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Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver
Wang, Wencai1; Chen, Siyun2; Zhang, Xianzhi3
2018-04-01
Source PublicationINTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
ISSN1422-0067
Volume19Issue:4Pages:1037
AbstractEucommia 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.
KeywordEucommia Ulmoides Chloroplast Genome Heterogeneous Divergence Mutation Hotspots Whole-genome Comparison
DOI10.3390/ijms19041037
Language英语
WOS IDWOS:000434978700116
Citation statistics
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/61420
Collection中国西南野生生物种质资源库
Affiliation1.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
Recommended Citation
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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.
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