes (DEGs) were identified. In addition, an in-depth weighted gene co-expression network analysis (WGCNA) was carried out to investigate the relationship between RNA-seq data and tiller number. The results indicated that DEGs were enriched in photosynthesis-related pathways and were further supported by chlorophyll content measurements. Moreover, tiller-development-related hub genes were identified in the D2R treatment, including F-box/LRR-repeat MAX2 homolog (D3), homeobox-leucine zipper protein HOX12-like (HOX12), and putative laccase-17 (LAC17). The consistency of RNA-seq and qRT-PCR data were validated by high Pearson’s correlation coefficients ranging from 0.899 to 0.998. This study can provide a new irrigation management strategy that might increase plant biomass with less water consumption. In addition, candidate photosynthesis and hub genes in regulating tiller growth may provide new insights for drought-resistant breeding. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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15 pages, 927 KiB  
Article
Microsatellite Content in 397 Nuclear Exons and Their Flanking Regions in the Fern Family Ophioglossaceae
by Darina Koubínová, GoFlag Consortium and Jason R. Grant
Plants 2024, 13(5), 713; https://doi.org/10.3390/plants13050713 - 04 Mar 2024
Viewed by 569
Abstract
Microsatellites or SSRs are small tandem repeats that are 1–6 bp long. They are usually highly polymorphic and form important portions of genomes. They have been extensively analyzed in humans, animals and model plants; however, information from non-flowering plants is generally lacking. Here, [...] Read more.
Microsatellites or SSRs are small tandem repeats that are 1–6 bp long. They are usually highly polymorphic and form important portions of genomes. They have been extensively analyzed in humans, animals and model plants; however, information from non-flowering plants is generally lacking. Here, we examined 29 samples of Ophioglossaceae ferns, mainly from the genera Botrychium and Sceptridium. We analyzed the SSR distribution, density and composition in almost 400 nuclear exons and their flanking regions. We detected 45 SSRs in exons and 1475 SSRs in the flanking regions. In the exons, only di-, tri- and tetranucleotides were found, and all of them were 12 bp long. The annotation of the exons containing SSRs showed that they were related to various processes, such as metabolism, catalysis, transportation or plant growth. The flanking regions contained SSRs from all categories, with the most numerous being dinucleotides, followed by tetranucleotides. More than one-third of all the SSRs in the flanking regions were 12 bp long. The SSR densities in the exons were very low, ranging from 0 to 0.07 SSRs/kb, while those in the flanking regions ranged from 0.24 to 0.81 SSRs/kb; and those in the combined dataset ranged from 0.2 to 0.81 SSRs/kb. The majority of the detected SSRs in the flanking regions were polymorphic and present at the same loci across two or more samples but differing in the number of repeats. The SSRs detected here may serve as a basis for further population genetic, phylogenetic or evolutionary genetic studies, as well as for further studies focusing on SSRs in the genomes and their roles in adaptation, evolution and diseases. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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15 pages, 5766 KiB  
Article
Transcriptome Analysis Reveals Key Genes Involved in the Response of Pyrus betuleafolia to Drought and High-Temperature Stress
by Panpan Ma, Guoling Guo, Xiaoqian Xu, Tingyue Luo, Yu Sun, Xiaomei Tang, Wei Heng, Bing Jia and Lun Liu
Plants 2024, 13(2), 309; https://doi.org/10.3390/plants13020309 - 20 Jan 2024
Cited by 1 | Viewed by 759
Abstract
Drought and high-temperature stress are the main abiotic stresses that alone or simultaneously affect the yield and quality of pears worldwide. However, studies on the mechanisms of drought or high-temperature resistance in pears remain elusive. Therefore, the molecular responses of Pyrus betuleafolia, [...] Read more.
