Correlation Analysis Reveals an Important Role of GC Content in Accumulation of Deletion Mutations in the Coding Region of Angiosperm Plastomes

doi:10.1007/s00239-020-09987-5

KIB OpenIR

	Correlation Analysis Reveals an Important Role of GC Content in Accumulation of Deletion Mutations in the Coding Region of Angiosperm Plastomes
	Yu,Ying ; Li,Hong-Tao ; Wu,Yu-Huan ; Li,De-Zhu
	2021
发表期刊	JOURNAL OF MOLECULAR EVOLUTION
ISSN	0022-2844
卷号	89 期号:1-2 页码:73-80
摘要	Variation in GC content is assumed to correlate with various processes, including mutation biases, recombination, and environmental parameters. To date, most genomic studies exploring the evolution of GC content have focused on nuclear genomes, but relatively few have concentrated on organelle genomes. We explored the mechanisms maintaining the GC content in angiosperm plastomes, with a particular focus on the hypothesis of phylogenetic dependence and the correlation with deletion mutations. We measured three genetic traits, namely, GC content, A/T tracts, and G/C tracts, in the coding region of plastid genomes for 1382 angiosperm species representing 350 families and 64 orders, and tested the phylogenetic signal. Then, we performed correlation analyses and revealed the variation in evolutionary rate of selected traits using RRphylo. The plastid GC content in the coding region varied from 28.10% to 43.20% across angiosperms, with a few non-photosynthetic species showing highly reduced values, highlighting the significance of functional constraints. We found strong phylogenetic signal in A/T tracts, but weak ones in GC content and G/C tracts, indicating adaptive potential. GC content was positively and negatively correlated with G/C and A/T tracts, respectively, suggesting a trade-off between these two deletion events. GC content evolved at various rates across the phylogeny, with significant increases in monocots and Lamiids, and a decrease in Fabids, implying the effects of some other factors. We hypothesize that variation in plastid GC content might be a mixed strategy of species to optimize fitness in fluctuating climates, partly through influencing the trade-off between AT -> GC and GC -> AT mutations.
关键词	Base composition variation AT-biased deletion mutation Phylogenetic relatedness Functional constraints Energy resource competition Rrphylo BIASED GENE CONVERSION EVOLUTIONARY RATE VARIATION BASE COMPOSITION PLASTID GENOMES PHYLOGENETIC SIGNAL MISMATCH REPAIR SELECTION SLIPPAGE PLANTS RATES
DOI	10.1007/s00239-020-09987-5
WOS记录号	WOS:000607343600001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/73201
专题	中国科学院昆明植物研究所
作者单位	1.[Yu, Ying 2.Hangzhou Normal Univ, Coll Life & Environm Sci, Hangzhou 311121, Peoples R China 3.[Li, Hong-Tao 4.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Yu,Ying,Li,Hong-Tao,Wu,Yu-Huan,et al. Correlation Analysis Reveals an Important Role of GC Content in Accumulation of Deletion Mutations in the Coding Region of Angiosperm Plastomes[J]. JOURNAL OF MOLECULAR EVOLUTION,2021,89(1-2):73-80.
APA	Yu,Ying,Li,Hong-Tao,Wu,Yu-Huan,&Li,De-Zhu.(2021).Correlation Analysis Reveals an Important Role of GC Content in Accumulation of Deletion Mutations in the Coding Region of Angiosperm Plastomes.JOURNAL OF MOLECULAR EVOLUTION,89(1-2),73-80.
MLA	Yu,Ying,et al."Correlation Analysis Reveals an Important Role of GC Content in Accumulation of Deletion Mutations in the Coding Region of Angiosperm Plastomes".JOURNAL OF MOLECULAR EVOLUTION 89.1-2(2021):73-80.