Chloroplast phylogenomic analysis provides insights into the evolution of the largest eukaryotic genome holder, Paris japonica (Melanthiaceae)
Yang, Lifang1,5; Yang, Zhenyan1; Liu, Changkun1; He, Zhengshan3; Zhang, Zhirong3; Yang, Jing3; Liu, Haiyang4; Yang, Junbo3; Ji, Yunheng1,2
Corresponding AuthorYang, Junbo(jbyang@mail.kib.ac.cn) ; Ji, Yunheng(jiyh@mail.kib.ac.cn)
2019-07-04
Source PublicationBMC PLANT BIOLOGY
ISSN1471-2229
Volume19Pages:11
AbstractBackgroundRobust phylogenies for species with giant genomes and closely related taxa can build evolutionary frameworks for investigating the origin and evolution of these genomic gigantisms. Paris japonica (Melanthiaceae) has the largest genome that has been confirmed in eukaryotes to date; however, its phylogenetic position remains unresolved. As a result, the evolutionary history of the genomic gigantisms in P. japonica remains poorly understood.ResultsWe used next-generation sequencing to generate complete plastomes of P. japonica, P. verticillata, Trillium govanianum, Ypsilandra thibetica and Y. yunnanensis. Together with published plastomes, the infra-familial relationships in Melanthiaceae and infra-generic phylogeny in Paris were investigated, and their divergence times were calculated. The results indicated that the expansion of the ancestral genome of extant Paris and Trillium occurred approximately from 59.16 Mya to 38.21 Mya. The sister relationship between P. japonica and the section Euthyra was recovered, and they diverged around the transition of the Oligocene/Miocene (20 Mya), when the Japan Islands were separated from the continent of Asia.ConclusionsThe genome size expansion in the most recent common ancestor for Paris and Trillium was most possibly a gradual process that lasted for approximately 20 million years. The divergence of P. japonica (section Kinugasa) and other taxa with thick rhizome may have been triggered by the isolation of the Japan Islands from the continent of Asia. This long-term separation, since the Oligocene/Miocene boundary, would have played an important role in the formation and evolution of the genomic gigantism in P. japonica. Moreover, our results support the taxonomic treatment of Paris as a genus rather than dividing it into three genera, but do not support the recognition of T. govanianum as the separate genus Trillidium.
KeywordPlastome Phylogenomics Giant genome Evolution Paris japonica Paris Trillium govanianum
DOI10.1186/s12870-019-1879-7
Indexed BySCI
Language英语
WOS Research AreaPlant Sciences
WOS SubjectPlant Sciences
WOS IDWOS:000474595500002
Citation statistics
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/67438
Collection植物化学与西部植物资源持续利用国家重点实验室
Corresponding AuthorYang, Junbo; Ji, Yunheng
Affiliation1.Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Divers & Biogeog East Asia, Kunming, Yunnan, Peoples R China
2.Chinese Acad Sci, Kunming Inst Bot, Yunnan Key Lab Integrat Conservat Plant Species E, Kunming, Yunnan, Peoples R China
3.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming, Yunnan, Peoples R China
4.Chinese Acad Sci, Kunming Inst Bot, State Key Lab Phytochem & Plant Resources West Ch, Kunming, Yunnan, Peoples R China
5.Yunnan Univ, Sch Life Sci, Kunming, Yunnan, Peoples R China
Recommended Citation
GB/T 7714
Yang, Lifang,Yang, Zhenyan,Liu, Changkun,et al. Chloroplast phylogenomic analysis provides insights into the evolution of the largest eukaryotic genome holder, Paris japonica (Melanthiaceae)[J]. BMC PLANT BIOLOGY,2019,19:11.
APA Yang, Lifang.,Yang, Zhenyan.,Liu, Changkun.,He, Zhengshan.,Zhang, Zhirong.,...&Ji, Yunheng.(2019).Chloroplast phylogenomic analysis provides insights into the evolution of the largest eukaryotic genome holder, Paris japonica (Melanthiaceae).BMC PLANT BIOLOGY,19,11.
MLA Yang, Lifang,et al."Chloroplast phylogenomic analysis provides insights into the evolution of the largest eukaryotic genome holder, Paris japonica (Melanthiaceae)".BMC PLANT BIOLOGY 19(2019):11.
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