Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns

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Francisconi, Ana Flavia ; Marroquin, Jonathan Andre Morales ; Cauz-Santos, Luiz Augusto ; van den Berg, Cassio ; Martins, Kauanne Karolline Moreno ; Costa, Marcones Ferreira ; Picanco-Rodrigues, Doriane ; de Alencar, Luciano Delmodes ; Zanello, Cesar Augusto ; Colombo, Carlos Augusto ; Hernandez, Brenda Gabriela Diaz ; Amaral, Danilo Trabuco ; Lopes, Maria Teresa Gomes ; Veasey, Elizabeth Ann ; Zucchi, Maria Imaculada

• Document type: Journal article
• Source: SCIENTIFIC REPORTS; v. 13, n. 1, p. 15-pg., 2023-11-23.

Abstract

The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; 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 S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). 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, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a 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. (AU)

• FAPESP's process: 21/10319-0 - Genome assembly, population genomics and associative mapping in Attalea Kunth., an important genus of native palms from the neotropical region
• Grantee: Maria Imaculada Zucchi
• Support Opportunities: Regular Research Grants