Jiaqi Wang, Yue Ding, Yinfeng Li, Xintong Gao, Xiangming Kong, Feng Long, Yishan Feng, Yan Zhang, Yu Li, Zijian Yu, Tianyu Lei, Li Wang, Xiu‐Qing Li, Jinpeng Wang
Oleaceae, a eudicot family with great species diversity, has attracted much attention from botanists because it contains many plants with important economic, medicinal, and ornamental values. However, the history of polyploidization and ancestral genome reshuffling of Oleaceae remains unclear. Here, we clarified an Oleaceae‐common hexaploidization (OCH) event occurring at ~53–61 million years ago (Ma) common in all Oleaceae plants and an Oleaceae‐recent tetraploidization (ORT) event occurring at ~18–21 Ma shared by the lineages of Syringa, Olea, Osmanthus, and Fraxinus. We found that high‐frequency polyploidization events drove the frequency of gene loss in Oleaceae genomes and extended the size of regions containing adjacent gene loss, thereby promoting the degree of genome fragmentation. We revealed that biased fractionation between the OCH‐ and ORT‐produced subgenomes is likely attributed to the origin of allopolyploidization in the OCH and ORT events. Significantly, through paleochromosome rearrangement comparisons, we proposed a "two‐step" genome duplication model for OCH and determined the duplicated orders of OCH tripled genome. We reconstructed 11 protochromosomes of the most recent ancestral Oleaceae karyotype (AOK) and elucidated the trajectories of immense paleochromosome reorganization of Oleaceae species from ancestral eudicot karyotype. Notably, we tracked the diversification history of secondary metabolite synthesis genes in the Oleaceae and explored the effects of paleogenome evolution on specialized metabolite synthesis. Our findings provide new insights into the polyploidization and paleogenomic evolution of Oleaceae and have important scientific significance for understanding the genetic basis of species and secondary metabolic diversity in Oleaceae.
{"title":"Allopolyploidization events and immense paleogenome reshuffling underlying the diversification of plants and secondary metabolites in Oleaceae","authors":"Jiaqi Wang, Yue Ding, Yinfeng Li, Xintong Gao, Xiangming Kong, Feng Long, Yishan Feng, Yan Zhang, Yu Li, Zijian Yu, Tianyu Lei, Li Wang, Xiu‐Qing Li, Jinpeng Wang","doi":"10.1111/jse.13116","DOIUrl":"https://doi.org/10.1111/jse.13116","url":null,"abstract":"Oleaceae, a eudicot family with great species diversity, has attracted much attention from botanists because it contains many plants with important economic, medicinal, and ornamental values. However, the history of polyploidization and ancestral genome reshuffling of Oleaceae remains unclear. Here, we clarified an Oleaceae‐common hexaploidization (OCH) event occurring at ~53–61 million years ago (Ma) common in all Oleaceae plants and an Oleaceae‐recent tetraploidization (ORT) event occurring at ~18–21 Ma shared by the lineages of <jats:italic>Syringa</jats:italic>, <jats:italic>Olea</jats:italic>, <jats:italic>Osmanthus</jats:italic>, and <jats:italic>Fraxinus</jats:italic>. We found that high‐frequency polyploidization events drove the frequency of gene loss in Oleaceae genomes and extended the size of regions containing adjacent gene loss, thereby promoting the degree of genome fragmentation. We revealed that biased fractionation between the OCH‐ and ORT‐produced subgenomes is likely attributed to the origin of allopolyploidization in the OCH and ORT events. Significantly, through paleochromosome rearrangement comparisons, we proposed a \"two‐step\" genome duplication model for OCH and determined the duplicated orders of OCH tripled genome. We reconstructed 11 protochromosomes of the most recent ancestral Oleaceae karyotype (AOK) and elucidated the trajectories of immense paleochromosome reorganization of Oleaceae species from ancestral eudicot karyotype. Notably, we tracked the diversification history of secondary metabolite synthesis genes in the Oleaceae and explored the effects of paleogenome evolution on specialized metabolite synthesis. Our findings provide new insights into the polyploidization and paleogenomic evolution of Oleaceae and have important scientific significance for understanding the genetic basis of species and secondary metabolic diversity in Oleaceae.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"17 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141501715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xing‐Hao Li, Ru‐Fan Li, Fang‐Jing Hu, Shuai Zheng, Fu‐Qiang Rao, Rong An, Yong‐Hong Li, De‐Guang Liu
The Cucujiformia, with remarkable morphological, ecological, and behavioral diversity, is the most evolutionarily successful group within Coleoptera. However, the phylogenetic relationships among superfamilies within Cucujiformia remain elusive. To address the issues, we conducted a transcriptome‐based macro‐evolutionary study of this lineage. We sequenced the genomes and transcriptomes of three species from the superfamily Curculionoidea (two from Curculionidae and one from Brentidae), and obtained a data set of more than 569 990 amino acid alignments from 143 species of Cucujiformia. With the most complete collection of whole genomes and transcriptomes so far, we compared the performance of different data matrices with universal‐single‐copy orthologs (USCO). The resultant trees based on different data sets were consistent for the majority of deep nodes. Two USCO amino acid matrices (i.e., USCO75 and USCO750‐abs80) provided well‐resolved topology. The analyses confirm that Cucujoidea sensu Robertson et al. 2015 is a nonmonophyletic group, consisting of Erotyloidea, Nitiduloidea, and Cucujoidea sensu Cai et al. 2022. Moreover, Erotyloidea is the early‐diverging group, followed by the clade Nitiduloidea. The preferred topologies supported a “basal” split of Coccinelloidea from the remaining superfamilies, and Cleroidea formed the second splitting group. The following phylogeny was supported at the superfamily level in Cucujiformia: (Coccinelloidea, (Cleroidea, ((Lymexyloidea, Tenebrionoidea), (Erotyloidea, (Nitiduloidea, (Cucujoidea, (Chrysomeloidea, Curculionoidea))))))). Our comprehensive analyses recovered well‐resolved higher‐level phylogenetic relationships within the Cucujiformia, providing a stable framework for comprehending its evolutionary history.
