Saussurea is one of the largest and most rapidly evolving genera within the Asteraceae,comprising approximately 520 species from the Northern Hemisphere.A comprehensive infrageneric classification,supported by robust ...Saussurea is one of the largest and most rapidly evolving genera within the Asteraceae,comprising approximately 520 species from the Northern Hemisphere.A comprehensive infrageneric classification,supported by robust phylogenetic trees and corroborated by morphological and other data,has not yet been published.For the first time,we recovered a well-resolved nuclear phylogeny of Saussurea consisting of four main clades,which was also supported by morphological data.Our analyses show that ancient hybridization is the most likely source of deep cytoplasmic-nuclear conflict in Saussurea,and a phylogeny based on nuclear data is more suitable than one based on chloroplast data for exploring the infrageneric classification of Saussurea.Based on the nuclear phylogeny obtained and morphological characters,we proposed a revised infrageneric taxonomy of Saussurea,which includes four subgenera and 13 sections.Specifically,1)S.sect.Cincta,S.sect.Gymnocline,S.sect.Lagurostemon,and S.sect.Strictae were moved from S.subg.Saussurea to S.subg.Amphilaena,2)S.sect.Pseudoeriocoryne was moved from S.subg.Eriocoryne to S.subg.Amphilaena,and 3)S.sect.Laguranthera was moved from S.subg.Saussurea to S.subg.Theodorea.展开更多
The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannot...The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannotating and utilizing plastome sequences remain challenging.Therefore,a streamlined phylogenomic pipeline spanning plastome annotation,phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome.Here,we develop PlastidHub,a novel web application employing innovative tools to analyze plastome sequences.In comparison with existing tools,key novel functionalities in PlastidHub include:(1)standardization of quadripartite structure;(2)improvement of annotation flexibility and consistency;(3)quantitative assessment of annotation completeness;(4)diverse extraction modes for canonical and specialized sequences;(5)intelligent screening of molecular markers for biodiversity studies;(6)genelevel visual comparison of structural variations and annotation completeness.PlastidHub features cloud-based web applications that do not require users to install,update,or maintain tools;detailed help documents including user guides,test examples,a static pop-up prompt box,and dynamic pop-up warning prompts when entering unreasonable parameter values;batch processing capabilities for all tools;intermediate results for secondary use;and easy-to-operate task flows between fileupload and download.A key feature of PlastidHub is its interrelated task-based user interface design.Give that PlastidHub is easy to use without specialized computational skills or resources,this new platform should be widely used among botanists and evolutionary biologists,improving and expediting research employing the plastome.PlastidHub is available at https://www.plastidhub.cn.展开更多
Dryopteridaceae are the largest fern family and include nearly 20%of extant fern diversity,with 24 currently recognized genera.Recognition and delineation of genera within this family have varied greatly.The three-sub...Dryopteridaceae are the largest fern family and include nearly 20%of extant fern diversity,with 24 currently recognized genera.Recognition and delineation of genera within this family have varied greatly.The three-subfamily classification of Dryopteridaceae was based primarily on molecular phylogenetic relationships but lacked morphological evidence,and the phylogenetic relationships of the subfamilies and genera of Dryopteridaceae are only partially resolved.A comprehensive and robust phylogeny is urgently needed.The heterogeneous morphology of the current members of Dryopteridaceae makes the family and its subfamilies difficult to define by single morphological characteristics or even character combinations.We carried out phylogenetic analyses to reconstruct a highly supported phylogeny of Dryopteridaceae.Our analyses recovered 24 strongly supported clades grouped into seven major clades of Dryopteridaceae.Seven morphological characters including habit,rhizome shape,frond morphology,rachis-costae architecture,appendages on stipe base and lamina,and soral arrangement were found to be informative for identifying different major clades and clades in Dryopteridaceae.Based on phylogenetic reconstruction and morphological analysis,we presented an updated infra-familial classification of Dryopteridaceae with seven subfamilies and 24 genera including four newly proposed subfamilies(Ctenitidoideae,Lastreopsidoideae,Pleocnemioideae,and Polystichopsidoideae).Morphological character combinations of each subfamily are summarized,and a key is provided.Most genera sensu PPG I are recognized,with Stigmatopetris reclassified into Dryopteridoideae and Arthrobotrya considered a synonym of Teratophyllum.A new genus Pseudarachniodes is introduced.This revised classification will serve as a foundational framework for future investigations on taxonomy,biogeography,and diversification of the most species-rich Dryopteridaceae in ferns.展开更多
