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23 pages, 10438 KiB

Open AccessArticle

Comparative Analysis of Chloroplast Genomes for the Genus Manglietia Blume (Magnoliaceae): Molecular Structure and Phylogenetic Evolution

by Tingzhang Li, Shuangyu Zhang, Yunfei Deng and Yuling Li

Genes 2024, 15(4), 406; https://doi.org/10.3390/genes15040406 - 26 Mar 2024

Viewed by 573

Abstract

Manglietia Blume, belonging to the Magnoliaceae family and mainly distributed in tropical and subtropical regions of Asia, has great scientific and economic value. In this study, we employed next-generation sequencing followed by de novo assembly to investigate the adaptive evolution of Manglietia using [...] Read more.

Manglietia Blume, belonging to the Magnoliaceae family and mainly distributed in tropical and subtropical regions of Asia, has great scientific and economic value. In this study, we employed next-generation sequencing followed by de novo assembly to investigate the adaptive evolution of Manglietia using plastid genetic information. We newly sequenced the complete or nearly complete plastomes of four Manglietia species (Manglietia aromatica, Manglietia calcarea, Manglietia kwangtungensis, and Manglietia glauca) and conducted comparative analysis with seventeen published plastomes to examine the evolutionary pattern within this genus. The plastomes of these five newly sequenced Manglietia species range from 157,093 bp (M. calcarea2) to 160,493 bp (M. kwangtungensis), all exhibiting circular structures when mapped. Nucleotide diversity was observed across the plastomes, leading us to identify 13 mutational hotspot regions, comprising eight intergenic spacer regions and five gene regions. Our phylogenetic analyses based on 77 protein-coding genes generated phylogenetic relationships with high support and resolution for Manglietia. This genus can be divided into three clades, and the previously proposed infrageneric classifications are not supported by our studies. Furthermore, the close affinity between M. aromatica and M. calcarea is supported by the present work, and further studies are necessary to conclude the taxonomic treatment for the latter. These results provide resources for the comparative plastome, breeding, and plastid genetic engineering of Magnoliaceae and flowering plants. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Adaptive Evolution in Trees)

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15 pages, 3205 KiB

Open AccessArticle

Population Structure and Genetic Diversity in the Natural Distribution of Neolamarckia cadamba in China

by Yan-Wen Lv, Zi-Han He, Yu Xiao, Kun-Xi Ouyang, Xi Wang and Xin-Sheng Hu

Genes 2023, 14(4), 855; https://doi.org/10.3390/genes14040855 - 31 Mar 2023

Cited by 1 | Viewed by 1549

Abstract

Neolamarckia cadamba (Roxb.) Bosser is a fast-growing deciduous tree species and belongs to the Neolamarckia genus of the Rubiaceae family. This species has great economic and medical values in addition to being an important timber species for multiple industrial purposes. However, few studies [...] Read more.

Neolamarckia cadamba (Roxb.) Bosser is a fast-growing deciduous tree species and belongs to the Neolamarckia genus of the Rubiaceae family. This species has great economic and medical values in addition to being an important timber species for multiple industrial purposes. However, few studies have examined the genetic diversity and population structure in the natural distribution of this species in China. Here, we applied both the haploid nrDNA ITS (619 bp for aligned sequences) and mtDNA (2 polymorphic loci) markers to investigate 10 natural populations (239 individuals in total) that covered most of the distribution of the species in China. The results showed that the nucleotide diversity was

π

= 0.1185 ± 0.0242 for the nrDNA ITS markers and

π

= 0.00038 ± 0.00052 for the mtDNA markers. The haplotype diversity for the mtDNA markers was

h

= 0.1952 ± 0.2532. The population genetic differentiation was small (

F_{s t (n)}

= 0.0294) for the nrDNA ITS markers but large (

F_{s t (m)}

= 0.6765) for the mtDNA markers. There were no significant effects of isolation by distance (IBD), by elevation, and by two climatic factors (annual average precipitation and tem perature). A geographic structure among populations (