葫芦形目具有显著的形态、生态和行为多样性，是鞘翅目中进化最成功的类群。然而，鳞翅目超科之间的系统发育关系仍然难以捉摸。为了解决这些问题，我们对这一支系进行了基于转录组的宏观进化研究。我们对Curculionoidea超科的三个物种（两个来自Curculionidae，一个来自Brentidae）的基因组和转录组进行了测序，并从143个Cucujiformia物种中获得了超过569 990个氨基酸比对的数据集。有了迄今为止最完整的全基因组和转录组，我们比较了不同数据矩阵与通用单拷贝直向同源物（USCO）的性能。基于不同数据集的结果树在大多数深度节点上是一致的。两个 USCO 氨基酸矩阵（即 USCO75 和 USCO750-abs80）提供了很好的拓扑结构。分析结果证实，Cucujoidea sensu Robertson 等（2015 年）是一个非单系群，由 Erotyloidea、Nitiduloidea 和 Cucujoidea sensu Cai 等（2022 年）组成。此外，Erotyloidea 是早期分化的类群，其次是 Nitiduloidea 支系。首选的拓扑结构支持 Coccinelloidea 从其余超科中 "基本 "分裂，Cleroidea 形成第二个分裂群。Cucujiformia 在超科水平上支持以下系统发生：（Coccinelloidea）、（Cleroidea）、（（Lymexyloidea）、（Tenebrionoidea）、（Erotyloidea）、（Nitiduloidea）、（Cucujoidea）、（Chrysomeloidea）、（Curculionoidea）)))))))。我们的综合分析恢复了葫芦形目中层次较高的系统发育关系，为理解其进化历史提供了一个稳定的框架。
{"title":"Comprehensive phylogenomic analyses revealed higher‐level phylogenetic relationships within the Cucujiformia","authors":"Xing‐Hao Li, Ru‐Fan Li, Fang‐Jing Hu, Shuai Zheng, Fu‐Qiang Rao, Rong An, Yong‐Hong Li, De‐Guang Liu","doi":"10.1111/jse.13079","DOIUrl":"https://doi.org/10.1111/jse.13079","url":null,"abstract":"The Cucujiformia, with remarkable morphological, ecological, and behavioral diversity, is the most evolutionarily successful group within Coleoptera. However, the phylogenetic relationships among superfamilies within Cucujiformia remain elusive. To address the issues, we conducted a transcriptome‐based macro‐evolutionary study of this lineage. We sequenced the genomes and transcriptomes of three species from the superfamily Curculionoidea (two from Curculionidae and one from Brentidae), and obtained a data set of more than 569 990 amino acid alignments from 143 species of Cucujiformia. With the most complete collection of whole genomes and transcriptomes so far, we compared the performance of different data matrices with universal‐single‐copy orthologs (USCO). The resultant trees based on different data sets were consistent for the majority of deep nodes. Two USCO amino acid matrices (i.e., USCO75 and USCO750‐abs80) provided well‐resolved topology. The analyses confirm that Cucujoidea <jats:italic>sensu</jats:italic> Robertson et al. 2015 is a nonmonophyletic group, consisting of Erotyloidea, Nitiduloidea, and Cucujoidea <jats:italic>sensu</jats:italic> Cai et al. 2022. Moreover, Erotyloidea is the early‐diverging group, followed by the clade Nitiduloidea. The preferred topologies supported a “basal” split of Coccinelloidea from the remaining superfamilies, and Cleroidea formed the second splitting group. The following phylogeny was supported at the superfamily level in Cucujiformia: (Coccinelloidea, (Cleroidea, ((Lymexyloidea, Tenebrionoidea), (Erotyloidea, (Nitiduloidea, (Cucujoidea, (Chrysomeloidea, Curculionoidea))))))). Our comprehensive analyses recovered well‐resolved higher‐level phylogenetic relationships within the Cucujiformia, providing a stable framework for comprehending its evolutionary history.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"30 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141194100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Enzo Jugieau, Victor Talmot, Cybill Staentzel, Sandra Noir, Laurent Hardion
The two invasive Reynoutria species, Reynoutria japonica var. japonica and Reynoutria sachalinensis, and their hybrid Reynoutria x bohemica are often misidentified by managers and nonspecialists. The taxonomic confusions are all the more exacerbated by the infraspecific variability of introduced populations in terms of morphology, genetic diversity, and ploidy level. We resolved the identity of North‐Eastern French invasive populations using 4582 single‐nucleotide polymorphisms (SNPs) from a RADseq analysis, DNA contents estimated by flow cytometry, and 12 vegetative morphometric variables. The SNPs supported only one single genotype for R. japonica over 11 localities, while the nine localities of Reynoutria x bohemica were represented by one genotype each. Estimation of genome size using DAPI staining and flow cytometry revealed only octoploid cytotypes for R. japonica and hexaploid cytotypes for R. x bohemica, whereas R. sachalinensis was represented by tetraploid and hexaploid cytotypes. Among morphometric variables, no single one allows for a clear differentiation of the three taxa. We propose a combination of characters to easily and quickly identify these three invasive taxa based on six vegetative criteria including leaf and apex length, as well as leaf shape, leaf base, and apex shape, and the extrafloral nectaries on the node.
