Comparative analyses of chloroplast genomes among three Firmiana species: Identification of mutational hotspots and phylogenetic relationship with other species of Malvaceae

Abstract

Firmiana is a small genus of subfamily Sterculioideae of family Malvaceae. Previously, Firmiana genus was ignored, and its phylogenetics was not elucidated at genus level. Here, we assembled the chloroplast genomes of Firmiana colorata and compared with reported chloroplast genome of F. major and F. pulcherrima. Firmiana colorata had total length of 160,700 bp, contained large single copy (LSC) region of 89,551 bp and small single copy (SSC) region of 20,001 bp that were separated by two inverted repeats regions (IRa and IRb) of 25,574 bp each. The chloroplast genome of Firmiana colorata consisted of 113 unique genes including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Firmiana colorata and Firmiana major showed similar genes content and organisation except some variations. Comparative analyses revealed Firmiana species had similar GC content, codon usage, RNA editing sites, simple sequence repeats, oligonucleotide repeats, and substitutions. The substitution and InDels analyses showed that IR regions were more conserved as compared to LSC region and SSC region. Here, we observed low transition and transversion ratio (Ts/Tv) of about 0.90 among Firmiana species. The ratio of non-synonymous substitutions and synonymous substitutions (Ka/Ks) revealed similar evolutionary rate for protein-coding genes of Firmiana. Comparison of protein coding sequences, introns, and intergenic spacer regions (IGS) among Firmiana species revealed 30 mutational hotspots with maxmium regions from IGS that including psbZ-trnG-GCC, trnR-UCU-atpA, ndhD-ccsA, petD-rpoA, rps4-trnT-UGU, rpl33-rps18, rpl32-ndhF, and psbK-psbI. Markers design from these mutational hotspots might be authentic, robust, and cost effective for inferring phylogeny of genus Firmiana and subfamily Sterculioideae of family Malvaceae.