Comparative And Phylogenetic Analyses of Six Kenya Polystachya (Orchidaceae) Species Based On The Complete Chloroplast Genome Sequences

Abstract

Background: Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with the centre of diversity in Africa. Chloroplast (cp) genomes of plants are highly conserved and can provide much more informative DNA sites and generate much better resolution for plant phylogenies. However, for Polystachya, the whole cp genome including its structure features are yet unknown and its phylogenetic placement of the genus within the Orchidaceae is still unclear.Results: In this study, the complete cp genomes of six Polystachya species were assembled based on genome skimming. We subjected them to comparative genomic analyses and reconstructed their phylogenetic relationships. The results exhibited that the cp genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The cp genomes of the six Polystachya species ranged from 145,484 bp to 149,274 bp in length and had almost similar GC content of 36.9%-37.0%. Gene annotation revealed 113 unique genes. In additions, 19 genes are duplicated in the inverted regions, and 17 gene possessed intron. Comparative analysis of the overall sequence identity among six complete cp genomes confirmed that for both coding and non-coding regions in Polystachya, SC regions exhibit higher sequence variation than IRs. Furthermore, there were various amplifications in the IR region among the six Polystachya species. Most of the protein-coding genes of these species had a high degree of codon preference. We screened out specific SSR and found seven relatively highly variable loci. Moreover, 13 genes were discovered with significant positive selection. Phylogenetic analysis suggested that the six Polystachya species formed a monophyletic clade and had more closely related to tribe Vandeae. Phylogenetic relationships of the family Orchidaceae inferred from the 85 cp genome sequences were generally consistent with previous studies and robust. Conclusions: Our study reported the complete cp genomes of the six Polystachya species, and provided detailed structural analysis and comparative analysis results, which can contribute to the development of DNA markers for use in the study of genetic variability and evolutionary studies in Polystachya. In addition, the present results further demonstrate the phylogenetic position of Polystachya.

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