Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae

Abstract

The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: <i>Lasia</i> <i>spinosa</i> (Lasioideae), <i>Stylochaeton bogneri</i>, <i>Zamioculcas zamiifolia</i> (Zamioculcadoideae), and <i>Orontium</i> <i>aquaticum</i> (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17-18 genes are duplicated in the inverted repeat (IR) regions, comprising 6-7 protein-coding (including trans-splicing gene <i>rps</i>12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The <i>inf</i>A gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in <i>S. bogneri,</i> including <i>ycf</i>2, <i>clp</i>P, and <i>rpl</i>36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.