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

Abstract

The subfamily Pothoideae belongs to the ecologically important plant family Araceae. Here, we report the chloroplast genomes of two species of the subfamily Pothoideae: Anthurium huixtlense (size: 163,116 bp) and Pothos scandens (size: 164,719 bp). The chloroplast genome of P. scandens showed unique contraction and expansion of inverted repeats (IRs), thereby increasing the size of the large single-copy region (LSC: 102,956 bp) and decreasing the size of the small single-copy region (SSC: 6779 bp). This led to duplication of many single-copy genes due to transfer to IR regions from the small single-copy (SSC) region, whereas some duplicate genes became single copy due to transfer to large single-copy regions. The rate of evolution of protein-coding genes was affected by the contraction and expansion of IRs; we found higher mutation rates for genes that exist in single-copy regions as compared to those in IRs. We found a 2.3-fold increase of oligonucleotide repeats in P. scandens when compared with A. huixtlense, whereas amino acid frequency and codon usage revealed similarities. The ratio of transition to transversion mutations was 2.26 in P. scandens and 2.12 in A. huixtlense. Transversion mutations mostly translated in non-synonymous substitutions. The phylogenetic inference of the limited species showed the monophyly of the Araceae subfamilies. Our study provides insight into the molecular evolution of chloroplast genomes in the subfamily Pothoideae and family Araceae.

Keywords: Anthurium; Araceae; Gene evolution; Gene rearrangement; Inverted repeat contraction and expansion; Pothoideae; Pothos.

Fig. 1

Circular diagram of chloroplast genomes of A. huixtlense and P. scandens. LSC, SSC, and IR represent large single-copy, small single-copy, and inverted repeat regions, respectively. The genes located inside are transcribed counterclockwise, whereas the genes located outside are transcribed clockwise

Fig. 2

Amino acid frequency in A. huixtlense and P. scandens. The x-axis shows amino acids, whereas the Y-axis shows percentage of amino acid frequency

Fig. 3

Analyses of repeats in A. huixtlense and P. scandens. a Types of repeats. b Distribution of repeats in the chloroplast genomes. c The size of repeats in the genome. F Forward, C complementary, R reverse, P palindromic, LSC large single copy, SSC small single copy, IR inverted repeat, LSC/SSC and LSC/IR represent shared repeats between regions

Fig. 4

Analyses of gene arrangements among the species of Araceae based on Mauve alignment. White boxes indicate protein-coding genes, red indicate rRNA, black indicate tRNA, green indicate intron-containing tRNA, and the line between two white boxes indicates intron-containing protein-coding genes

Fig. 5

Comparative analysis of junction sites in Araceae chloroplast genomes. Abbreviations denote junction site of the plastid genome JLA (IRa/LSC), JLB (IRb/LSC), JSA (SSC/IRa) and JSB (IRb/SSC). Genes are represented by colored boxes while arrows are showing the coordinate positions of each gene near the junctions. Genes displayed on the top appear on the negative strand, while genes present bellow and found on the positive strand of the genome

Fig. 6

Maximum likelihood phylogenetic tree of the Araceae family reconstructed from plastid genome data. a Phylogenetic tree and b cladogram