Drought and high-temperature stress are the main abiotic stresses that alone or simultaneously affect the yield and quality of pears worldwide. However, studies on the mechanisms of drought or high-temperature resistance in pears remain elusive. Therefore, the molecular responses of Pyrus betuleafolia, the widely used rootstock in pear production, to drought and high temperatures require further study. Here, drought- or high-temperature-resistant seedlings were selected from many Pyrus betuleafolia seedlings. The leaf samples collected before and after drought or high-temperature treatment were used to perform RNA sequencing analysis. For drought treatment, a total of 11,731 differentially expressed genes (DEGs) were identified, including 4444 drought-induced genes and 7287 drought-inhibited genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these DEGs were more significantly enriched in plant hormone signal transduction, flavonoid biosynthesis, and glutathione metabolism. For high-temperature treatment, 9639 DEGs were identified, including 5493 significantly upregulated genes and 4146 significantly downregulated genes due to high-temperature stress. KEGG analysis showed that brassinosteroid biosynthesis, arginine metabolism, and proline metabolism were the most enriched pathways for high-temperature response. Meanwhile, the common genes that respond to both drought and high-temperature stress were subsequently identified, with a focus on responsive transcription factors, such as MYB, HSF, bZIP, and WRKY. These results reveal potential genes that function in drought or high-temperature resistance. This study provides a theoretical basis and gene resources for the genetic improvement and molecular breeding of pears. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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19 pages, 5432 KiB  
Article
Population Structure and Genetic Diversity Analyses Provide New Insight into the Endemic Species Aster spathulifolius Maxim. and Its Evolutionary History
by Gurusamy Raman, Kyoung Su Choi and SeonJoo Park
Plants 2024, 13(1), 88; https://doi.org/10.3390/plants13010088 - 27 Dec 2023
Cited by 1 | Viewed by 707
Abstract
Aster spathulifolius, an ecologically significant plant species native to the coastal regions of Korea and Japan, remains understudied in terms of its genetic structure and evolutionary history. In this study, we employed four chloroplast markers and the nuclear ITS region from 15 populations [...] Read more.
Aster spathulifolius, an ecologically significant plant species native to the coastal regions of Korea and Japan, remains understudied in terms of its genetic structure and evolutionary history. In this study, we employed four chloroplast markers and the nuclear ITS region from 15 populations of A. spathulifolius from both Korea and Japan, including their islands, to unravel the spatial genetic structure, differentiation, gene flow, phylogenetic, and biogeographical relationships. Analysis based on multiple methods identified a low level of genetic diversity, genetic differentiation and gene flow among A. spathulifolius populations. Network analysis and principal coordinates analysis showed that 15 populations could be divided into two groups: mainland and island. Furthermore, UPGMA, neighbor-net, maximum-likelihood and Bayesian inference-based phylogenetic tree confirmed that these populations formed two distinct clades. Therefore, the island populations might be treated as A. spathulifolius populations rather than A. oharai populations. Divergence time analysis estimated the divergence of A. spathulifolius lineages approximately 23.09 million years ago, while ancestral area reconstruction analysis suggested Korea as the potential origin, conflicting with alternative scenarios. These findings contribute to a comprehensive understanding of the evolutionary history, genetic structure, and adaptive strategies of A. spathulifolius in coastal environments. Our study challenges previous assumptions and underscores the necessity for further population studies to elucidate the intricate dynamics of this distinctive plant species. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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15 pages, 3464 KiB  
Article
A Genome-Wide Analysis and Expression Profile of Heat Shock Transcription Factor (Hsf) Gene Family in Rhododendron simsii
by Yanan Xu, Ying Jin, Dan He, Haochen Di, Ying Liang and Yanxia Xu
Plants 2023, 12(22), 3917; https://doi.org/10.3390/plants12223917 - 20 Nov 2023
Viewed by 810
Abstract
Heat shock transcription factors are key players in a number of transcriptional regulatory pathways that function during plant growth and development. However, their mode of action in Rhododendron simsii is still unclear. In this study, 22 RsHsf genes were identified from genomic data of [...] Read more.