Living gymnosperms comprise four major groups:cycads,Ginkgo,conifers,and gnetophytes.Relationships among/within these lineages have not been fully resolved.Next generation sequencing has made available a large number ...Living gymnosperms comprise four major groups:cycads,Ginkgo,conifers,and gnetophytes.Relationships among/within these lineages have not been fully resolved.Next generation sequencing has made available a large number of sequences,including both plastomes and single-copy nuclear genes,for reconstruction of solid phylogenetic trees.Recent advances in gymnosperm phylogenomic studies have updated our knowledge of gymnosperm systematics.Here,we review major advances of gymnosperm phylogeny over the past 10 years and propose an updated classification of extant gymnosperms.This new classification includes three classes(Cycadopsida,Ginkgoopsida,and Pinopsida),five subclasses(Cycadidae,Ginkgoidae,Cupressidae,Pinidae,and Gnetidae),eight orders(Cycadales,Ginkgoales,Araucariales,Cupressales,Pinales,Ephedrales,Gnetales,and Welwitschiales),13 families,and 86 genera.We also described six new tribes including Acmopyleae Y.Yang,Austrocedreae Y.Yang,Chamaecyparideae Y.Yang,Microcachrydeae Y.Yang,Papuacedreae Y.Yang,and Prumnopityeae Y.Yang,and made 27 new combinations in the genus Sabina.展开更多
The rapid expansion of next-generation sequencing （NGS） has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets o...The rapid expansion of next-generation sequencing （NGS） has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genome- partitioning approaches in plant phylogenomics： genome skimming, transcriptome sequencing （RNA- seq）, restriction site associated DNA sequencing （RAD-Seq）, and targeted capture （Hyb-seq）. Of these four genome-partitioning approaches, targeted capture （especially Hyb-seq） shows the greatest promise for plant phy^ogenetics over the next fex~ years. This reviex~ wi~ aid ~esea^chers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion ofwhole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.展开更多
The cosmopolitan family Solanaceae,which originated and first diversified in South America,is economically important.The tribe Hyoscyameae is one of the three clades in Solanaceae that occurs outside of the New World;...The cosmopolitan family Solanaceae,which originated and first diversified in South America,is economically important.The tribe Hyoscyameae is one of the three clades in Solanaceae that occurs outside of the New World;Hyoscyameae genera are distributed mainly in Europe and Asia,and have centers of species diversity in the Qinghai-Tibet Plateau and adjacent regions.Although many phylogenetic studies have focused on Solanaceae,the phylogenetic relationships within the tribe Hyoscyameae and its biogeographic history remain obscure.In this study,we reconstructed the phylogeny of Hyoscyameae based on whole chloroplast genome data,and estimated lineage divergence times according to the newly reported fruit fossil from the Eocene Patagonia,Physalis infinemundi,the earliest known fossil of Solanaceae.We reconstructed a robust phylogeny of Hyoscyameae that reveals the berry fruit-type Atropa is sister to the six capsule-bearing genera(Hyoscyameae sensu stricto),Atropanthe is sister to the clade(Scopolia,Physochlaina,Przewalskia),and together they are sister to the robustly supported AnisoduseHyoscyamus clade.The stem age of Hyoscyameae was inferred to be in the Eocene(47.11 Ma,95%HPD:36.75e57.86 Ma),and the crown ages of Hyoscyameae sensu stricto were estimated as the early Miocene(22.52 Ma,95%HPD:15.19e30.53 Ma),which shows a close correlation with the rapid uplift of the Qinghai-Tibet Plateau at the Paleogene/Neogene boundary.Our results provide insights into the phylogenetic relationships and the history of the biogeographic diversification of the tribe Hyoscyameae,as well as plant diversification on the Qinghai-Tibet Plateau.展开更多
