Complete chloroplast genomes of six Neotropical palm tree species: genome structure comparison, identification of repeats sequences and evolutionary dynamic patterns

Abstract

Abstract The Arecaceae family has a worldwide distribution, specially in the tropical and subtropical regions. We sequenced the chloroplast genome of Acrocomia intumescens and A. totai, widely used in the food and energy industry, Bactris gasipaes, important for palm heart, Copernicia alba and C. prunifera, worldwide known for wax utilization, and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while B. gasipaes presented the smallest (155,078 bp). Copernicia spp. had two more gene copies (trnL-GAG) than the others, and S. romanzoffianaunderwent pseudogenization in one copy of rps19. Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closer phylogenetically species shared more sites. Almost all nodes of the phylogenetic analysis showed posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.