两种入侵的栗树（Reynoutria japonica var. japonica 和 Reynoutria sachalinensis）及其杂交种 Reynoutria x bohemica 经常被管理人员和非专业人员误认。引入种群在形态、遗传多样性和倍性水平方面的种下变异更加剧了分类上的混乱。我们利用 RADseq 分析得出的 4582 个单核苷酸多态性（SNPs）、流式细胞仪估算的 DNA 含量以及 12 个无性系形态变量，确定了法国东北部入侵种群的身份。这些 SNPs 只支持 11 个地方的 R. japonica 的一个单一基因型，而 Reynoutria x bohemica 的 9 个地方各有一个基因型。使用 DAPI 染色和流式细胞仪估算基因组大小时发现，R. japonica 只有八倍体细胞型，R. x bohemica 有六倍体细胞型，而 R. sachalinensis 则有四倍体和六倍体细胞型。在形态计量变量中，没有一个变量能明确区分这三个类群。我们根据叶片和顶端长度、叶片形状、叶基部和顶端形状以及节上的花外蜜腺等六个无性系标准，提出了一种特征组合，以方便快捷地识别这三个入侵类群。
{"title":"A knot of hybrids: Differentiating Asian knotweeds in North‐Eastern France using genetic, cytological, and morphological data","authors":"Enzo Jugieau, Victor Talmot, Cybill Staentzel, Sandra Noir, Laurent Hardion","doi":"10.1111/jse.13075","DOIUrl":"https://doi.org/10.1111/jse.13075","url":null,"abstract":"The two invasive <jats:italic>Reynoutria</jats:italic> species, <jats:italic>Reynoutria japonica</jats:italic> var. <jats:italic>japonica</jats:italic> and <jats:italic>Reynoutria sachalinensis</jats:italic>, and their hybrid <jats:italic>Reynoutria</jats:italic> x <jats:italic>bohemica</jats:italic> are often misidentified by managers and nonspecialists. The taxonomic confusions are all the more exacerbated by the infraspecific variability of introduced populations in terms of morphology, genetic diversity, and ploidy level. We resolved the identity of North‐Eastern French invasive populations using 4582 single‐nucleotide polymorphisms (SNPs) from a RADseq analysis, DNA contents estimated by flow cytometry, and 12 vegetative morphometric variables. The SNPs supported only one single genotype for <jats:italic>R. japonica</jats:italic> over 11 localities, while the nine localities of <jats:italic>Reynoutria</jats:italic> x <jats:italic>bohemica</jats:italic> were represented by one genotype each. Estimation of genome size using DAPI staining and flow cytometry revealed only octoploid cytotypes for <jats:italic>R. japonica</jats:italic> and hexaploid cytotypes for <jats:italic>R</jats:italic>. x <jats:italic>bohemica</jats:italic>, whereas <jats:italic>R. sachalinensis</jats:italic> was represented by tetraploid and hexaploid cytotypes. Among morphometric variables, no single one allows for a clear differentiation of the three taxa. We propose a combination of characters to easily and quickly identify these three invasive taxa based on six vegetative criteria including leaf and apex length, as well as leaf shape, leaf base, and apex shape, and the extrafloral nectaries on the node.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"18 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140942234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ryan A. Folk, Aliasghar A. Maassoumi, Carolina M. Siniscalchi, Heather R. Kates, Douglas E. Soltis, Pamela S. Soltis, Michael B. Belitz, Robert P. Guralnick
Astragalus (Fabaceae) is astoundingly diverse in temperate, cold arid regions of Earth, positioning this group as a model clade for investigating the distribution of plant diversity in the face of environmental challenges. Here, we identify the spatial distribution of diversity and endemism in Astragalus using species distribution models for 752 species and a phylogenetic tree comprising 847 species. We integrated these to map centers of species richness (SR) and relative phylogenetic diversity (RPD) and used randomization approaches to investigate centers of endemism. We also used clustering methods to identify phylogenetic regionalizations. We then assembled predictor variables of current climate conditions to test environmental factors predicting these phylogenetic diversity results, especially temperature and precipitation seasonality. We find that SR centers are distributed globally at temperate middle latitudes in arid regions, but the Mediterranean Basin is the most important center of RPD. Endemism centers also occur globally, but Iran represents a key endemic area with a concentration of both paleo‐ and neoendemism. Phylogenetic regionalization recovered an east‐west gradient in Eurasia and an amphitropical disjunction across North and South America; American phyloregions are overall most closely related to east and central Asia. SR, RPD, and lineage turnover are driven mostly by precipitation and seasonality, but endemism is driven primarily by diurnal temperature variation. Endemism and regionalization results point to western Asia and especially Iran as a biogeographic gateway between Europe and Asia. RPD and endemism highlight the importance of temperature and drought stress in determining plant diversity and endemism centers.