Spiders are among the most varied terrestrial predators,with highly diverse morphology,ecology,and behavior.Morphological and molecular data have greatly contributed to advances in the phylogeny and evolutionary dynam...Spiders are among the most varied terrestrial predators,with highly diverse morphology,ecology,and behavior.Morphological and molecular data have greatly contributed to advances in the phylogeny and evolutionary dynamics of spiders.Here,we performed comprehensive mitochondrial phylogenomics analysis on 78 mitochondrial genomes(mitogenomes)representing 29 families;of these,23 species from eight families were newly generated.Mesothelae retained the same gene arrangement as the arthropod ancestor(Limulus polyphemus),while Opisthothelae showed extensive rearrangement,with 12 rearrangement types in transfer RNAs(tRNAs)and control region.Most spider tRNAs were extremely truncated and lacked typical dihydrouridine or TΨC arms,showing high tRNA structural diversity;in particular,trnS1 exhibited anticodon diversity across the phylogeny.The evolutionary rates of mitochondrial genes were potentially associated with gene rearrangement or truncated tRNAs.Both mitogenomic sequences and rearrangements possessed phylogenetic characteristics,providing a robust backbone for spider phylogeny,as previously reported.The monophyly of suborder,infraorder,retrolateral tibial apophysis clade,and families(except for Pisauridae)was separately supported,and high-level relationships were resolved as(Mesothelae,(Mygalomorphae,(Entelegynae,(Synspermiata,Hypochilidae)))).The phylogenetic positions of several families were also resolved(e.g.,Eresidae,Oecobiidae and Titanoecidae).Two reconstructions of ancestral web type obtained almost identical results,indicating that the common ancestor of spiders likely foraged using a silk-lined burrow.This study,the largest mitochondrial phylogenomics analysis of spiders to date,highlights the usefulness of mitogenomic data not only for providing efficient phylogenetic signals for spider phylogeny,but also for characterizing trait diversification in spider evolution.展开更多
基金supported by the National Natural Science Foundation of China(grant no.32200172)Guangzhou Science and technology project(grant no.2023A04J0715).
文摘Saussurea is one of the largest and most rapidly evolving genera within the Asteraceae,comprising approximately 520 species from the Northern Hemisphere.A comprehensive infrageneric classification,supported by robust phylogenetic trees and corroborated by morphological and other data,has not yet been published.For the first time,we recovered a well-resolved nuclear phylogeny of Saussurea consisting of four main clades,which was also supported by morphological data.Our analyses show that ancient hybridization is the most likely source of deep cytoplasmic-nuclear conflict in Saussurea,and a phylogeny based on nuclear data is more suitable than one based on chloroplast data for exploring the infrageneric classification of Saussurea.Based on the nuclear phylogeny obtained and morphological characters,we proposed a revised infrageneric taxonomy of Saussurea,which includes four subgenera and 13 sections.Specifically,1)S.sect.Cincta,S.sect.Gymnocline,S.sect.Lagurostemon,and S.sect.Strictae were moved from S.subg.Saussurea to S.subg.Amphilaena,2)S.sect.Pseudoeriocoryne was moved from S.subg.Eriocoryne to S.subg.Amphilaena,and 3)S.sect.Laguranthera was moved from S.subg.Saussurea to S.subg.Theodorea.
基金the Natural Science Foundation of Shandong Province(ZR2020QC022)the Science and Technology Basic Resources Investigation Program of China(No.2019FY100900)+2 种基金the Major Program for Basic Research Project of Yunnan Province(202401BC070001)Yunnan Revitalization Talent Support Program:Yunling Scholar Project to Tingshuang Yithe open research project of“Cross Cooperative Team”of the Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences.
文摘The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannotating and utilizing plastome sequences remain challenging.Therefore,a streamlined phylogenomic pipeline spanning plastome annotation,phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome.Here,we develop PlastidHub,a novel web application employing innovative tools to analyze plastome sequences.In comparison with existing tools,key novel functionalities in PlastidHub include:(1)standardization of quadripartite structure;(2)improvement of annotation flexibility and consistency;(3)quantitative assessment of annotation completeness;(4)diverse extraction modes for canonical and specialized sequences;(5)intelligent screening of molecular markers for biodiversity studies;(6)genelevel visual comparison of structural variations and annotation completeness.PlastidHub features cloud-based web applications that do not require users to install,update,or maintain tools;detailed help documents including user guides,test examples,a static pop-up prompt box,and dynamic pop-up warning prompts when entering unreasonable parameter values;batch processing capabilities for all tools;intermediate results for secondary use;and easy-to-operate task flows between fileupload and download.A key feature of PlastidHub is its interrelated task-based user interface design.Give that PlastidHub is easy to use without specialized computational skills or resources,this new platform should be widely used among botanists and evolutionary biologists,improving and expediting research employing the plastome.PlastidHub is available at https://www.plastidhub.cn.