Heat shock transcription factors are key players in a number of transcriptional regulatory pathways that function during plant growth and development. However, their mode of action in Rhododendron simsii is still unclear. In this study, 22 RsHsf genes were identified from genomic data of R. simsii. The 22 genes were randomly distributed on 12 chromosomes, and were divided into three major groups according to their phylogenetic relationships. The structures and conserved motifs were predicted for the 22 genes. Analysis of cis-acting elements revealed stress-responsive and phytohormone-responsive elements in the gene promoter regions, but the types and number varied among the different groups of genes. Transcriptional profile analyses revealed that RsHsfs were expressed in a tissue-specific manner, with particularly high transcript levels in the roots. The transcriptional profiles under abiotic stress were detected by qRT-PCR, and the results further validated the critical function of RsHsfs. This study provides basic information about RsHsf family in R. simsii, and paves the way for further research to clarify their precise roles and to breed new stress-tolerant varieties. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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23 pages, 2561 KiB  
Article
Transcriptome Analysis Reveals Changes in Whole Gene Expression, Biological Process, and Molecular Functions Induced by Nickel in Jack Pine (Pinus banksiana)
by Alistar Moy, Karolina Czajka, Paul Michael and Kabwe Nkongolo
Plants 2023, 12(15), 2889; https://doi.org/10.3390/plants12152889 - 07 Aug 2023
Cited by 1 | Viewed by 892
Abstract
Understanding the genetic response of plants to nickel stress is a necessary step to improving the utility of plants in environmental remediation and restoration. The main objective of this study was to generate whole genome expression profiles of P. banksiana exposed to nickel [...] Read more.
Understanding the genetic response of plants to nickel stress is a necessary step to improving the utility of plants in environmental remediation and restoration. The main objective of this study was to generate whole genome expression profiles of P. banksiana exposed to nickel ion toxicity compared to reference genotypes. Pinus banksiana seedlings were screened in a growth chamber setting using a high concentration of 1600 mg of nickel per 1 kg of soil. RNA was extracted and sequenced using the Illumina platform, followed by de novo transcriptome assembly. Overall, 25,552 transcripts were assigned gene ontology. The biological processes in water-treated samples were analyzed, and 55% of transcripts were distributed among five categories: DNA metabolic process (19.3%), response to stress (13.3%), response to chemical stimuli (8.7%), signal transduction (7.7%) and response to biotic stimulus (6.0%). For molecular function, the highest percentages of genes were involved in nucleotide binding (27.6%), nuclease activity (27.3%) and kinase activity (10.3%). Sixty-two percent of genes were associated with cellular compartments. Of these genes, 21.7% were found in the plasma membrane, 16.1% in the cytosol, 12.4% with the chloroplast and 11.9% in the extracellular region. Nickel ions induced changes in gene expression, resulting in the emergence of differentially regulated categories. Overall, there were significant changes in gene expression with a total 4128 genes upregulated and 3754 downregulated genes detected in nickel-treated genotypes compared to water-treated control plants. For biological processes, the highest percentage of upregulated genes in plants exposed to nickel were associated with the response to stress (15%), the response to chemicals (11,1%), carbohydrate metabolic processes (7.4%) and catabolic processes (7.4%). The largest proportions of downregulated genes were associated with the biosynthetic process (21%), carbohydrate metabolic process (14.3%), response to biotic stimulus (10.7%) and response to stress (10.7%). For molecular function, genes encoding for enzyme regulatory and hydrolase activities represented the highest proportion (61%) of upregulated gene. The majority of downregulated genes were involved in the biosynthetic processes. Overall, 58% of upregulated genes were located in the extracellular region and the nucleus, while 42% of downregulated genes were localized to the plasma membrane and 33% to the extracellular region. This study represents the first report of a transcriptome from a conifer species treated with nickel. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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20 pages, 6763 KiB  
Article
Comparative Analysis and Identification of Terpene Synthase Genes in Convallaria keiskei Leaf, Flower and Root Using RNA-Sequencing Profiling
by Sivagami-Jean Claude, Gurusamy Raman and Seon-Joo Park
Plants 2023, 12(15), 2797; https://doi.org/10.3390/plants12152797 - 28 Jul 2023
Viewed by 1041
Abstract
The ‘Lilly of the Valley’ species, Convallaria, is renowned for its fragrant white flowers and distinctive fresh and green floral scent, attributed to a rich composition of volatile organic compounds (VOCs). However, the molecular mechanisms underlying the biosynthesis of this floral scent [...] Read more.
