Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis

NWIPB OpenIR

	Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis
	Zhang, Jinkui; Zhou, Dangwei; Chen, Weidong; Lin, Pengcheng; Zhao, Suqin; Wang, Min; Wang, Huan; Shi, Shengbo; Mehmood, Furrukh; Ye, Xing; Meng, Jing; Zhuang, Wenyuan
	2024
发表期刊	BMC PLANT BIOLOGY
卷号	24 期号:1
摘要	BackgroundHabenaria, a genus in the family Orchidaceae, are the nearly cosmopolitan orchids, and most species have significant medicinal and ornamental values. Despite the morphological and molecular data that have been studied in recent years, the phylogenetic relationship is still unclear.ResultsWe sequenced, assembled, and annotated the chloroplast (cp) genomes of two species (Habenaria aitchisonii Rchb.f. and Habenaria tibetica Schltr.ex Limpricht) of Habenaria grown on the Qinghai-Tibetan Plateau (QTP), and compared them with seven previously published cp genomes which may aid in the genomic profiling of these species. The two genomes ranged from 155,259-155,269 bp in length and both included 132 genes, encoding 86 proteins, 38 tRNAs and 8 rRNAs. In the cp genomes, the tandem repeats (797), SSRs (2195) and diverse loci (3214) were identified. Comparative analyses of codon usage, amino frequency, microsatellite, oligo repeats and transition and transversion substitutions revealed similarities between the species. Moreover, we identified 16 highly polymorphic regions with a nucleotide diversity above 0.02, which may be suitable for robust authentic barcoding and inferring in the phylogeny of Habenaria species. Among the polymorphic regions, positive selection was significantly exerted on several genes, such as cemA, petA, and ycf1. This finding may suggest an important adaptation strategy for the two Habenaria species on the QTP. The phylogenetic relationship revealed that H. aitchisonii and H. tibetica were more closely related to each other than to the other species, and the other seven species were clustered in three groups. In addition, the estimated divergence time suggested that the two species separated from the others approximately 0.39 Mya in the Neogene period. Our findings also suggest that Habenaria can be divided into different sections.ConclusionsThe results of this study enriched the genomics resources of Habenaria, and SSR marker may aid in the conservation management of two endangered species.
收录类别	SCIE
文献类型	期刊论文
条目标识符	http://210.75.249.4/handle/363003/61912
专题	中国科学院西北高原生物研究所
推荐引用方式 GB/T 7714	Zhang, Jinkui,Zhou, Dangwei,Chen, Weidong,et al. Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis[J]. BMC PLANT BIOLOGY,2024,24(1).
APA	Zhang, Jinkui.,Zhou, Dangwei.,Chen, Weidong.,Lin, Pengcheng.,Zhao, Suqin.,...&Zhuang, Wenyuan.(2024).Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis.BMC PLANT BIOLOGY,24(1).
MLA	Zhang, Jinkui,et al."Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis".BMC PLANT BIOLOGY 24.1(2024).