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.

Keywords: Araceae; chloroplast genome; contraction and expansion; gene evolution; inverted repeats; phylogenetics; substitutions.

Figure 1

Vegetative and reproductive stages of bisexual and unisexual species. (a) L. spinosa, tropical Southeast Asian aculeate colony-forming evergreen herbs with deeply pinnatifid hastate-sagittate leaf blades and spadix at antithesis. (b) L. spinosa, solitary inflorescence of bisexual flowers. (c) O. aquaticum, temperate east North American seasonally dormant, aquatic herbs with oblong-elliptic blades held above water. (d) O. aquaticum, numerous bisexual inflorescences held above water level with disintegrated spathe not visible. (e) S. bogneri, tropical and southeast subtropical African evergreen herb with cordate-sagittate leaf blades. (f) Z. zamiifolia, tropical east to subtropical southeast African seasonally dormant or evergreen herb with pinnatisect leaf blades and an inflorescence of unisexual flowers with basal female and apical male flowers [43].

Figure 2

Circular maps of chloroplast genomes. Genes present inside the circle are transcribed counter-clockwise, whereas genes present outside the circle are transcribed clockwise. Genes are color-coded based on functionality. LSC, IRb, SSC, and IRa of the inner circle represent quadripartite structure of genomes.

Figure 3

Colinear block-based analyses of gene arrangement in the chloroplast genomes. (a) O. aquaticum, (b) L. spinosa, (c) Z. zamiifolia, and (d) S. bogneri. The black block: transfer RNA genes, green block: transfer RNA genes with introns, white block: coding genes, and red block: ribosomal RNA genes. Light green and dark green blocks show differential existence of ycf1 and rps15 due to contraction and expansion of inverted repeats.

Figure 4

Comparison of quadripartite junction sites among chloroplast genomes of four assembled species. Genes present on top of track transcribe on the negative strand, whereas genes present below the track transcribe on the positive strand. The T scale bar shows integration of genes between two adjacent regions. The junctions of genomes are represented as follows: JLB: IRb/LSC, JSB: IRb/SSC, JSA: SSC/IRa, and JLA: IRa/LSC.

Figure 5

Comparison of repeats among chloroplast genomes of four species. (a) Microsatellites distribution in regions of chloroplast genomes. (b) Numbers of different types of microsatellites. (c) Distribution of oligonucleotide repeats in regions of chloroplast genomes. (d) Types of oligonucleotide repeats. (e) Number of repeats based on size. LSC: large single copy, SSC: small single copy, IR: inverted repeats; LSC/SSC, LSC/IR, and SSC/IR represent those repeat pairs in which one copy exists in one region and another copy in another region. 14–20, 21–26, 27–32, and >32 showed a range of repeat sizes.

Figure 6

Maximum likelihood tree based on multiple alignment of 30 species of Araceae. (a) Phylogenetic tree; (b) cladogram. The bootstrapping support values are similar for the phylogenetic tree and the cladogram and are shown only on the cladogram for easy visualization. The four species reported in the current study are highlighted with yellow boxes.