Complete Chloroplast Genomes and Comparative Analyses of Three Paraphalaenopsis (Aeridinae, Orchidaceae) Species

Jinliao Chen; Fei Wang; Zhuang Zhao; Minghe Li; Zhongjian Liu; Donghui Peng

doi:10.3390/ijms241311167

Complete Chloroplast Genomes and Comparative Analyses of Three Paraphalaenopsis (Aeridinae, Orchidaceae) Species

Int J Mol Sci. 2023 Jul 6;24(13):11167. doi: 10.3390/ijms241311167.

Authors

Jinliao Chen¹, Fei Wang¹, Zhuang Zhao¹, Minghe Li¹, Zhongjian Liu¹, Donghui Peng¹

Affiliation

¹ Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Abstract

Paraphalaenopsis, a genus of perennial herbs from the family Orchidaceae, contains a number of ornamental species. However, there is no information on the chloroplast genomes of Paraphalaenopsis, which limits our studies of this genus. In this study, we reported the chloroplast genomes of three species of Paraphalaenopsis (P. labukensis, P. denevel, and P. laycockii 'Semi-alba') and performed comprehensive comparative analysis. These three chloroplast genomes showed a typical quadripartile structure. Their lengths ranged from 147,311 bp to 149,240 bp. Each genome contained 120 unique genes, including 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Comparative analysis revealed major differences in sequence divergence in the three chloroplast genomes. In addition, six hypervariable regions were identified (psbM-trnD^GUC, psbB, ccsA, trnK^UUU, trnS^GCU-trnG^UCC, rps16-trnQ^UUG) that can be used as DNA molecular markers. Phylogenetic relationships were determined using the chloroplast genomes of 28 species from 12 genera of Aeridinae. Results suggested that Paraphalaenopsis was a clade of Aeridinae that was sister to the Holcoglossum-Vanda clade, with 100% bootstrap support within Aeridinae. The findings of this study provided the foundation for future studies on the phylogenetic analysis of Aeridinae.

Keywords: Aeridinae; Paraphalaenopsis; chloroplast genome; phylogenetic analysis.

MeSH terms

Genetic Markers
Genome, Chloroplast*
Orchidaceae* / genetics
Phylogeny

Substances

Genetic Markers

Grants and funding

This research was supported by the following fundings: one is the Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University (No. 72202200205), and the Outstanding Youth Scientific Fund of Fujian Agriculture and Forestry University (Grant No. XJQ202005), and the Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province (No. 115-PTJH16005).