{"title":"Phylogenetic diversity and regionalization in the temperate arid zone","authors":"Ryan A. Folk, Aliasghar A. Maassoumi, Carolina M. Siniscalchi, Heather R. Kates, Douglas E. Soltis, Pamela S. Soltis, Michael B. Belitz, Robert P. Guralnick","doi":"10.1111/jse.13077","DOIUrl":"https://doi.org/10.1111/jse.13077","url":null,"abstract":"<jats:italic>Astragalus</jats:italic> (Fabaceae) is astoundingly diverse in temperate, cold arid regions of Earth, positioning this group as a model clade for investigating the distribution of plant diversity in the face of environmental challenges. Here, we identify the spatial distribution of diversity and endemism in <jats:italic>Astragalus</jats:italic> using species distribution models for 752 species and a phylogenetic tree comprising 847 species. We integrated these to map centers of species richness (SR) and relative phylogenetic diversity (RPD) and used randomization approaches to investigate centers of endemism. We also used clustering methods to identify phylogenetic regionalizations. We then assembled predictor variables of current climate conditions to test environmental factors predicting these phylogenetic diversity results, especially temperature and precipitation seasonality. We find that SR centers are distributed globally at temperate middle latitudes in arid regions, but the Mediterranean Basin is the most important center of RPD. Endemism centers also occur globally, but Iran represents a key endemic area with a concentration of both paleo‐ and neoendemism. Phylogenetic regionalization recovered an east‐west gradient in Eurasia and an amphitropical disjunction across North and South America; American phyloregions are overall most closely related to east and central Asia. SR, RPD, and lineage turnover are driven mostly by precipitation and seasonality, but endemism is driven primarily by diurnal temperature variation. Endemism and regionalization results point to western Asia and especially Iran as a biogeographic gateway between Europe and Asia. RPD and endemism highlight the importance of temperature and drought stress in determining plant diversity and endemism centers.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"47 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140942174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ya‐Nan Cao, Meng‐Hao Wang, Hang Ran, Bin Tian, Lu‐Xian Liu, Qing‐Nan Wu, Yan‐Yan Liu, Hong‐Wei Wang, Shan‐Shan Zhu
Dipelta Maxim. (Caprifoliaceae) is a Tertiary relic genus endemic to China, which includes three extant species, Dipelta floribunda, Dipelta yunnanensis, and Dipelta elegans. Recent progress in the systematics and phylogeographics of Dipelta has greatly broadened our knowledge about its origin and evolution, however, conflicted phylogenetic relationships and divergence times have been reported and warrant further investigation. Here, we utilized chloroplast genomes and population‐level genomic data restriction site‐associated DNA‐single nucleotide polymorphisms (RAD‐SNPs) to evaluate the interspecific relationships, population genetic structure and demographic histories of this genus. Our results confirmed the sister relationship between D. elegans and the D. yunnanensis–D. floribunda group, but with cyto‐nuclear phylogenetic discordance observed in the latter. Coalescent simulations suggested that this discordance might be attributed to asymmetric “chloroplast capture” through introgressive hybridization between the two parapatric species. Our fossil‐calibrated plastid chronogram of Dipsacales and the coalescent modeling based on nuclear RAD‐SNPs simultaneously suggested that the three species of Dipelta diversified at the late Miocene, which may be related to the uplift of the eastern part of Qinghai–Tibet Plateau (QTP) and adjacent southwest China, and increasing Asian interior aridification since the late Miocene; while in the mid‐Pleistocene, the climatic transition and continuous uplift of the QTP, triggered allopatric speciation via geographical isolation for D. floribunda and D. yunnanensis regardless of bidirectional gene flow. Based on both plastid and nuclear genome‐scale data, our findings provide the most comprehensive and reliable phylogeny and evolutionary histories for Dipelta and enable further understanding of the origin and evolution of floristic endemisms of China.