N_{s t} < G_{s t}

) was absent. Phylogenetic analysis showed a highly genetic mixture among individuals of the ten populations. Pollen flow was substantially greater than seed flow (

m_{p} / m_{s} ≫

1.0) and played a dominant role in shaping population genetic structure. The nrDNA ITS sequences were neutral and all local populations did not undergo demographic expansion. The overall results provide fundamental information for the genetic conservation and breeding of this miraculous tree. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Adaptive Evolution in Trees)

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19 pages, 3678 KiB

Open AccessArticle

Phylogeography of Toona ciliata (Meliaceae) Complex in China Inferred from Cytonuclear Markers

by Yu Xiao, Xin-Xin Zhang, Ying Hu, Xi Wang, Pei Li, Zi-Han He, Yan-Wen Lv, Xiao-Yang Chen and Xin-Sheng Hu

Genes 2023, 14(1), 116; https://doi.org/10.3390/genes14010116 - 31 Dec 2022

Cited by 10 | Viewed by 1813

Abstract

Toona ciliata is an important timber species but is recognized as an endangered species at level II in China. Its genetic conservation is of increasing concern. Provenance trials and other breeding programs were conducted to develop seed transfer rules and multiplications. Here, we [...] Read more.

Toona ciliata is an important timber species but is recognized as an endangered species at level II in China. Its genetic conservation is of increasing concern. Provenance trials and other breeding programs were conducted to develop seed transfer rules and multiplications. Here, we investigated twenty-nine populations sampled across the natural distribution of the T. ciliata complex using mtDNA and nrDNA ITS (ribosomal internal transcribed spacer) markers. Haplotype diversity was h = 0.190 ± 0.202 and nucleotide diversity was π = 0.000383 ± 0.000536 for mtDNA marker. Nucleotide diversity for ITS sequences was 0.00837 ± 0.000783. Haplotypes exhibited phylogeographic structure in spatial distribution. The extent of genetic differentiation was significant (F_st = 0.6994 ± 0.0079 for ITS and 0.8870 ± 0.0077 for mtDNA marker). Isolation by distance (IBD) and by elevation (IBE) occurred among populations. Phylogenetic relationships from mtDNA marker indicated three genetically distinct regions, each without IBD effects. Compared with pollen flow, seed flow was strongly impeded in the western region, but extensive in the central region, and less impeded in the eastern region. Most populations did not exhibit expansion, with only a few populations showing expansion after bottleneck effects. We discussed a strategy of region-based genetic conservation and proposed to conserve multiple populations in the western and eastern regions and a few populations in the central region. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Adaptive Evolution in Trees)

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15 pages, 2067 KiB

Open AccessArticle

Evolution and Expression Patterns of the Fructose 1,6-Bisphosptase Gene Family in a Miracle Tree (Neolamarckia cadamba)

by Qingmin Que, Xiaohan Liang, Huiyun Song, Chunmei Li, Pei Li, Ruiqi Pian, Xiaoyang Chen, Wei Zhou and Kunxi Ouyang

Genes 2022, 13(12), 2349; https://doi.org/10.3390/genes13122349 - 13 Dec 2022

Cited by 1 | Viewed by 1313

Abstract

Neolamarckia cadamba (N. cadamba) is a fast-growing tree species with tremendous economic and ecological value; the study of the key genes regulating photosynthesis and sugar accumulation is very important for the breeding of N. cadamba. Fructose 1,6-bisphosptase (FBP) [...] Read more.

Neolamarckia cadamba (N. cadamba) is a fast-growing tree species with tremendous economic and ecological value; the study of the key genes regulating photosynthesis and sugar accumulation is very important for the breeding of N. cadamba. Fructose 1,6-bisphosptase (FBP) gene has been found to play a key role in plant photosynthesis, sugar accumulation and other growth processes. However, no systemic analysis of FBPs has been reported in N. cadamba. A total of six FBP genes were identifed and cloned based on the N. cadamba genome, and these FBP genes were sorted into four groups. The characteristics of the NcFBP gene family were analyzed such as phylogenetic relationships, gene structures, conserved motifs, and expression patterns. A cis-acting element related to circadian control was first found in the promoter region of FBP gene. Phylogenetic and quantitative real-time PCR analyses showed that NcFBP5 and NcFBP6 may be chloroplast type 1 FBP and cytoplasmic FBP, respectively. FBP proteins from N. cadamba and 22 other plant species were used for phylogenetic analyses, indicating that FBP family may have expanded during the evolution of algae to mosses and differentiated cpFBPase1 proteins in mosses. This work analyzes the internal relationship between the evolution and expression of the six NcFBPs, providing a scientific basis for the evolutionary pattern of plant FBPs, and promoting the functional studies of FBP genes. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Adaptive Evolution in Trees)

