Complete chloroplast genome of two Brachycorythis (Orchidaceae) species from China: comparative analysis and phylogenetic implications.

BACKGROUND

Brachycorythis Lindl. (Orchidinae, Orchidaceae) was characterized by a large and densely leafy stem throughout its length, comprising about 35 species with African-Asian disjunct distribution. However, the intergeneric and infrageneric phylogeny of Brachycorythis has been debated based on morphological and molecular data. The chloroplast (cp.) genomes of B. henryi and B. menglianensis were investigated in detail and compared with those of related taxa for providing new evidence for the phylogenetics of Brachycorythis.

RESULTS

The cp. genomes of B. henryi and B. menglianensis exhibited conserved quadripartite structures, measured 153,006 bp and 152,932 bp in length, with an identical GC content of 37.2%. Gene annotations identified 133 genes, 20 duplicated in the inverted repeat regions. Comparative analysis across their related species confirmed stable sequence identity and higher variation in single-copy regions. Phylogenetic analysis based on complete cp. genomic data revealed that these two Brachycorythis species formed an independent clade exhibiting distinct branch lengths, representing a sister lineage to their related taxa in Orchidinae s. s. It was also supported that six species of Brachycorythis formed a monophyletic clade based on matK + rbcL sequences. Among them, three species from Asia and other three species from Africa, respectively, formed two independent clades. Notably, it was also showed that B. macowaniana was not clustered with other six Brachycorythis species.

CONCLUSIONS

This is the first report on complete cp. genomic data of Brachycorythis, providing some phylogenetic implications. Some varied cp. genomic features for phylogenetic implications were discussed, including overall genome structure, codon usage, repeat sequences, IR boundaries, DNA polymorphisms, and phylogenetic reconstruction. Based on chloroplast genomic data and matK + rbcL sequence analysis, phylogenetic results revealed that Brachycorythis was not closely related to any of the five genera assumed to be related. Three species from Asia and other three species from Africa, respectively, formed two independent clades, which was consistent well with the African-Asian disjunct distribution of Brachycorythis. And, it was supported that Gyaladenia should be re-established, considering the uncertain species of B. macowaniana. In addition, it was revealed that B. menglianensis was not a synonym of B. henryi, and each of them was a distinct species based on cp. genomic and morphological data. Therefore, the intergeneric and infrageneric relationship of Brachycorythis should be understood better by more cp. genomic data.