Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome

doi:10.1186/s12864-024-10278-2

KIB OpenIR

	Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome
	He, Shuilian; Xu, Bin; Chen, Siyun; Li, Gengyun; Zhang, Jie; Xu, Junqiang; Wu, Hang; Li, Xuejiao; Yang, Zhengan
	2024
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	25 期号:1 页码:384
摘要	Background Curcubita ficifolia Bouche (Cucurbitaceae) has high value as a food crop and medicinal plant, and also has horticultural value as rootstock for other melon species. China is home to many different cultivars, but the genetic diversity of these resources and the evolutionary relationships among them, as well as the differences between C. ficifolia and other Cucurbita species, remain unclear.Results We investigated the chloroplast (cp) genomes of 160 C. ficifolia individuals from 31 populations in Yunnan, a major C. ficifolia production area in China. We found that the cp genome of C. ficifolia is similar to 151 kb and contains 128 genes, of which 86 are protein coding genes, 34 encode tRNA, and eight encode rRNAs. We also identified 64 SSRs, mainly AT repeats. The cp genome was found to contain a total of 204 SNP and 57 indels, and a total of 21 haplotypes were found in the 160 study individuals. The reverse repeat (IR) region of C. ficifolia contained a few differences compared with this region in the six other Cucurbita species. Sequence difference analysis demonstrated that most of the variable regions were concentrated in the single copy (SC) region. Moreover, the sequences of the coding regions were found to be more similar among species than those of the non-coding regions. The phylogenies reconstructed from the cp genomes of 61 representative species of Cucurbitaceae reflected the currently accepted classification, in which C. ficifolia is sister to the other Cucurbita species, however, different interspecific relationships were found between Cucurbita species.Conclusions These results will be valuable in the classification of C. ficifolia genetic resources and will contribute to our understanding of evolutionary relationships within the genus Cucurbita.
DOI	10.1186/s12864-024-10278-2
WOS记录号	WOS:001205532900003
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75864
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	He, Shuilian,Xu, Bin,Chen, Siyun,et al. Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome[J]. BMC GENOMICS,2024,25(1):384.
APA	He, Shuilian.,Xu, Bin.,Chen, Siyun.,Li, Gengyun.,Zhang, Jie.,...&Yang, Zhengan.(2024).Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome.BMC GENOMICS,25(1),384.
MLA	He, Shuilian,et al."Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome".BMC GENOMICS 25.1(2024):384.

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
10.1186_s12864-024-1（6772KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	浏览下载