基金funded by the National Natural Science Foundation of China(Grant No.31970232)the National Key Basic Research Program of China(Grant No.2014CB954100).
文摘Dryopteridaceae are the largest fern family and include nearly 20%of extant fern diversity,with 24 currently recognized genera.Recognition and delineation of genera within this family have varied greatly.The three-subfamily classification of Dryopteridaceae was based primarily on molecular phylogenetic relationships but lacked morphological evidence,and the phylogenetic relationships of the subfamilies and genera of Dryopteridaceae are only partially resolved.A comprehensive and robust phylogeny is urgently needed.The heterogeneous morphology of the current members of Dryopteridaceae makes the family and its subfamilies difficult to define by single morphological characteristics or even character combinations.We carried out phylogenetic analyses to reconstruct a highly supported phylogeny of Dryopteridaceae.Our analyses recovered 24 strongly supported clades grouped into seven major clades of Dryopteridaceae.Seven morphological characters including habit,rhizome shape,frond morphology,rachis-costae architecture,appendages on stipe base and lamina,and soral arrangement were found to be informative for identifying different major clades and clades in Dryopteridaceae.Based on phylogenetic reconstruction and morphological analysis,we presented an updated infra-familial classification of Dryopteridaceae with seven subfamilies and 24 genera including four newly proposed subfamilies(Ctenitidoideae,Lastreopsidoideae,Pleocnemioideae,and Polystichopsidoideae).Morphological character combinations of each subfamily are summarized,and a key is provided.Most genera sensu PPG I are recognized,with Stigmatopetris reclassified into Dryopteridoideae and Arthrobotrya considered a synonym of Teratophyllum.A new genus Pseudarachniodes is introduced.This revised classification will serve as a foundational framework for future investigations on taxonomy,biogeography,and diversification of the most species-rich Dryopteridaceae in ferns.
基金supported by the National Natural Science Foundation of China(31970205,31870206)the Metasequoia funding of the Nanjing Forestry University,China。
文摘Living gymnosperms comprise four major groups:cycads,Ginkgo,conifers,and gnetophytes.Relationships among/within these lineages have not been fully resolved.Next generation sequencing has made available a large number of sequences,including both plastomes and single-copy nuclear genes,for reconstruction of solid phylogenetic trees.Recent advances in gymnosperm phylogenomic studies have updated our knowledge of gymnosperm systematics.Here,we review major advances of gymnosperm phylogeny over the past 10 years and propose an updated classification of extant gymnosperms.This new classification includes three classes(Cycadopsida,Ginkgoopsida,and Pinopsida),five subclasses(Cycadidae,Ginkgoidae,Cupressidae,Pinidae,and Gnetidae),eight orders(Cycadales,Ginkgoales,Araucariales,Cupressales,Pinales,Ephedrales,Gnetales,and Welwitschiales),13 families,and 86 genera.We also described six new tribes including Acmopyleae Y.Yang,Austrocedreae Y.Yang,Chamaecyparideae Y.Yang,Microcachrydeae Y.Yang,Papuacedreae Y.Yang,and Prumnopityeae Y.Yang,and made 27 new combinations in the genus Sabina.
基金supported by the Large-scale Scientific Facilities of the Chinese Academy of Sciences (Grant No: 2017-LSFGBOWS-01)the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31000000)the Program of Science and Technology Talents Training of Yunnan Province (2017HA014)
文摘The rapid expansion of next-generation sequencing （NGS） has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genome- partitioning approaches in plant phylogenomics： genome skimming, transcriptome sequencing （RNA- seq）, restriction site associated DNA sequencing （RAD-Seq）, and targeted capture （Hyb-seq）. Of these four genome-partitioning approaches, targeted capture （especially Hyb-seq） shows the greatest promise for plant phy^ogenetics over the next fex~ years. This reviex~ wi~ aid ~esea^chers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion ofwhole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.