{"title":"Phylogenetic and molecular dating analyses of Chinese endemic genus Dipelta (Caprifoliaceae) based on nuclear RAD‐Seq and chloroplast genome data","authors":"Ya‐Nan Cao, Meng‐Hao Wang, Hang Ran, Bin Tian, Lu‐Xian Liu, Qing‐Nan Wu, Yan‐Yan Liu, Hong‐Wei Wang, Shan‐Shan Zhu","doi":"10.1111/jse.13076","DOIUrl":"https://doi.org/10.1111/jse.13076","url":null,"abstract":"<jats:italic>Dipelta</jats:italic> Maxim. (Caprifoliaceae) is a Tertiary relic genus endemic to China, which includes three extant species, <jats:italic>Dipelta floribunda, Dipelta yunnanensis</jats:italic>, and <jats:italic>Dipelta elegans</jats:italic>. Recent progress in the systematics and phylogeographics of <jats:italic>Dipelta</jats:italic> has greatly broadened our knowledge about its origin and evolution, however, conflicted phylogenetic relationships and divergence times have been reported and warrant further investigation. Here, we utilized chloroplast genomes and population‐level genomic data restriction site‐associated DNA‐single nucleotide polymorphisms (RAD‐SNPs) to evaluate the interspecific relationships, population genetic structure and demographic histories of this genus. Our results confirmed the sister relationship between <jats:italic>D. elegans</jats:italic> and the <jats:italic>D. yunnanensis</jats:italic>–<jats:italic>D. floribunda</jats:italic> group, but with cyto‐nuclear phylogenetic discordance observed in the latter. Coalescent simulations suggested that this discordance might be attributed to asymmetric “chloroplast capture” through introgressive hybridization between the two parapatric species. Our fossil‐calibrated plastid chronogram of Dipsacales and the coalescent modeling based on nuclear RAD‐SNPs simultaneously suggested that the three species of <jats:italic>Dipelta</jats:italic> diversified at the late Miocene, which may be related to the uplift of the eastern part of Qinghai–Tibet Plateau (QTP) and adjacent southwest China, and increasing Asian interior aridification since the late Miocene; while in the mid‐Pleistocene, the climatic transition and continuous uplift of the QTP, triggered allopatric speciation via geographical isolation for <jats:italic>D. floribunda</jats:italic> and <jats:italic>D. yunnanensis</jats:italic> regardless of bidirectional gene flow. Based on both plastid and nuclear genome‐scale data, our findings provide the most comprehensive and reliable phylogeny and evolutionary histories for <jats:italic>Dipelta</jats:italic> and enable further understanding of the origin and evolution of floristic endemisms of China.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"61 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140812964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Taxonomy of Populus is a challenging task, especially in regions with complex topography, such as the Qinghai–Tibet Plateau because of the effect of hybridization, incomplete lineage sorting, phenotypic plasticity, and convergence. In the Flora of China, Populus pseudoglanca and Populus wuana are classified into sect. Leucoides and sect. Tacamahaca, respectively, but their taxonomy remains unclear. By conducting a systematic investigation for all taxa of Populus on the plateau, we found 31 taxa from the two sections. Through identification based on morphology and habitats, we confirmed that the “P. pseudoglanca” recorded in the Flora of Sichuan is not true P. pseudoglanca, while P. pseudoglanca and P. wuana recorded in the Flora of China may refer to the same species. By performing whole‐genome re‐sequencing of 150 individuals from the 31 taxa, we derived 2.28 million single nucleotide polymorphisms (SNPs). Further genetic and phylogenetic analyses demonstrated that the genetic structure of P. wuana is extremely consistent with P. pseudoglanca, and they all originate through the natural hybridization between Populus ciliata in sect. Leucoides and Populus curviserrata in sect. Tacamahaca. Our results suggested that P. wuana should be merged with P. pseudoglanca taxonomically. This study not only clarifies the taxonomic confusions related to P. pseudoglanca and P. wuana but also provides a new framework based on the integration of morphology, distribution, habitat, and genome to solve complex taxonomic problems.
杨树的分类是一项具有挑战性的任务，尤其是在地形复杂的地区，如青藏高原，因为杂交、不完全的品系分类、表型可塑性和趋同性的影响。在《中国植物志》中，杨属植物假杨和杨属植物圆叶杨被划分为杨科（sect.Leucoides科和Tacamahaca科。但它们的分类仍不清楚。通过对高原上所有杨属植物的系统调查，我们发现了这两个科的 31 个类群。通过基于形态和生境的鉴定，我们确认了《四川植物志》中记载的 "P. pseudoglanca "并非真正的P. pseudoglanca，而《中国植物志》中记载的P. pseudoglanca和P. wuana可能指的是同一物种。通过对 31 个类群中的 150 个个体进行全基因组重测序，我们获得了 228 万个单核苷酸多态性（SNPs）。进一步的遗传和系统进化分析表明，P. wuana 的遗传结构与 P. pseudoglanca 极其一致，它们都起源于杨科（Populus ciliata in sect.Leucoides科的杨树 ciliata 和 Tacamahaca 科的杨树 curviserrata 之间的自然杂交。Tacamahaca。我们的研究结果表明，在分类学上应将 P. wuana 与 P. pseudoglanca 合并。这项研究不仅澄清了与 P. pseudoglanca 和 P. wuana 相关的分类混淆，还提供了一个基于形态学、分布、生境和基因组整合的新框架，以解决复杂的分类问题。