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14 pages, 680 KiB

Open AccessArticle

Mating Systems of Single Families and Population Genetic Diversity of Endangered Ormosia hosiei in South China

by Fengqing Li, Huanwei Chen, Suzhen Liu, Huacong Zhang and Zhichun Zhou

Genes 2022, 13(11), 2117; https://doi.org/10.3390/genes13112117 - 15 Nov 2022

Cited by 2 | Viewed by 1309

Abstract

Ormosia hosiei is a tree species native to China that has been extensively used for ornamental and furniture purposes due to its valued timber. The mating system has substantial impact on genetic diversity and structure of plant natural population. Such information should be [...] Read more.

Ormosia hosiei is a tree species native to China that has been extensively used for ornamental and furniture purposes due to its valued timber. The mating system has substantial impact on genetic diversity and structure of plant natural population. Such information should be considered when planning tree planting for forest restoration. Here we used 12 microsatellite markers and described the mating system of single families and the population genetic diversity of O. hosiei. A high level of genetic diversity was observed in both adults and progenies, although slight differences existed among populations and their progenies, with the expected heterozygosity ranging from 0.763 to 0.794. Overall, O. hosiei displayed a predominantly outcrossed mating. The estimate of multi-locus outcrossing rate (tm) was high with low variations among families, ranged from 0.997 to 1.000. The value of tm-ts, ranged from 0.000 to 0.139, indicated that biparental inbreeding occurred in progenies. Therefore, to obtain a reasonable genetic representation of native tree species and prevent problems associated with inbreeding depression, we suggested effective in situ conservation by replanting seedlings, but seedling production for restoration purposes may require a much larger sampling effort than is currently used. Moreover, it is necessary to conduct further multiple population and multi-year experiments to verify our conclusions. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Adaptive Evolution in Trees)

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10 pages, 1579 KiB

Open AccessArticle

Inbreeding in Chinese Fir: Insight into the Rare Self-Fertilizing Event from a Genetic View

by Rong Huang, Weishan Zeng, Houyin Deng, Dehuo Hu, Runhui Wang and Huiquan Zheng

Genes 2022, 13(11), 2105; https://doi.org/10.3390/genes13112105 - 13 Nov 2022

Cited by 3 | Viewed by 1205

Abstract

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is a fast-growing conifer with great forestation value and prefers outcrossing with high inbreeding depression effect. Previously, we captured a special Chinese fir parent clone named as ‘cx569’ that lacks early inbreeding depression. In view of [...] Read more.

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is a fast-growing conifer with great forestation value and prefers outcrossing with high inbreeding depression effect. Previously, we captured a special Chinese fir parent clone named as ‘cx569’ that lacks early inbreeding depression. In view of the fact that very little has been published about the rare self-fertilizing event in Chinese fir from a genetic view, herein, we conduct an SSR-based study on the variation of open- and self-pollinated offspring of this parent to gain a view of the rare self-fertilizing event. The results indicated that genetic diversity of self-pollinated offspring was significantly reduced by half (Ho: 0.302, vs. 0.595, p = 0.001; He: 0.274 vs. 0.512, p = 0.002) when compared to an open-pollinated set. Self-pollinated offspring also had significantly positive F_IS values (F_IS = 0.057, p = 0.034) with a much higher proportion of common allele (20.59% vs. 0), reflecting their heterozygote deficiency. Clustering analysis further indicated a separation of the self- and opened- pollinated groups, implying a natural preference of outcrossing for cx569. However, the cx569 still had 6% acceptance for selfing. When accepted 100% for its own pollen, the cx569 led to a genetically unique selfing group. Additionally, this selfing group seemed to be consistently homozygous at seven particular loci. These findings gave us more genetic clues to gain insight into the rare self-fertilizing event in conifer (Chinese fir). Full article

