Does IR-loss promote plastome structural variation and sequence evolution?

doi:10.3389/fpls.2022.888049

KIB OpenIR

	Does IR-loss promote plastome structural variation and sequence evolution?
	Wang, Zi-Xun; Wang, Ding-Jie; Yi, Ting-Shuang
	2022
发表期刊	FRONTIERS IN PLANT SCIENCE
卷号	13 页码:888049
摘要	Plastids are one of the main distinguishing characteristics of the plant cell. The plastid genome (plastome) of most autotrophic seed plants possesses a highly conserved quadripartite structure containing a large single-copy (LSC) and a small single-copy (SSC) region separated by two copies of the inverted repeat (termed as IRA and IRB). The IRs have been inferred to stabilize the plastid genome via homologous recombination-induced repair mechanisms. IR loss has been documented in seven autotrophic flowering plant lineages and two autotrophic gymnosperm lineages, and the plastomes of these species (with a few exceptions) are rearranged to a great extent. However, some plastomes containing normal IRs also show high structural variation. Therefore, the role of IRs in maintaining plastome stability is still controversial. In this study, we first integrated and compared genome structure and sequence evolution of representative plastomes of all nine reported IR-lacking lineages and those of their closest relative(s) with canonical inverted repeats (CRCIRs for short) to explore the role of the IR in maintaining plastome structural stability and sequence evolution. We found the plastomes of most IR-lacking lineages have experienced significant structural rearrangement, gene loss and duplication, accumulation of novel small repeats, and acceleration of synonymous substitution compared with those of their CRCIRs. However, the IR-lacking plastomes show similar structural variation and sequence evolution rate, and even less rearrangement distance, dispersed repeat number, tandem repeat number, indels frequency and GC3 content than those of IR-present plastomes with variation in Geraniaceae. We argue that IR loss is not a driver of these changes but is instead itself a consequence of other processes that more broadly shape both structural and sequence-level plastome evolution.
关键词	plastid genome evolution structural variation inverted repeat region loss substitution rate comparative genomics CHLOROPLAST GENOME SEQUENCE INVERTED REPEAT NUCLEOTIDE SUBSTITUTION PHYLOGENETIC ANALYSIS MOLECULAR EVOLUTION NONCODING RNAS RATES REARRANGEMENTS ORGANIZATION CUPRESSOPHYTES
DOI	10.3389/fpls.2022.888049
收录类别	SCI
WOS记录号	WOS:000868553600001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75628
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Wang, Zi-Xun,Wang, Ding-Jie,Yi, Ting-Shuang. Does IR-loss promote plastome structural variation and sequence evolution?[J]. FRONTIERS IN PLANT SCIENCE,2022,13:888049.
APA	Wang, Zi-Xun,Wang, Ding-Jie,&Yi, Ting-Shuang.(2022).Does IR-loss promote plastome structural variation and sequence evolution?.FRONTIERS IN PLANT SCIENCE,13,888049.
MLA	Wang, Zi-Xun,et al."Does IR-loss promote plastome structural variation and sequence evolution?".FRONTIERS IN PLANT SCIENCE 13(2022):888049.

条目包含的文件		下载所有文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
10.3389_fpls.2022.88（2423KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	浏览下载