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

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.

Figure 1

Gene map of (a) Acrocomia intumescens, (b) A. totai, (c) Bactris gasipaes var. gasipaes, (d) Copernicia alba, (e) C. prunifera, and (f) Syagrus romanzoffiana chloroplast genomes. Genes represented inside the large circle are oriented clockwise, and those outside are oriented counterclockwise. The distinct colors represent functional groups, and the darker gray in the inner circle indicates the GC content. The quadripartite structure is also reported as: LSC large single copy, SSC small single copy, IRA inverted repeat A, IRB inverted repeat B.

Figure 2

Synteny and divergence in the small single copy (SSC) size detected in Arecaceae chloroplast genomes using the Mauve multiple-genome alignment program. A sample of 16 different chloroplast genomes is shown. Color bars indicate syntenic blocks, and the lines indicate the correspondence between them. Blocks on the top row are in the same orientation, while blocks on the bottom row are in the opposite orientation.

Figure 3

Comparison of the inverted repeats A and B (IRA and IRB) borders among Brazilian palms. The numbers indicate the lengths of IGSs, genes, and spacers between IR-LSC and IR-SSC junctions. The ycf1* and rps19* genes have incomplete CDSs. LSC large single copy, SSC small single copy.

Figure 4

Distribution, classification, and motifs of single sequence repeats (SSR) in the chloroplast genomes of Acrocomia intumescens, A. totai, Bactris gasipaes var. gasipaes, Copernicia alba, C. prunifera, and Syagrus romanzoffiana. (a) Number of SSR types (mono-, di-, tri-, tetra-, penta-, and hexanucleotides) present in the six chloroplast genomes; (b) number of SSR in the different chloroplast genome regions; (c) number of different SSR motifs distributed in the six chloroplast genomes. SSC small single copy, LSC large single copy, IRA inverted repeat A, IRB inverted repeat B.

Figure 5

Distribution and classification of dispersed repeats in the chloroplast genomes of Acrocomia intumesces, A. totai, Bactris gasipaes var. gasipaes, Copernicia alba, C. prunifera, and Syagrus romanzoffiana. (a) Frequency distribution of different types of repeats; (b) number of dispersed repeats present in different chloroplast genome regions; (c) number of dispersed repeat sizes among the six palm species. F forward, P palindrome, R reverse, C complement, SSC small single copy, LSC large single copy, IRA inverted repeat A, IRB inverted repeat B.

Figure 6

RNA editing sites shared by the species Acrocomia intumescens, A. totai, Bactris gasipaes var. gasipaes, Copernicia alba, C. prunifera, and Syagrus romanzoffiana. (a) Number of RNA editing sites shared among the six species; (b) Pairwise comparison of RNA editing sites found between the species.

Figure 7

Majority-rule consensus tree of 30,000 trees obtained from a Bayesian inference analysis of chloroplast protein-coding genes of 66 taxa. Posterior probabilities (PP) for each are indicated above the branches.