Exceptionally high rates of positive selection on the rbcL gene in the genus Ilex (Aquifoliaceae)

doi:10.1186/s12862-019-1521-1

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	Exceptionally high rates of positive selection on the rbcL gene in the genus Ilex (Aquifoliaceae)
	Yao,Xin 1,2; Tan,Yun-hong 1,2,3; Yang,Jun-bo 4; Wang,Yan 5; Corlett,Richard T.1,2; Manen,Jean-Fran?ois 6
通讯作者	Yao,Xin(yaoxin@xtbg.org.cn) ; Corlett,Richard T.(corlett@xtbg.org.cn) ; Manen,Jean-Fran?ois(jean-francois.manen@wanadoo.fr)
	2019-10-21
发表期刊	BMC Evolutionary Biology
ISSN	1471-2148
卷号	19 期号:1 页码:13
摘要	AbstractBackgroundThe genus Ilex (Aquifoliaceae) has a near-cosmopolitan distribution in mesic habitats from tropical to temperate lowlands and in alpine forests. It has a high rate of hybridization and plastid capture, and comprises four geographically structured plastid groups. A previous study showed that the plastid rbcL gene, coding for the large subunit of Rubisco, has a particularly high rate of non-synonymous substitutions in Ilex, when compared with other plant lineages. This suggests a strong positive selection on rbcL, involved in yet unknown adaptations. We therefore investigated positive selection on rbcL in 240 Ilex sequences from across the global range.ResultsThe rbcL gene shows a much higher rate of positive selection in Ilex than in any other plant lineage studied so far (>?3000 species) by tests in both PAML and SLR. Most positively selected residues are on the surface of the folded large subunit, suggesting interaction with other subunits and associated chaperones, and coevolution between positively selected residues is prevalent, indicating compensatory mutations to recover molecular stability. Coevolution between positively selected sites to restore global stability is common.ConclusionsThis study has confirmed the predicted high incidence of positively selected residues in rbcL in Ilex, and shown that this is higher than in any other plant lineage studied so far. The causes and consequences of this high incidence are unclear, but it is probably associated with the similarly high incidence of hybridization and introgression in Ilex, even between distantly related lineages, resulting in large cytonuclear discordance in the phylogenies.
关键词	Rubisco Positive selection PALM Environmental adaptation Molecular adaptation
DOI	10.1186/s12862-019-1521-1
收录类别	SCI ; SCI
语种	英语
WOS记录号	BMC:10.1186/s12862-019-1521-1
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/69360
专题	中国科学院昆明植物研究所
通讯作者	Yao,Xin; Corlett,Richard T.; Manen,Jean-Fran?ois
作者单位	1. 2. 3. 4. 5. 6.
推荐引用方式 GB/T 7714	Yao,Xin,Tan,Yun-hong,Yang,Jun-bo,et al. Exceptionally high rates of positive selection on the rbcL gene in the genus Ilex (Aquifoliaceae)[J]. BMC Evolutionary Biology,2019,19(1):13.
APA	Yao,Xin,Tan,Yun-hong,Yang,Jun-bo,Wang,Yan,Corlett,Richard T.,&Manen,Jean-Fran?ois.(2019).Exceptionally high rates of positive selection on the rbcL gene in the genus Ilex (Aquifoliaceae).BMC Evolutionary Biology,19(1),13.
MLA	Yao,Xin,et al."Exceptionally high rates of positive selection on the rbcL gene in the genus Ilex (Aquifoliaceae)".BMC Evolutionary Biology 19.1(2019):13.

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