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 (IRa and IRb) of 25,574 bp. 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 analysis showed that IR was more conserved as compared to LSC and SSC. Here, we observed low transition and transversion ratio (Ts/Tv) of 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 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 of phylogenetics in genus Firmiana and subfamily Sterculioideae of family Malvaceae.