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).

Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

“…In summary, the Ka/Ks values here provide comparative results for detection of selective pressure in mangrove chloroplasts. The genes that involve photosynthesis and energy metabolism for chloroplasts are conserved with very low Ka/Ks ratio, and this kind of evolutionary pattern has been generally observed in other plant chloroplasts [22,32]. The potential positive selection or relax pressure of ycf1 , rpl23 , rps7 , rpl36 , petL , psaI were also detected in mangroves, indicating their fast evolve rate and divergence in different species in spite of its ambiguous function in chloroplast genomes.…”

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

“…The trn K intron is important because it expresses an unusual form of a group II intron derived from a mobile group of mitochondrial-like intron open reading frames (ORFs) (Hausner et al, 2006). As in the plastid genomes of many land plants, the abundance of A/T content at 3 rd base of codons was reported due to high concentration of A/T nucleotides in the whole plastid genome (Menezes et al, 2018).…”

“…The plastomes of land plants have conserved structure but diversity prevails at the border position of LSC/SSC/IR of the genome. The size range of LSC, SSC and IR varies between the plastid genomes of species that advances to alterations in several genes and leads to the deletion of one copy of a gene or duplication of functional and non-functional genes of different sizes (Menezes et al, 2018; Saina et al, 2018). In the current study, all these ten Nicotiana species showed similarities with some variation as compared to the Nicotiana tabacum: in all these plants except Nicotiana tomentosiformis which have 60 bp in IRb region, the rps19 gene is present entirely in the LSC region but in Nicotiana tabacum rps19 gene extended 5bp in the IR region.…”

“…In the current study, all these ten Nicotiana species showed similarities with some variation as compared to the Nicotiana tabacum: in all these plants except Nicotiana tomentosiformis which have 60 bp in IRb region, the rps19 gene is present entirely in the LSC region but in Nicotiana tabacum rps19 gene extended 5bp in the IR region. The fluctuations at the border positions of various regions of the plastid genome might be helpful in determining the evolution of species (Menezes et al, 2018). Liu et al, (2018) reported that the similarities at the junction regions may be useful in explaining the relationship between the species and that those plants which have a high level of relatedness show minimal fluctuations at the junctions of the chloroplast genome.…”

“…(Ahmed et al, 2013; Ahmad, 2014; Nguyen et al, 2017). Previously, in several studies, polymorphic loci were identified based on comparisons of chloroplast genome to provide information about suitable loci for the development of molecular markers (Choi, Chung & Park, 2016; Li et al, 2018; Menezes et al, 2018). We found 20 polymorphic regions such as infA, rps12 intron, rps16-trnQ-UUG which have 0.25942, 0.15275, 0.08451 nucleotide diversity respectively that were more polymorphic than frequently used markers such as rbcL , and matK .…”