Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns

doi:10.1111/tpj.13583

	Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns
	Shen, Hui ; Jin, Dongmei ; Shu, Jiang-Ping ; Zhou, Xi-Le ; Lei, Ming 2; Wei, Ran ; Shang, Hui ; Wei, Hong-Jin ; Zhang, Rui ; Liu, Li ; Gu, Yu-Feng ; Zhang, Xian-Chun; Yan, Yue-Hong
	2017
发表期刊	GIGASCIENCE
ISSN	2047-217X
卷号	7 期号:2
摘要	Background: Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. Results: With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Conclusions: Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants.
关键词	phylogenomic monilophytes evolution sporangium transcriptome
学科领域	Plant Sciences
DOI	10.1111/tpj.13583
收录类别	SCI
语种	英语
WOS关键词	RNA-SEQ ; MOLECULAR PHYLOGENY ; CLASSIFICATION ; TREE ; MORPHOLOGY ; EVOLUTION ; RELATIVES ; INSIGHTS
WOS记录号	WOS:000405572800010
出版者	OXFORD UNIV PRESS
文献子类	Article
出版地	OXFORD
资助机构	Shanghai Landscaping and City Appearance Administrative Bureau of China [G142433, G152420, F112422] ; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31370234]
作者邮箱	yhyan@sibs.ac.cn
作品OA属性	Bronze
引用统计	被引频次：19[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/22283
专题	系统与进化植物学国家重点实验室
作者单位	1.Chinese Acad Sci, Shanghai Chenshan Plant Sci Res Ctr, 3888 Chenhua Rd, Shanghai 201602, Peoples R China 2.Shanghai Chenshan Bot Garden, Shanghai Key Lab Plant Funct Genom & Resources, 3888 Chenhua Rd, Shanghai 201602, Peoples R China 3.Majorbio Bioinformat Res Inst, Bldg 3,Lane 3399,Kangxin Rd,Int Med Pk, Shanghai 201320, Peoples R China 4.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, 20 Nanxincun, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Shen, Hui,Jin, Dongmei,Shu, Jiang-Ping,et al. Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns[J]. GIGASCIENCE,2017,7(2).
APA	Shen, Hui.,Jin, Dongmei.,Shu, Jiang-Ping.,Zhou, Xi-Le.,Lei, Ming.,...&Yan, Yue-Hong.(2017).Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns.GIGASCIENCE,7(2).
MLA	Shen, Hui,et al."Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns".GIGASCIENCE 7.2(2017).

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