气候变化领域集成服务门户(CCPortal): Lineage-specific plastid degradation in subtribe Gentianinae (Gentianaceae)

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DOI	10.1002/ece3.7281
	Lineage-specific plastid degradation in subtribe Gentianinae (Gentianaceae)
	Fu, Peng-Cheng; Sun, Shan-Shan; Twyford, Alex D.; Li, Bei-Bei; Zhou, Rui-Qi; Chen, Shi-Long; Gao, Qing-Bo; Favre, Adrien
通讯作者	Favre, A (通讯作者)，Senckenberg Res Inst, Frankfurt, Germany. ; Favre, A (通讯作者)，Nat Hist Museum, Frankfurt, Germany.
发表日期	2021
ISSN	2045-7758
起始页码	3286
结束页码	3299
卷号	11 期号:7
英文摘要	The structure and sequence of plastid genomes is highly conserved across most land plants, except for a minority of lineages that show gene loss and genome degradation. Understanding the early stages of plastome degradation may provide crucial insights into the repeatability and predictability of genomic evolutionary trends. We investigated these trends in subtribe Gentianinae of the Gentianaceae, which encompasses ca. 450 species distributed around the world, particularly in alpine and subalpine environments. We sequenced, assembled, and annotated the plastomes of 41 species, representing all six genera in subtribe Gentianinae and all main sections of the species-rich genus Gentiana L. We reconstructed the phylogeny, estimated divergence times, investigated the phylogenetic distribution of putative gene losses, and related these to substitution rate shifts and species' habitats. We obtained a strongly supported topology consistent with earlier studies, with all six genera in Gentianinae recovered as monophyletic and all main sections of Gentiana having full support. While closely related species have very similar plastomes in terms of size and structure, independent gene losses, particularly of the ndh complex, have occurred in multiple clades across the phylogeny. Gene loss was usually associated with a shift in the boundaries of the small single-copy and inverted repeat regions. Substitution rates were variable between clades, with evidence for both elevated and decelerated rate shifts. Independent lineage-specific loss of ndh genes occurred at a wide range of times, from Eocene to Pliocene. Our study illustrates that diverse degradation patterns shape the evolution of the plastid in this species-rich plant group.
关键词	CHLOROPLAST GENOME NDH GENES EVOLUTIONARY DYNAMICS SUBSTITUTION RATES INVERTED REPEAT SEQUENCES ACCURATE ANNOTATION DIVERSITY PLASTOMES
英文关键词	divergence dating; molecular evolution; ndh complex; plastome; substitution rate; subtribe Gentianinae
语种	英语
WOS研究方向	Environmental Sciences & Ecology ; Evolutionary Biology
WOS类目	Ecology ; Evolutionary Biology
WOS记录号	WOS:000620371600001
来源期刊	ECOLOGY AND EVOLUTION
来源机构	中国科学院西北生态环境资源研究院
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/254488
作者单位	[Fu, Peng-Cheng; Sun, Shan-Shan; Li, Bei-Bei; Zhou, Rui-Qi] Luoyang Normal Univ, Sch Life Sci, Luoyang, Peoples R China; [Twyford, Alex D.] Univ Edinburgh, Inst Evolutionary Biol, Ashworth Labs, Edinburgh, Midlothian, Scotland; [Twyford, Alex D.] Royal Bot Garden Edinburgh, Edinburgh, Midlothian, Scotland; [Chen, Shi-Long; Gao, Qing-Bo] Chinese Acad Sci, Northwest Inst Plateau Biol, Key Lab Adaptat & Evolut Plateau Biota, Xining, Peoples R China; [Chen, Shi-Long; Gao, Qing-Bo] Qinghai Prov Key Lab Crop Mol Breeding, Xining, Peoples R China; [Favre, Adrien] Senckenberg Res Inst, Frankfurt, Germany; [Favre, Adrien] Nat Hist Museum, Frankfurt, Germany
推荐引用方式 GB/T 7714	Fu, Peng-Cheng,Sun, Shan-Shan,Twyford, Alex D.,et al. Lineage-specific plastid degradation in subtribe Gentianinae (Gentianaceae)[J]. 中国科学院西北生态环境资源研究院,2021,11(7).
APA	Fu, Peng-Cheng.,Sun, Shan-Shan.,Twyford, Alex D..,Li, Bei-Bei.,Zhou, Rui-Qi.,...&Favre, Adrien.(2021).Lineage-specific plastid degradation in subtribe Gentianinae (Gentianaceae).ECOLOGY AND EVOLUTION,11(7).
MLA	Fu, Peng-Cheng,et al."Lineage-specific plastid degradation in subtribe Gentianinae (Gentianaceae)".ECOLOGY AND EVOLUTION 11.7(2021).