Chloroplast phylogenomic analysis provides insights into the evolution of the largest eukaryotic genome holder, Paris japonica (Melanthiaceae)

doi:10.1186/s12870-019-1879-7

	Chloroplast phylogenomic analysis provides insights into the evolution of the largest eukaryotic genome holder, Paris japonica (Melanthiaceae)
	Yang, Lifang 1,5; Yang, Zhenyan 1; Liu, Changkun 1; He, Zhengshan 3; Zhang, Zhirong3 ; Yang, Jing3 ; Liu, Haiyang4 ; Yang, Junbo 3; Ji, Yunheng1,2
通讯作者	Yang, Junbo(jbyang@mail.kib.ac.cn) ; Ji, Yunheng(jiyh@mail.kib.ac.cn)
	2019-07-04
发表期刊	BMC PLANT BIOLOGY
ISSN	1471-2229
卷号	19 页码:11
摘要	BackgroundRobust 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.
关键词	Plastome Phylogenomics Giant genome Evolution Paris japonica Paris Trillium govanianum
DOI	10.1186/s12870-019-1879-7
收录类别	SCI
语种	英语
WOS记录号	WOS:000474595500002
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/67438
专题	植物化学与西部植物资源持续利用国家重点实验室
通讯作者	Yang, Junbo; Ji, Yunheng
作者单位	1.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
推荐引用方式 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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