Chloroplast genomes of Byrsonima species (Malpighiaceae): comparative analysis and screening of high divergence sequences

Abstract

Byrsonima is the third largest genus (about 200 species) in the Malpighiaceae family, and one of the most common in Brazilian savannas. However, there is no molecular phylogeny available for the genus and taxonomic uncertainties at the generic and family level still remain. Herein, we sequenced the complete chloroplast genome of B. coccolobifolia and B. crassifolia, the first ones described for Malpighiaceae, and performed comparative analyses with sequences previously published for other families in the order Malpighiales. The chloroplast genomes assembled had a similar structure, gene content and organization, even when compared with species from other families. Chloroplast genomes ranged between 160,212 bp in B. crassifolia and 160,329 bp in B. coccolobifolia, both containing 115 genes (four ribosomal RNA genes, 28 tRNA genes and 83 protein-coding genes). We also identified sequences with high divergence that might be informative for phylogenetic inferences in the Malpighiales order, Malpighiaceae family and within the genus Byrsonima. The phylogenetic reconstruction of Malpighiales with these regions highlighted their utility for phylogenetic studies. The comparative analyses among species in Malpighiales provided insights into the chloroplast genome evolution in this order, including the presence/absence of three genes (infA, rpl32 and rps16) and two pseudogenes (ycf1 and rps19).

Figure 1

Chloroplast genome circular map of Byrsonima coccolobifolia Kunth and B. crassifolia (L.) Kunth (Malpighiaceae) with annotated genes. Genes inside the circle are transcribed clockwise, genes outside are transcribed counter-clockwise. Genes are color coded according to functional groups. Boundaries of the small (SSC) and large (LSC) single copy regions and inverted repeat (IRa and IRb) regions are noted in the inner circle for each species. Picture of B. crassiflora was taken by Dr. Daniel L. Nickrent (source: http://www.phytoimages.siu.edu). Picture of B. coccolobifolia was provided by Maurício Mercadante.

Figure 2

Comparisons of percentage identity of chloroplast genomes for six species belonging to five different families within the order Malpighiales. Bc: Byrsonima coccolobifolia; Br: Byrsonima crassifolia (Malpighiaceae); Ci: Chrysobalanus icaco (Chrysobalanaceae); Vs: Viola seoulensis (Violaceae); Pa: Populus alba (Salicaceae), Rc: Ricinus communis (Euphorbiaceae). The percentage of identity is shown in the vertical axis, ranging from 50% to 100%, while the horizontal axis shows the position within the chloroplast genome. Each arrow displays the annotated genes and direction of their transcription in the reference genome (Byrsonima coccolobifolia). Genome regions are color coded as exon, untranslated region (UTR), conserved noncoding sequences (CNS) and mRNA.

Figure 3

Maximum likelihood trees for the order Malpighiales inferred from complete chloroplast genomes of nine species of the order (using all putative 1–1 orthologs - right) and from five highly variable coding sequences identified in this study (accD, matK, rpoA, ycf2 and rps7 - left). Bootstrap values are indicated above branches.

Figure 4

Details of boundary positions between inverted repeat regions (IR) and large and small single copy regions (LSC and SSC) among nine chloroplast genomes within the order Malpighiales. Bc: Byrsonima coccolobifolia; Br: B. crassifolia (Malpighiaceae); Ci: Chrysobalanus icaco; Hr: Hirtela racemosa (Chrysobalanaceae); Vs: Viola seoulensis (Violaceae); Sp: Salix purpurea, Pa: Populus alba (Salicaceae), Rc: Ricinus communis, Me: Manihot esculenta (Euphorbiaceae). Both Byrsonima species sequences are represented together at the top of the figure given that there are no differences between their boundaries. The direction of arrows shows the direction of transcription (right is forward and left is reverse). Ψ indicates a pseudogene. Length of arrows is illustrative. Number of base pairs (bp) indicates distance from the boundary to the end of the gene. Complete chloroplast genome sizes are noted on the right-hand side of the panel.