Chloroplast genomes of Vanilla spp. (Orchidaceae) provide new evolutionary insights into the genus

Abstract

The genus Vanilla (Orchidaceae) holds significant economic value due to its production of aromatic compounds; however, numerous species are increasingly threatened by overexploitation and habitat destruction, underscoring the need for comprehensive genomic resources to support evolutionary and conservation efforts. In this study, we sequenced and assembled the complete chloroplast (cp) genomes of eight Vanilla species from Peru and Brazil. Additionally, two genomes were assembled from publicly available data. These were analyzed alongside seven chloroplast genomes from NCBI, yielding a dataset of 17 cp genomes. Genomic DNA extracted from young leaves was sequenced using the Illumina NovaSeq platform. Chloroplast genomes were assembled through a combination of de novo and reference-guided strategies and subsequently annotated using online platforms. The assembled cp genomes displayed the typical quadripartite structure, ranging from 147,372 to 163,306 bp in length and encoding 121–122 genes. Three highly variable regions (π > 0.3) and four genes (clpP, rpl32, rps18, and infA) with high nucleotide diversity were identified and proposed as promising molecular markers. Codon-based likelihood analyses provided convergent evidence of positive selection in five genes (atpA, atpB, cemA, clpP, and ycf2), supported by significant likelihood-ratio tests and high-probability Bayesian Empirical Bayes (BEB) sites. Phylogenetic analysis of concatenated coding sequences confirmed Vanilla as a monophyletic genus, with three well-supported clades corresponding to the current subgenus classification. These results provide important insights into the molecular evolution of Vanilla cp genomes, with relevant implications for phylogenetic, taxonomic, and conservation studies.