{"title":"A study on the distribution, origin, and taxonomy of Populus pseudoglauca and Populus wuana","authors":"Jia‐Xuan Mi, Jin‐Liang Huang, Yu‐Jie Shi, Fei‐Fei Tian, Jing Li, Fan‐Yu Meng, Fang He, Yu Zhong, Han‐Bo Yang, Fan Zhang, Liang‐Hua Chen, Xue‐Qin Wan","doi":"10.1111/jse.13074","DOIUrl":"https://doi.org/10.1111/jse.13074","url":null,"abstract":"Taxonomy of <jats:italic>Populus</jats:italic> is a challenging task, especially in regions with complex topography, such as the Qinghai–Tibet Plateau because of the effect of hybridization, incomplete lineage sorting, phenotypic plasticity, and convergence. In the <jats:italic>Flora of China</jats:italic>, <jats:italic>Populus pseudoglanca</jats:italic> and <jats:italic>Populus wuana</jats:italic> are classified into sect. <jats:italic>Leucoides</jats:italic> and sect. <jats:italic>Tacamahaca</jats:italic>, respectively, but their taxonomy remains unclear. By conducting a systematic investigation for all taxa of <jats:italic>Populus</jats:italic> on the plateau, we found 31 taxa from the two sections<jats:italic>.</jats:italic> Through identification based on morphology and habitats, we confirmed that the “<jats:italic>P. pseudoglanca</jats:italic>” recorded in the <jats:italic>Flora of Sichuan</jats:italic> is not true <jats:italic>P. pseudoglanca</jats:italic>, while <jats:italic>P. pseudoglanca</jats:italic> and <jats:italic>P. wuana</jats:italic> recorded in the <jats:italic>Flora of China</jats:italic> may refer to the same species. By performing whole‐genome re‐sequencing of 150 individuals from the 31 taxa, we derived 2.28 million single nucleotide polymorphisms (SNPs). Further genetic and phylogenetic analyses demonstrated that the genetic structure of <jats:italic>P. wuana</jats:italic> is extremely consistent with <jats:italic>P. pseudoglanca</jats:italic>, and they all originate through the natural hybridization between <jats:italic>Populus ciliata</jats:italic> in sect. <jats:italic>Leucoides</jats:italic> and <jats:italic>Populus curviserrata</jats:italic> in sect. <jats:italic>Tacamahaca</jats:italic>. Our results suggested that <jats:italic>P. wuana</jats:italic> should be merged with <jats:italic>P. pseudoglanca</jats:italic> taxonomically. This study not only clarifies the taxonomic confusions related to <jats:italic>P. pseudoglanca</jats:italic> and <jats:italic>P. wuana</jats:italic> but also provides a new framework based on the integration of morphology, distribution, habitat, and genome to solve complex taxonomic problems.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"9 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140799544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xin‐Lin Yan, Sheng‐Long Kan, Mei‐Xia Wang, Yong‐Yao Li, Luke R. Tembrock, Wen‐Chuang He, Li‐Yun Nie, Guan‐Jing Hu, Dao‐Jun Yuan, Xiong‐Feng Ma, Zhi‐Qiang Wu
Cotton (Gossypium spp.) is a vital global source of renewable fiber and ranks among the world's most important cash crops. While extensive nuclear genomic data of Gossypium has been explored, the organellar genomic resources of allotetraploid cotton, remain largely untapped at the population level. The plastid genome (plastome) is well suited for studying plant species relationships and diversity due to its nonrecombinant uniparental inheritance. Here, we conducted de novo assembly of 336 Gossypium plastomes, mainly from domesticated cultivars, and generated a pan‐plastome level resource for population structure and genetic diversity analyses. The assembled plastomes exhibited a typical quadripartite structure and varied in length from 160 103 to 160 597 bp. At the species level, seven allotetraploid species were resolved into three clades, where Gossypium tomentosum and Gossypium mustelinum formed an early diverging clade rooted by diploids, followed by splitting two sister clades of Gossypium darwinii–Gossypium barbadense and Gossypium hirsutum–Gossypium ekmanianum–Gossypium stephensii. Within the G. hirsutum clade the resolution of cultivated accessions was less polyphyletic with landrace and wild accessions than in G. barbadense suggesting some selection on plastome in the domestication of this adaptable species of cotton. The nucleotide diversity of G. hirsutum was higher than that of G. barbadense. We specifically compared the plastomes of G. hirsutum and G. barbadense to find mutational hotspots within each species as potential molecular markers. These findings contribute a valuable resource for exploring cotton evolution as well as in the breeding of new cotton cultivars and the preservation of wild and cultivated germplasm.
