Journal of Systematics and Evolution最新文献

{"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}

{"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}

{"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}

{"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}

{"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}

{"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}

{"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}

{"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}

{"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}

{"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}