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

Abdullah Abdullah,Thomas B Croat,Zain Ali,Ibrar Ahmed,Mohammad Tahir Waheed,Iram Shahzadi,Furrukh Mehmood,Peter Poczai,Claudia L Henriquez

doi:10.3390/plants9060737

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.

Highlights

The chloroplast is an important double membrane-bounded organelle that plays a crucial role in photosynthesis and metabolism of fatty acids and amino acids in plant cells [1]
We report de novo assembled and fully annotated chloroplast genomes of four species from three subfamilies of Araceae: Lasia spinosa (L.) Thwaites (Lasioideae), Stylochaeton bogneri and Zamioculcas zamiifolia (Lodd.) Engl. (Zamioculcadoideae), and Orontium aquaticum L
Region ranged from 13,967 bp (O. aquaticum) to 20,497 bp (S. bogneri); large single-copy (LSC) ranged from 87,269 bp (O. aquaticum) to 91,357 bp (Z. zamiifolia); the size of each inverted repeat (IR) region ranged from 26,702 bp (S. bogneri) to 32,053 bp (L. spinosa) (Table 2)

Summary

Introduction

The chloroplast is an important double membrane-bounded organelle that plays a crucial role in photosynthesis and metabolism of fatty acids and amino acids in plant cells [1]. The structure of chloroplast genomes is conserved regarding gene organization, gene content, and intron content [1,10,11,12,13]. Large-scale events of gene rearrangement, gene loss/generation of pseudogenes, and intron loss are reported in various plant lineages [11,14,15,16,17,18]. Inverted repeat contraction and expansion in chloroplast genomes create pseudogenes, cause gene duplication, or convert duplicates into single-copy genes [11,12]. Availability of chloroplast genomes provides quality tools for endangered species conservation, accurate barcoding, and avoiding intentional and unintentional adulteration of medicinal plants [1,29,30]. Chloroplast genomes play an important role in the identification and determination of the purity of commercial cultivars [1,31]

Methods

Results

Conclusion