The ‘Lilly of the Valley’ species, Convallaria, is renowned for its fragrant white flowers and distinctive fresh and green floral scent, attributed to a rich composition of volatile organic compounds (VOCs). However, the molecular mechanisms underlying the biosynthesis of this floral scent remain poorly understood due to a lack of transcriptomic data. In this study, we conducted the first comparative transcriptome analysis of C. keiskei, encompassing the leaf, flower, and root tissues. Our aim was to investigate the terpene synthase (TPS) genes and differential gene expression (DEG) patterns associated with essential oil biosynthesis. Through de novo assembly, we generated a substantial number of unigenes, with the highest count in the root (146,550), followed by the flower (116,434) and the leaf (72,044). Among the identified unigenes, we focused on fifteen putative ckTPS genes, which are involved in the synthesis of mono- and sesquiterpenes, the key aromatic compounds responsible for the essential oil biosynthesis in C. keiskei. The expression of these genes was validated using quantitative PCR analysis. Both DEG and qPCR analyses revealed the presence of ckTPS genes in the flower transcriptome, responsible for the synthesis of various compounds such as geraniol, germacrene, kaurene, linalool, nerolidol, trans-ocimene and valencene. The leaf transcriptome exhibited genes related to the biosynthesis of kaurene and trans-ocimene. In the root, the identified unigenes were associated with synthesizing kaurene, trans-ocimene and valencene. Both analyses indicated that the genes involved in mono- and sesquiterpene biosynthesis are more highly expressed in the flower compared to the leaf and root. This comprehensive study provides valuable resources for future investigations aiming to unravel the essential oil-biosynthesis-related genes in the Convallaria genus. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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23 pages, 5370 KiB  
Article
Deciphering the Genetic Mechanisms of Salt Tolerance in Sorghum bicolor L.: Key Genes and SNP Associations from Comparative Transcriptomic Analyses
by Donghyun Jeon, Jin-Baek Kim, Beum-Chang Kang and Changsoo Kim
Plants 2023, 12(14), 2639; https://doi.org/10.3390/plants12142639 - 13 Jul 2023
Viewed by 1106
Abstract
Sorghum bicolor L. is a vital cereal crop for global food security. Its adaptability to diverse climates make it economically, socially, and environmentally valuable. However, soil salinization caused by climate extremes poses a threat to sorghum. This study aimed to identify candidate salt-tolerant [...] Read more.
Sorghum bicolor L. is a vital cereal crop for global food security. Its adaptability to diverse climates make it economically, socially, and environmentally valuable. However, soil salinization caused by climate extremes poses a threat to sorghum. This study aimed to identify candidate salt-tolerant genes and single nucleotide polymorphisms (SNPs) by performing a comparative transcriptome analysis on a mutant sorghum line and its wild type. The mutant line was generated through gamma ray exposure and selection for salt tolerance. Phenotypic measurements were taken, followed by mRNA sequencing and variant calling. In this study, potential genes and non-synonymous SNPs associated with salt tolerance were inferred, including LOC8071970, LOC8067721, LOC110430887, LOC8070256, and LOC8056880. These genes demonstrated notable differences in nsSNPs in comparison to the wild type, suggesting their potential roles in salt tolerance. Additionally, LOC8060874 (cyanohydrin beta-glucosyltransferase) was suggested as a key gene involved in salt tolerance due to its possible role in dhurrin biosynthesis under salt stress. In upcoming research, additional reverse genetics studies will be necessary in order to verify the function of those candidate genes in relation to salt stress. In conclusion, this study underscores the significance of investigating salt tolerance mechanisms and the potential key genes associated with salt tolerance in sorghum. Our findings may provide insights for future breeding strategies aimed at enhancing salinity tolerance and crop productivity. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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13 pages, 3455 KiB  
Article
Differential RNA-Seq Analysis Predicts Genes Related to Terpene Tailoring in Caryopteris × clandonensis
by Manfred Ritz, Nadim Ahmad, Thomas Brueck and Norbert Mehlmer
Plants 2023, 12(12), 2305; https://doi.org/10.3390/plants12122305 - 13 Jun 2023
Viewed by 1126
Abstract
Enzymatic terpene functionalization is an essential part of plant secondary metabolite diversity. Within this, multiple terpene-modifying enzymes are required to enable the chemical diversity of volatile compounds essential in plant communication and defense. This work sheds light on the differentially transcribed genes within [...] Read more.
