Complete chloroplast genome structural characterization of two Phalaenopsis (Orchidaceae) species and comparative analysis with their alliance

BMC Genomics

Research

Hanning Duan¹  Lu Li¹  Kaifeng Tao¹  Lei Tao²  Yan Luo³  Qingqing Li⁴ 

[1] Department of Biological Conservation, Southwest Forestry University, 650224, Kunming, Yunnan, China;Department of Biological Conservation, Southwest Forestry University, 650224, Kunming, Yunnan, China;Department of Life Science, Southwest Forestry University, 650224, Kunming, Yunnan, China;Department of Horticulture and Gardening, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Mengla, Yunnan, China;Department of Life Science, Southwest Forestry University, 650224, Kunming, Yunnan, China;Kunming Xianghao Technology Co. Ltd., 650204, Kunming, Yunnan, China;

关键词: Phalaenopsis storbartiana;    Phalaenopsis wilsonii;    Chloroplast genome;    Orchidaceae;    Structural characterization;   

DOI  :  10.1186/s12864-023-09448-5

 received in 2022-10-13, accepted in 2023-06-14,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundThe taxonomy and infrageneric delimitation of Phalaenopsis Blume has been significantly disputed due to some overlapping morphological features between species related, which needed further evidence for clarification. The structural characterization of complete chloroplast genomes of P. storbatiana and P. wilsonii were analyzed and compared with those of related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny.ResultsIt was shown that chloroplast genomes of Phalaenopsis storbatiana and P. wilsonii had a typical quadripartite structure with conserved genome arrangements and moderate divergence. The chloroplast genomes of P. storbatiana and P. wilsonii were 145,885 bp and 145,445 bp in length, respectively, and shared a similar GC content of 36.8%. Gene annotations of two species revealed 109 single-copy genes consistently. In addition, 20 genes duplicated in the inverted regions, 16 genes each possessed one or more introns, and five ndh (NA (D)H dehydrogenase) genes were observed in both. Comparative analysis of the total cp genomes of P. storbatiana and P. wilsonii with those of other six related Phalaenopsis species confirmed the stable sequence identity for coding and non-coding regions and higher sequence variation in SC regions than IR regions. Most of their protein-coding genes had a high degree of codon preference. Moreover, 45 genes were discovered with significantly positive selection. However, different amplifications in IR regions were observed in these eight species. Phylogenetic analysis based on CDS from 60 species representing main clades in Orchidaceae indicated that Phalaenopsis species including P. stobartiana and P. wilsonii formed a monophyletic clade with high bootstrap nested in tribe Vandeae of Epidendroideae, which was consistent with those from previous studies.ConclusionsThe results could provide insight into understanding the plastome evolution and phylogenetic relationships of Phalaenopsis.

【 授权许可】

CC BY   
© The Author(s) 2023

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