Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver

doi:10.3390/ijms19041037

	Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver
	Wang, Wencai 1; Chen, Siyun 2; Zhang, Xianzhi3
	2018-04-01
发表期刊	INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
ISSN	1422-0067
卷号	19 期号:4 页码:1037
摘要	Eucommia ulmoides (E. ulmoides), the sole species of Eucommiaceae with high importance of medicinal and industrial values, is a Tertiary relic plant that is endemic to China. However, the population genetics study of E. ulmoides lags far behind largely due to the scarcity of genomic data. In this study, one complete chloroplast (cp) genome of E. ulmoides was generated via the genome skimming approach and compared to another available E. ulmoides cp genome comprehensively at the genome scale. We found that the structure of the cp genome in E. ulmoides was highly consistent with genome size variation which might result from DNA repeat variations in the two E. ulmoides cp genomes. Heterogeneous sequence divergence patterns were revealed in different regions of the E. ulmoides cp genomes, with most (59 out of 75) of the detected SNPs (single nucleotide polymorphisms) located in the gene regions, whereas most (50 out of 80) of the indels (insertions/deletions) were distributed in the intergenic spacers. In addition, we also found that all the 40 putative coding-region-located SNPs were synonymous mutations. A total of 71 polymorphic cpDNA fragments were further identified, among which 20 loci were selected as potential molecular markers for subsequent population genetics studies of E. ulmoides. Moreover, eight polymorphic cpSSR loci were also developed. The sister relationship between E. ulmoides and Aucuba japonica in Garryales was also confirmed based on the cp phylogenomic analyses. Overall, this study will shed new light on the conservation genomics of this endangered plant in the future.
关键词	Eucommia Ulmoides Chloroplast Genome Heterogeneous Divergence Mutation Hotspots Whole-genome Comparison
DOI	10.3390/ijms19041037
语种	英语
WOS记录号	WOS:000434978700116
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/61420
专题	中国西南野生生物种质资源库
作者单位	1.Guangzhou Univ Chinese Med, Inst Clin Pharmacol, Guangzhou 510000, Guangdong, Peoples R China 2.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China 3.Northwest A&F Univ, Coll Forestry, Yangling 712100, Shaanxi, Peoples R China
推荐引用方式 GB/T 7714	Wang, Wencai,Chen, Siyun,Zhang, Xianzhi. Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2018,19(4):1037.
APA	Wang, Wencai,Chen, Siyun,&Zhang, Xianzhi.(2018).Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,19(4),1037.
MLA	Wang, Wencai,et al."Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 19.4(2018):1037.