Zetao Jin, Dai-Kun Ma, Guang-Ning Liu, Richard G. J. Hodel, Yan Jiang, Bin‐Jie Ge, Shuai Liao, Lei Duan, Chen Ren, Chao Xu, Junyao Wu, Bing Liu
{"title":"推进梨属的系统发育:基于深度基因组略读的推断与旁系分析产生了一个稳健的系统发育骨架,并更新了梨属(马列,蔷薇科)的属下分类","authors":"Zetao Jin, Dai-Kun Ma, Guang-Ning Liu, Richard G. J. Hodel, Yan Jiang, Bin‐Jie Ge, Shuai Liao, Lei Duan, Chen Ren, Chao Xu, Junyao Wu, Bing Liu","doi":"10.1002/tax.13163","DOIUrl":null,"url":null,"abstract":"The lack of a robust phylogenetic backbone has posed significant challenges to proposing an infrageneric taxonomic classification of the pear genus, Pyrus, a widely distributed Eurasian lineage of Rosaceae. This issue has been exacerbated by limited informative loci and inaccessible taxon sampling. To address these limitations, we conducted extensive taxon sampling, encompassing 78 Pyrus ingroup individuals representing 32 species, along with 4 outgroup species. This comprehensive sampling strategy covers a wide range of morphological and geographical variations. To enable accurate phylogenomic inference, we assembled 801 single‐copy nuclear genes and 72 plastid coding sequences from deep genome skimming (DGS) data. Additionally, we employed a tree‐based method for nuclear orthology inference, which led to the generation of three orthologous datasets: one‐to‐one orthologs (1to1), monophyletic outgroups (MO), and rooted ingroups (RT). The results yielded from both nuclear and plastid analyses consistently support the monophyly of Pyrus, and two well‐supported clades, the Occidental and Oriental clades, were recovered in nine nuclear and three plastid trees. Integrating evidence from morphology and phylogenomics, we propose an updated infrageneric classification of Pyrus, which consists of two subgenera: P. subg. Pyrus and P. subg. Pashia stat. nov. This revised classification provides a more robust framework for understanding the evolutionary relationships within the pear genus.","PeriodicalId":49448,"journal":{"name":"Taxon","volume":null,"pages":null},"PeriodicalIF":3.0000,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Advancing Pyrus phylogeny: Deep genome skimming‐based inference coupled with paralogy analysis yields a robust phylogenetic backbone and an updated infrageneric classification of the pear genus (Maleae, Rosaceae)\",\"authors\":\"Zetao Jin, Dai-Kun Ma, Guang-Ning Liu, Richard G. J. 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Additionally, we employed a tree‐based method for nuclear orthology inference, which led to the generation of three orthologous datasets: one‐to‐one orthologs (1to1), monophyletic outgroups (MO), and rooted ingroups (RT). The results yielded from both nuclear and plastid analyses consistently support the monophyly of Pyrus, and two well‐supported clades, the Occidental and Oriental clades, were recovered in nine nuclear and three plastid trees. Integrating evidence from morphology and phylogenomics, we propose an updated infrageneric classification of Pyrus, which consists of two subgenera: P. subg. Pyrus and P. subg. Pashia stat. nov. 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Advancing Pyrus phylogeny: Deep genome skimming‐based inference coupled with paralogy analysis yields a robust phylogenetic backbone and an updated infrageneric classification of the pear genus (Maleae, Rosaceae)
The lack of a robust phylogenetic backbone has posed significant challenges to proposing an infrageneric taxonomic classification of the pear genus, Pyrus, a widely distributed Eurasian lineage of Rosaceae. This issue has been exacerbated by limited informative loci and inaccessible taxon sampling. To address these limitations, we conducted extensive taxon sampling, encompassing 78 Pyrus ingroup individuals representing 32 species, along with 4 outgroup species. This comprehensive sampling strategy covers a wide range of morphological and geographical variations. To enable accurate phylogenomic inference, we assembled 801 single‐copy nuclear genes and 72 plastid coding sequences from deep genome skimming (DGS) data. Additionally, we employed a tree‐based method for nuclear orthology inference, which led to the generation of three orthologous datasets: one‐to‐one orthologs (1to1), monophyletic outgroups (MO), and rooted ingroups (RT). The results yielded from both nuclear and plastid analyses consistently support the monophyly of Pyrus, and two well‐supported clades, the Occidental and Oriental clades, were recovered in nine nuclear and three plastid trees. Integrating evidence from morphology and phylogenomics, we propose an updated infrageneric classification of Pyrus, which consists of two subgenera: P. subg. Pyrus and P. subg. Pashia stat. nov. This revised classification provides a more robust framework for understanding the evolutionary relationships within the pear genus.
期刊介绍:
TAXON is the bi-monthly journal of the International Association for Plant Taxonomy and is devoted to systematic and evolutionary biology with emphasis on plants and fungi. It is published bimonthly by the International Bureau for Plant Taxonomy and Nomenclature, c/o Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, SLOVAKIA. Details of page charges are given in the Guidelines for authors. Papers will be reviewed by at least two specialists.