棉花（棉属植物）是全球重要的可再生纤维来源，也是世界上最重要的经济作物之一。虽然人们已经探索了棉花的大量核基因组数据，但在群体水平上，异源四倍体棉花的细胞器基因组资源在很大程度上仍未得到开发。质体基因组（plastome）具有非重组单亲遗传性，非常适合研究植物物种关系和多样性。在此，我们对主要来自驯化栽培品种的 336 个格桑花质粒进行了从头组装，并生成了用于种群结构和遗传多样性分析的泛质粒级资源。组装的质粒表现出典型的四方结构，长度从 160 103 到 160 597 bp 不等。在物种水平上，7 个异源四倍体物种被分解为三个支系，其中 Gossypium tomentosum 和 Gossypium mustelinum 形成了以二倍体为根的早期分化支系，随后分裂出 Gossypium darwinii-Gossypium barbadense 和 Gossypium hirsutum-Gossypium ekmanianum-Gossypium stephensii 两个姐妹支系。在 G. hirsutum 支系中，与 G. barbadense 相比，栽培品种与陆地栽培品种和野生品系的多态性较低，这表明在驯化这一适应性强的棉花品种的过程中对质体进行了一些选择。G. hirsutum 的核苷酸多样性高于 G. barbadense。我们特别比较了 G. hirsutum 和 G. barbadense 的质体，以发现每个物种中作为潜在分子标记的突变热点。这些发现为探索棉花进化、培育棉花新品种以及保存野生和栽培种质提供了宝贵的资源。
{"title":"Genetic diversity and evolution of the plastome in allotetraploid cotton (Gossypium spp.)","authors":"Xin‐Lin Yan, Sheng‐Long Kan, Mei‐Xia Wang, Yong‐Yao Li, Luke R. Tembrock, Wen‐Chuang He, Li‐Yun Nie, Guan‐Jing Hu, Dao‐Jun Yuan, Xiong‐Feng Ma, Zhi‐Qiang Wu","doi":"10.1111/jse.13070","DOIUrl":"https://doi.org/10.1111/jse.13070","url":null,"abstract":"Cotton (<jats:italic>Gossypium</jats:italic> spp.) is a vital global source of renewable fiber and ranks among the world's most important cash crops. While extensive nuclear genomic data of <jats:italic>Gossypium</jats:italic> has been explored, the organellar genomic resources of allotetraploid cotton, remain largely untapped at the population level. The plastid genome (plastome) is well suited for studying plant species relationships and diversity due to its nonrecombinant uniparental inheritance. Here, we conducted <jats:italic>de novo</jats:italic> assembly of 336 <jats:italic>Gossypium</jats:italic> plastomes, mainly from domesticated cultivars, and generated a pan‐plastome level resource for population structure and genetic diversity analyses. The assembled plastomes exhibited a typical quadripartite structure and varied in length from 160 103 to 160 597 bp. At the species level, seven allotetraploid species were resolved into three clades, where <jats:italic>Gossypium tomentosum</jats:italic> and <jats:italic>Gossypium mustelinum</jats:italic> formed an early diverging clade rooted by diploids, followed by splitting two sister clades of <jats:italic>Gossypium darwinii</jats:italic>–<jats:italic>Gossypium barbadense</jats:italic> and <jats:italic>Gossypium hirsutum</jats:italic>–<jats:italic>Gossypium ekmanianum</jats:italic>–<jats:italic>Gossypium stephensii</jats:italic>. Within the <jats:italic>G. hirsutum</jats:italic> clade the resolution of cultivated accessions was less polyphyletic with landrace and wild accessions than in <jats:italic>G. barbadense</jats:italic> suggesting some selection on plastome in the domestication of this adaptable species of cotton. The nucleotide diversity of <jats:italic>G. hirsutum</jats:italic> was higher than that of <jats:italic>G. barbadense</jats:italic>. We specifically compared the plastomes of <jats:italic>G. hirsutum</jats:italic> and <jats:italic>G. barbadense</jats:italic> to find mutational hotspots within each species as potential molecular markers. These findings contribute a valuable resource for exploring cotton evolution as well as in the breeding of new cotton cultivars and the preservation of wild and cultivated germplasm.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"225 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140612736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alexandra N. Muellner‐Riehl, Fabien Anthelme, Thomas Ibanez
{"title":"Past, present, and future of mountain and island systems","authors":"Alexandra N. Muellner‐Riehl, Fabien Anthelme, Thomas Ibanez","doi":"10.1111/jse.13073","DOIUrl":"https://doi.org/10.1111/jse.13073","url":null,"abstract":"","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"53 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140589505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zhi‐Fang Liu, Shi‐Fang Zhang, Alex D. Twyford, Xiu‐Qin Ci, Lang Li, Xiao‐Yan Zhang, Jian‐Lin Hu, Jia‐Chuan Tan, Guang‐Da Tang, Sheng‐Yuan Qin, Ling Hu, Xin Ding, Hong‐Hu Meng, Li‐Na Dong, Ting Huang, Hui Ma, Jian‐Hua Xiao, Chao‐Nan Cai, John G. Conran, Qi Wang, Peter M. Hollingsworth, Jie Li
Species delimitation remains a challenge worldwide, especially in highly diverse tropical and subtropical regions. Here, we use an integrative approach that combines morphology, phylogenomics, and species distribution modeling (SDM) to clarify the cryptic differentiation within the enigmatic hemiparasitic love vine Cassytha filiformis (Lauraceae) in China and adjacent regions. We generated complete plastid genomes and nuclear ribosomal sequences for diverse samples from across the species range and compared results with previously published plastid data, recovering two well‐supported monophyletic clades. Further, the analysis revealed significant differences in two morphological characters and SDM, indicating distinct environmental factors influencing their distributions. Fossil‐calibrated analyses to estimate the origins and diversification patterns for the cryptic species gave divergence age estimates corresponding to the Oligo‐Miocene; a period of new ecological opportunities associated with the prevailing East Asian monsoon. Multivariate analyses support the conclusion that southern China and adjacent regions have a different, previously unknown, cryptic lineage of C. filiformis. Our study highlights the importance of using multivariate approach to characterize plant species, as well as the significant role that past climatic changes have played in driving speciation in parasitic plants in tropical and subtropical zones.
