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: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (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 rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA 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 S. bogneri, including ycf2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.

Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae): Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution

“…The higher rate of synonymous substitutions than non-synonymous substitutions is indicative of strong purifying selection pressure acting on these genes during the course of evolution (Matsuoka et al 2002 ). The observation of purifying selection in our study are consistent with previous studies on angiosperm chloroplast genomes, including other aroid (Menezes et al 2018 ; Abdullah et al 2019a , 2020a , b ; Henriquez et al 2020a ; Shahzadi et al 2020 ). In current study, some codons sites in three protein-coding genes ( rpl 22, ycf 1, and ycf 2) were found under positive selection pressure in the subfamily Pothoideae based on the results of FUBAR.…”

“…The higher rate of synonymous substitutions than nonsynonymous substitutions is indicative of strong purifying selection pressure acting on these genes during the course of evolution (Matsuoka et al 2002). The observation of purifying selection in our study are consistent with previous studies on angiosperm chloroplast genomes, including other aroid (Menezes et al 2018;Abdullah et al 2019aAbdullah et al , 2020aHenriquez et al 2020a;Shahzadi et al 2020).…”

“…The rpl22 is encoding the large subunit of ribosomes (Mache 1990) while ycf1 and ycf2 are the largest protein-coding genes in the chloroplast genome that are part of the chloroplast inner envelope membrane protein translocon (Kikuchi et al 2013). These genes were also found under positive selection in species of Araceae and other angiosperms (Fan et al 2018;Liu et al 2018;Zhong et al 2019;Henriquez et al 2020a;Abdullah et al 2020a). The presence of positively selected codons revealed the role of these genes in adaptation of the species in their ecological niches.…”

“…The presence of positively selected codons revealed the role of these genes in adaptation of the species in their ecological niches. Previously, only seven genes in subfamily Monsteroideae were found under positive selection (Henriquez et al 2020a ), whereas in comparison of chloroplast genomes of four species from the three subfamilies of Araceae three genes were reported under positive selection (Abdullah et al 2020a ). In another study of Araceae, most genes (62/71) were reported under positive selection (Kim et al 2019 ) based on the evaluation of K a / K s values in DnaSP.…”

TheGASAGene Family inTheobroma cacao: Genome wide Identification and Expression Analysis

“…The number of introns were variable in tcGASA within genes that cluster together in phylogeny. The loss and gain of introns occurs in the course of evolution within protein-coding genes of the plants and is also reported within the GASA of other plant species (Abdullah et al, 2020a;Ahmad et al, 2019Ahmad et al, , 2020bAhmadizadeh et al, 2020;Ding et al, 2020;Heidari et al, 2019).…”