Enzymatic terpene functionalization is an essential part of plant secondary metabolite diversity. Within this, multiple terpene-modifying enzymes are required to enable the chemical diversity of volatile compounds essential in plant communication and defense. This work sheds light on the differentially transcribed genes within Caryopteris × clandonensis that are capable of functionalizing cyclic terpene scaffolds, which are the product of terpene cyclase action. The available genomic reference was subjected to further improvements to provide a comprehensive basis, where the number of contigs was minimized. RNA-Seq data of six cultivars, Dark Knight, Grand Bleu, Good as Gold, Hint of Gold, Pink Perfection, and Sunny Blue, were mapped on the reference, and their distinct transcription profile investigated. Within this data resource, we detected interesting variations and additionally genes with high and low transcript abundancies in leaves of Caryopteris × clandonensis related to terpene functionalization. As previously described, different cultivars vary in their modification of monoterpenes, especially limonene, resulting in different limonene-derived molecules. This study focuses on predicting the cytochrome p450 enzymes underlying this varied transcription pattern between investigated samples. Thus, making them a reasonable explanation for terpenoid differences between these plants. Furthermore, these data provide the basis for functional assays and the verification of putative enzyme activities. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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22 pages, 3212 KiB  
Article
Cellular Morphology and Transcriptome Comparative Analysis of Astragalus membranaceus Bunge Sprouts Cultured In Vitro under Different LED Light
by Ji Won Seo, Jae Geun Lee, Ji Hye Yoo, Jung Dae Lim, Ik Young Choi, Myong Jo Kim, Chang Yeon Yu and Eun Soo Seong
Plants 2023, 12(9), 1914; https://doi.org/10.3390/plants12091914 - 08 May 2023
Cited by 1 | Viewed by 1317
Abstract
Astragalus membranaceus, the major components of which are saponins, flavonoids, and polysaccharides, has been established to have excellent pharmacological activity. After ginseng, it is the second most used medicinal plant. To examine the utility of A. membranaceus as a sprout crop for [...] Read more.
Astragalus membranaceus, the major components of which are saponins, flavonoids, and polysaccharides, has been established to have excellent pharmacological activity. After ginseng, it is the second most used medicinal plant. To examine the utility of A. membranaceus as a sprout crop for plant factory cultivation, we sought to establish a functional substance control model by comparing the transcriptomes of sprouts grown in sterile, in vitro culture using LED light sources. Having sown the seeds of A. membranaceus, these were exposed to white LED light (continuous spectrum), red LED light (632 nm, 1.58 μmol/m2/s), or blue LED light (465 nm, 1.44 μmol/m2/s) and grown for 6 weeks; after which, the samples were collected for transcriptome analysis. Scanning electron microscopy analysis of cell morphology in plants exposed to the three light sources revealed that leaf cell size was largest in those plants exposed to red light, where the thickest stem was observed in plants exposed to white light. The total number of genes in A. membranaceus spouts determined via de novo assembly was 45,667. Analysis of differentially expressed genes revealed that for the comparisons of blue LED vs. red LED, blue LED vs. white LED, and red LED vs. white LED, the numbers of upregulated genes were 132, 148, and 144, respectively. Binding, DNA integration, transport, phosphorylation, DNA biosynthetic process, membrane, and plant-type secondary cell wall biogenesis were the most enriched in the comparative analysis of blue LED vs. red LED, whereas Binding, RNA-templated DNA biosynthetic process, DNA metabolic process, and DNA integration were the most enriched in the comparative analysis of blue vs. white LED, and DNA integration and resolution of meiotic recombination intermediates were the most enrichment in the comparison between red LED vs. white LED. The GO term associated with flavonoid biosynthesis, implying the functionality of A. membranaceus, was the flavonoid biosynthetic process, which was enriched in the white LED vs. red LED comparison. The findings of this study thus indicate that different LED light sources can differentially influence the transcriptome expression pattern of A. membranaceus sprouts, which can provide a basis for establishing a flavonoid biosynthesis regulation model and thus, the cultivation of high-functional Astragalus sprouts. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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18 pages, 3645 KiB  
Article
Isolation and Characterization of the Genes Involved in the Berberine Synthesis Pathway in Asian Blue Cohosh, Caulophyllum robustum
by Nam-Il Park, Neha Samir Roy, Yeri Park, Beom-Soon Choi, Mi Jin Jeon, Ji Yeon Oh, Bo-Yun Kim, Young-Dong Kim, Yong-In Kim, Taeyoung Um, Hwan Jong Kwak, Nam-Soo Kim, Soonok Kim and Ik-Young Choi
Plants 2023, 12(7), 1483; https://doi.org/10.3390/plants12071483 - 28 Mar 2023
Cited by 1 | Viewed by 1651
Abstract
Caulophyllum robustum, commonly named Asian blue cohosh, is a perennial herb in the family Berberidaceae. It has traditionally been used for folk medicine in China. We isolated berberine from the leaves, stem, roots, and fruits of C. robustum, and this is [...] Read more.