(This article belongs to the Special Issue Molecular Mechanisms of Adaptive Evolution in Trees)

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17 pages, 7206 KiB

Open AccessArticle

Climate-Driven Adaptive Differentiation in Melia azedarach: Evidence from a Common Garden Experiment

by Boyong Liao, Qingmin Que, Xingming Xu, Wei Zhou, Kunxi Ouyang, Pei Li, Huaqiang Li, Can Lai and Xiaoyang Chen

Genes 2022, 13(11), 1924; https://doi.org/10.3390/genes13111924 - 22 Oct 2022

Viewed by 1369

Abstract

Studies of local adaptation in populations of chinaberry (Melia azedarach L.) are important for clarifying patterns in the population differentiation of this species across its natural range. M. azedarach is an economically important timber species, and its phenotype is highly variable across [...] Read more.

Studies of local adaptation in populations of chinaberry (Melia azedarach L.) are important for clarifying patterns in the population differentiation of this species across its natural range. M. azedarach is an economically important timber species, and its phenotype is highly variable across its range in China. Here, we collected M. azedarach seeds from 31 populations across its range and conducted a common garden experiment. We studied patterns of genetic differentiation among populations using molecular markers (simple sequence repeats) and data on phenotypic variation in six traits collected over five years. Our sampled populations could be subdivided into two groups based on genetic analyses, as well as patterns of isolation by distance and isolation by environment. Significant differentiation in growth traits was observed among provenances and families within provenances. Geographic distance was significantly correlated with the quantitative genetic differentiation (Q_ST) in height (HEIT) and crown breadth. Climate factors were significantly correlated with the Q_ST for each trait. A total of 23 climatic factors were examined. There was a significant effect of temperature on all traits, and minimum relative humidity had a significant effect on the survival rate over four years. By comparing the neutral genetic differentiation (F_ST) with the Q_ST, the mode of selection acting on survival rate varied, whereas HEIT and the straightness of the main trunk were subject to the same mode of selection. The variation in survival rate was consistent with the variation in genetic differentiation among populations, which was indicative of local adaptation. Overall, our findings provide new insights into the responses of the phenological traits of M. azedarach to changes in the climate conditions of China. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Adaptive Evolution in Trees)

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14 pages, 2179 KiB

Open AccessArticle

Evolutionary Divergence between Toona ciliata and Toona sinensis Assayed with Their Whole Genome Sequences

by Xi Wang, Yu Xiao, Zi-Han He, Ling-Ling Li, Yan-Wen Lv and Xin-Sheng Hu

Genes 2022, 13(10), 1799; https://doi.org/10.3390/genes13101799 - 05 Oct 2022

Cited by 8 | Viewed by 1852

Abstract

Toona ciliata and Toona sinensis belong to the Toona genus of the Meliaceae family and are important timber species in China. T. ciliata is an endangered species at level II due to overcutting and a low rate of natural regeneration. T. sinensis was [...] Read more.

Toona ciliata and Toona sinensis belong to the Toona genus of the Meliaceae family and are important timber species in China. T. ciliata is an endangered species at level II due to overcutting and a low rate of natural regeneration. T. sinensis was cultivated as an economic and nutritious tree for more than 2000 years. The two species differ in flower and leaf morphological traits, reproductive systems, and range size of natural distribution. To reveal the potential molecular basis of these divergences, we examined the similarities and differences in their whole genome sequences. Results indicate that T. ciliata had a higher number of expanded gene families than T. sinensis. The whole genome duplication (WGD) occurred before their speciation. The long-terminal repeats (LTRs) insertion was earlier in the T. ciliata genome (3.2985 ± 2.5007 Mya) than in the T. sinensis genome (3.1516 ± 2.2097 Mya). Twenty-five gene families in the T. ciliata genome were detected to be under positive selection compared with background branches of ten different land species. The T. ciliata genome was highly collinear with the T. sinensis genome, but had low collinearity with the genomes of more distant species. These genomic and evolutionary divergences are potentially associated with the differences between T. ciliata and T. sinensis in terms of their reproductive systems and ecological adaptation. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Adaptive Evolution in Trees)

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