{"title":"Dense infraspecific sampling reveals cryptic differentiation in the enigmatic hemiparasitic love vine Cassytha filiformis (Lauraceae)","authors":"Zhi‐Fang Liu, Shi‐Fang Zhang, Alex D. Twyford, Xiu‐Qin Ci, Lang Li, Xiao‐Yan Zhang, Jian‐Lin Hu, Jia‐Chuan Tan, Guang‐Da Tang, Sheng‐Yuan Qin, Ling Hu, Xin Ding, Hong‐Hu Meng, Li‐Na Dong, Ting Huang, Hui Ma, Jian‐Hua Xiao, Chao‐Nan Cai, John G. Conran, Qi Wang, Peter M. Hollingsworth, Jie Li","doi":"10.1111/jse.13069","DOIUrl":"https://doi.org/10.1111/jse.13069","url":null,"abstract":"Species delimitation remains a challenge worldwide, especially in highly diverse tropical and subtropical regions. Here, we use an integrative approach that combines morphology, phylogenomics, and species distribution modeling (SDM) to clarify the cryptic differentiation within the enigmatic hemiparasitic love vine <jats:italic>Cassytha filiformis</jats:italic> (Lauraceae) in China and adjacent regions. We generated complete plastid genomes and nuclear ribosomal sequences for diverse samples from across the species range and compared results with previously published plastid data, recovering two well‐supported monophyletic clades. Further, the analysis revealed significant differences in two morphological characters and SDM, indicating distinct environmental factors influencing their distributions. Fossil‐calibrated analyses to estimate the origins and diversification patterns for the cryptic species gave divergence age estimates corresponding to the Oligo‐Miocene; a period of new ecological opportunities associated with the prevailing East Asian monsoon. Multivariate analyses support the conclusion that southern China and adjacent regions have a different, previously unknown, cryptic lineage of <jats:italic>C. filiformis</jats:italic>. Our study highlights the importance of using multivariate approach to characterize plant species, as well as the significant role that past climatic changes have played in driving speciation in parasitic plants in tropical and subtropical zones.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"67 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140589584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qiang He, Yuqing Miao, Xinyuan Zheng, Yaru Wang, Yitao Wang, Zheng Jia, Hongyu Zhang, Yu Wang, Yao Xiao, Cailian Du, Wei Li, Longsheng Xing, Huilong Du
Reynoutria multiflora is a widely used medicinal plant in China. Its medicinal compounds are mainly stilbenes and anthraquinones which possess important pharmacological activities in anti-aging, anti-inflammatory and anti-oxidation, but their biosynthetic pathways are still largely unresolved. Here, we reported a near-complete genome assembly of R. multiflora consisting of 1.39 Gb with a contig N50 of 122.91 Mb and only one gap left. Genome evolution analysis revealed that two recent bursts of long terminal repeats (LTRs) contributed significantly to the increased genome size of R. multiflora, and numerous large chromosome rearrangements were observed between R. multiflora and Fagopyrum tataricum genomes. Comparative genomics analysis revealed that a recent whole-genome duplication specific to Polygonaceae led to a significant expansion of gene families associated with disease tolerance and the biosynthesis of stilbenes and anthraquinones in R. multiflora. Combining transcriptomic and metabolomic analyses, we elucidated the molecular mechanisms underlying the dynamic changes in content of medicinal ingredients in R. multiflora roots across different growth years. Additionally, we identified several putative key genes responsible for anthraquinone and stilbene biosynthesis. We identified a stilbene synthase gene PM0G05131 highly expressed in roost, which may exhibit an important role in the accumulation of stilbenes in R. multiflora. These genomic data will expedite the discovery of anthraquinone and stilbenes biosynthesis pathways in medicinal plants.
{"title":"The near-complete genome assembly of Reynoutria multiflora reveals the genetic basis of stilbenes and anthraquinones biosynthesis","authors":"Qiang He, Yuqing Miao, Xinyuan Zheng, Yaru Wang, Yitao Wang, Zheng Jia, Hongyu Zhang, Yu Wang, Yao Xiao, Cailian Du, Wei Li, Longsheng Xing, Huilong Du","doi":"10.1111/jse.13068","DOIUrl":"https://doi.org/10.1111/jse.13068","url":null,"abstract":"<i>Reynoutria multiflora</i> is a widely used medicinal plant in China. Its medicinal compounds are mainly stilbenes and anthraquinones which possess important pharmacological activities in anti-aging, anti-inflammatory and anti-oxidation, but their biosynthetic pathways are still largely unresolved. Here, we reported a near-complete genome assembly of <i>R. multiflora</i> consisting of 1.39 Gb with a contig N50 of 122.91 Mb and only one gap left. Genome evolution analysis revealed that two recent bursts of long terminal repeats (LTRs) contributed significantly to the increased genome size of <i>R. multiflora</i>, and numerous large chromosome rearrangements were observed between <i>R. multiflora</i> and <i>Fagopyrum tataricum</i> genomes. Comparative genomics analysis revealed that a recent whole-genome duplication specific to Polygonaceae led to a significant expansion of gene families associated with disease tolerance and the biosynthesis of stilbenes and anthraquinones in <i>R. multiflora</i>. Combining transcriptomic and metabolomic analyses, we elucidated the molecular mechanisms underlying the dynamic changes in content of medicinal ingredients in <i>R. multiflora</i> roots across different growth years. Additionally, we identified several putative key genes responsible for anthraquinone and stilbene biosynthesis. We identified a stilbene synthase gene <i>PM0G05131</i> highly expressed in roost, which may exhibit an important role in the accumulation of stilbenes in <i>R. multiflora</i>. These genomic data will expedite the discovery of anthraquinone and stilbenes biosynthesis pathways in medicinal plants.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"16 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140325754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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