基金We thank Dr.Xiao-Feng Chi and Dr.Ofelia Vargas-Ponce for contributing the whole chloroplast genome sequences of Anisodus tanguticus(Maxim.)Pascher and Physalis philadelphica Lam.before the release in NCBI.This work was supported by the Beijing Natural Science Foundation(Grant No.5192012)National Natural Science Foundation of China(grant number 32070235)the China Scholarship Council(Grant No.201906515009)。
文摘The cosmopolitan family Solanaceae,which originated and first diversified in South America,is economically important.The tribe Hyoscyameae is one of the three clades in Solanaceae that occurs outside of the New World;Hyoscyameae genera are distributed mainly in Europe and Asia,and have centers of species diversity in the Qinghai-Tibet Plateau and adjacent regions.Although many phylogenetic studies have focused on Solanaceae,the phylogenetic relationships within the tribe Hyoscyameae and its biogeographic history remain obscure.In this study,we reconstructed the phylogeny of Hyoscyameae based on whole chloroplast genome data,and estimated lineage divergence times according to the newly reported fruit fossil from the Eocene Patagonia,Physalis infinemundi,the earliest known fossil of Solanaceae.We reconstructed a robust phylogeny of Hyoscyameae that reveals the berry fruit-type Atropa is sister to the six capsule-bearing genera(Hyoscyameae sensu stricto),Atropanthe is sister to the clade(Scopolia,Physochlaina,Przewalskia),and together they are sister to the robustly supported AnisoduseHyoscyamus clade.The stem age of Hyoscyameae was inferred to be in the Eocene(47.11 Ma,95%HPD:36.75e57.86 Ma),and the crown ages of Hyoscyameae sensu stricto were estimated as the early Miocene(22.52 Ma,95%HPD:15.19e30.53 Ma),which shows a close correlation with the rapid uplift of the Qinghai-Tibet Plateau at the Paleogene/Neogene boundary.Our results provide insights into the phylogenetic relationships and the history of the biogeographic diversification of the tribe Hyoscyameae,as well as plant diversification on the Qinghai-Tibet Plateau.
基金supported by the Second Tibetan Plateau Scientific Expedition and Research(STEP)Program(2019QZKK0302)Natural Science Foundation of Gansu Province(20JR5RA252)Innovation and Entrepreneurship Project of Lanzhou University(20210010020,20210010002)。
文摘Spiders are among the most varied terrestrial predators,with highly diverse morphology,ecology,and behavior.Morphological and molecular data have greatly contributed to advances in the phylogeny and evolutionary dynamics of spiders.Here,we performed comprehensive mitochondrial phylogenomics analysis on 78 mitochondrial genomes(mitogenomes)representing 29 families;of these,23 species from eight families were newly generated.Mesothelae retained the same gene arrangement as the arthropod ancestor(Limulus polyphemus),while Opisthothelae showed extensive rearrangement,with 12 rearrangement types in transfer RNAs(tRNAs)and control region.Most spider tRNAs were extremely truncated and lacked typical dihydrouridine or TΨC arms,showing high tRNA structural diversity;in particular,trnS1 exhibited anticodon diversity across the phylogeny.The evolutionary rates of mitochondrial genes were potentially associated with gene rearrangement or truncated tRNAs.Both mitogenomic sequences and rearrangements possessed phylogenetic characteristics,providing a robust backbone for spider phylogeny,as previously reported.The monophyly of suborder,infraorder,retrolateral tibial apophysis clade,and families(except for Pisauridae)was separately supported,and high-level relationships were resolved as(Mesothelae,(Mygalomorphae,(Entelegynae,(Synspermiata,Hypochilidae)))).The phylogenetic positions of several families were also resolved(e.g.,Eresidae,Oecobiidae and Titanoecidae).Two reconstructions of ancestral web type obtained almost identical results,indicating that the common ancestor of spiders likely foraged using a silk-lined burrow.This study,the largest mitochondrial phylogenomics analysis of spiders to date,highlights the usefulness of mitogenomic data not only for providing efficient phylogenetic signals for spider phylogeny,but also for characterizing trait diversification in spider evolution.