Caulophyllum robustum, commonly named Asian blue cohosh, is a perennial herb in the family Berberidaceae. It has traditionally been used for folk medicine in China. We isolated berberine from the leaves, stem, roots, and fruits of C. robustum, and this is the first report on berberine in this species. Transcriptome analysis was conducted for the characterization of berberine biosynthesis genes in C. robustum, in which, all the genes for berberine biosynthesis were identified. From 40,094 transcripts, using gene ontology (GO) analysis, 26,750 transcripts were assigned their functions in the categories of biological process, molecular function, and cellular component. In the analysis of genes expressed in different tissues, the numbers of genes in the categories of intrinsic component of membrane and transferase activity were up-regulated in leaves versus stem. The berberine synthesis genes in C. robustum were characterized by phylogenetic analysis with corresponding genes from other berberine-producing species. The co-existence of genes from different plant families in the deepest branch subclade implies that the differentiation of berberine synthesis genes occurred early in the evolution of berberine-producing plants. Furthermore, the copy number increment of the berberine synthesis genes was detected at the species level. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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Review

Jump to: Research

26 pages, 3622 KiB  
Review
The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms
by Kaiyue Hong, Yasmina Radian, Teja Manda, Haibin Xu and Yuming Luo
Plants 2023, 12(23), 4006; https://doi.org/10.3390/plants12234006 - 28 Nov 2023
Cited by 1 | Viewed by 2121
Abstract
Genome sequencing is widely recognized as a fundamental pillar in genetic research and legal studies of biological phenomena, providing essential insights for genetic investigations and legal analyses of biological events. The field of genome sequencing has experienced significant progress due to rapid improvements [...] Read more.
Genome sequencing is widely recognized as a fundamental pillar in genetic research and legal studies of biological phenomena, providing essential insights for genetic investigations and legal analyses of biological events. The field of genome sequencing has experienced significant progress due to rapid improvements in scientific and technological developments. These advancements encompass not only significant improvements in the speed and quality of sequencing but also provide an unparalleled opportunity to explore the subtle complexities of genomes, particularly in the context of rare species. Such a wide range of possibilities has successfully supported the validation of plant gene functions and the refinement of precision breeding methodologies. This expanded scope now includes a comprehensive exploration of the current state and conservation efforts of gymnosperm gene sequencing, offering invaluable insights into their genomic landscapes. This comprehensive review elucidates the trajectory of development and the diverse applications of genome sequencing. It encompasses various domains, including crop breeding, responses to abiotic stress, species evolutionary dynamics, biodiversity, and the unique challenges faced in the conservation and utilization of gymnosperms. It highlights both ongoing challenges and the unveiling of forthcoming developmental trajectories. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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22 pages, 3699 KiB  
Review
Genomics and Transcriptomics Reveal Genetic Contribution to Population Diversity and Specific Traits in Coconut
by Kobra Yousefi, Siti Nor Akmar Abdullah, Muhammad Asyraf Md Hatta and Kong Lih Ling
Plants 2023, 12(9), 1913; https://doi.org/10.3390/plants12091913 - 08 May 2023
Cited by 1 | Viewed by 2983
Abstract
Coconut is an economically important palm species with a long history of human use. It has applications in various food, nutraceuticals, and cosmetic products, and there has been renewed interest in coconut in recent years due to its unique nutritional and medicinal properties. [...] Read more.
