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

Content Provider	Springer Nature : BioMed Central
Author	Tao, Lei Duan, Hanning Tao, Kaifeng Luo, Yan Li, Qingqing Li, Lu
Abstract	Background The 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. Results It 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. Conclusions The results could provide insight into understanding the plastome evolution and phylogenetic relationships of Phalaenopsis.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-023-09448-5.pdf
Ending Page	15
Page Count	15
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-023-09448-5
Journal	BMC Genomics
Issue Number	1
Volume Number	24
Language	English
Publisher	BioMed Central
Publisher Date	2023-06-27
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Phalaenopsis storbartiana Phalaenopsis wilsonii Chloroplast genome Orchidaceae Structural characterization
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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