Coconut is an economically important palm species with a long history of human use. It has applications in various food, nutraceuticals, and cosmetic products, and there has been renewed interest in coconut in recent years due to its unique nutritional and medicinal properties. Unfortunately, the sustainable growth of the coconut industry has been hampered due to a shortage of good quality seedlings. Genetic improvement through the traditional breeding approach faced considerable obstacles due to its perennial nature, protracted juvenile period, and high heterozygosity. Molecular biotechnological tools, including molecular markers and next-generation sequencing (NGS), could expedite genetic improvement efforts in coconut. Researchers have employed various molecular markers to reveal genetic diversity among coconut populations and for the construction of a genetic map for exploitation in coconut breeding programs worldwide. Whole genome sequencing and transcriptomics on the different varieties have generated a massive amount of publicly accessible sequence data, substantially improving the ability to analyze and understand molecular mechanisms affecting crop performance. The production of high-yielding and disease-resilient coconuts and the deciphering of the complex coconut genome’s structure can profit tremendously from these technologies. This paper aims to provide a comprehensive review of the progress of coconut research, using genomics, transcriptomics, and molecular markers initiatives. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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19 pages, 1808 KiB  
Review
Molecular Genetic Research and Genetic Engineering of Taraxacum kok-saghyz L.E. Rodin
by Bulat Kuluev, Kairat Uteulin, Gabit Bari, Elvina Baimukhametova, Khalit Musin and Alexey Chemeris
Plants 2023, 12(8), 1621; https://doi.org/10.3390/plants12081621 - 12 Apr 2023
Cited by 7 | Viewed by 2426
Abstract
Natural rubber (NR) remains an indispensable raw material with unique properties that is used in the manufacture of a large number of products and the global demand for it is growing every year. The only industrially important source of NR is the tropical [...] Read more.
Natural rubber (NR) remains an indispensable raw material with unique properties that is used in the manufacture of a large number of products and the global demand for it is growing every year. The only industrially important source of NR is the tropical tree Hevea brasiliensis (Willd. ex A.Juss.) Müll.Arg., thus alternative sources of rubber are required. For the temperate zone, the most suitable source of high quality rubber is the Russian (Kazakh) dandelion Taraxacum kok-saghyz L.E. Rodin (TKS). An obstacle to the widespread industrial cultivation of TKS is its high heterozygosity, poor growth energy, and low competitiveness in the field, as well as inbreeding depression. Rapid cultivation of TKS requires the use of modern technologies of marker-assisted and genomic selection, as well as approaches of genetic engineering and genome editing. This review is devoted to describing the progress in the field of molecular genetics, genomics, and genetic engineering of TKS. Sequencing and annotation of the entire TKS genome made it possible to identify a large number of SNPs, which were subsequently used in genotyping. To date, a total of 90 functional genes have been identified that control the rubber synthesis pathway in TKS. The most important of these proteins are part of the rubber transferase complex and are encoded by eight genes for cis-prenyltransferases (TkCPT), two genes for cis-prenyltransferase-like proteins (TkCPTL), one gene for rubber elongation factor (TkREF), and nine genes for small rubber particle proteins (TkSRPP). In TKS, genes for enzymes of inulin metabolism have also been identified and genome-wide studies of other gene families are also underway. Comparative transcriptomic and proteomic studies of TKS lines with different accumulations of NR are also being carried out, which help to identify genes and proteins involved in the synthesis, regulation, and accumulation of this natural polymer. A number of authors already use the knowledge gained in the genetic engineering of TKS and the main goal of these works is the rapid transformation of the TKS into an economically viable rubber crop. There are no great successes in this area so far, therefore work on genetic transformation and genome editing of TKS should be continued, considering the recent results of genome-wide studies. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genomics and Transcriptome Analysis)
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