The Chloroplast Genome Sequence of Mungbean (Vigna radiata) Determined by High-throughput Pyrosequencing: Structural Organization and Phylogenetic Relationships

Abstract

Mungbean is an economically important crop which is grown principally for its protein-rich dry seeds. However, genomic research of mungbean has lagged behind other species in the Fabaceae family. Here, we reported the complete chloroplast (cp) genome sequence of mungbean obtained by the 454 pyrosequencing technology. The mungbean cp genome is 151 271 bp in length which includes a pair of inverted repeats (IRs) of 26 474 bp separated by a small single-copy region of 17 427 bp and a large single-copy region of 80 896 bp. The genome contains 108 unique genes and 19 of these genes are duplicated in the IR. Of these, 75 are predicted protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. Relative to other plant cp genomes, we observed two distinct rearrangements: a 50-kb inversion between accD/rps16 and rbcL/trnK-UUU, and a 78-kb rearrangement between trnH/rpl14 and rps19/rps8. We detected sequence length polymorphism in the cp homopolymeric regions at the intra- and inter-specific levels in the Vigna species. Phylogenetic analysis demonstrated a close relationship between Vigna and Phaseolus in the phaseolinae subtribe and provided a strong support for a monophyletic group of the eurosid I.

Different status of the gene for ribosomal protein S16 in the chloroplast genome during evolution of the genus Arabidopsis and closely related species

“…Six complete legume chloroplast genomes have been reported to date (G. max, L. japonicus. M. truncatula, P. vulgaris, C. arietinum, and V. radiata) (Jansen et al, 2008;Tangphatsornruang et al, 2010). A similar tendency to lose the cp rps16 in selfcompatible plants is observed in these species.…”

“…Although the number of genes and their order are generally conserved among angiosperm chloroplast genomes, exceptional gene losses have been identified (e.g., rpl33 in Phaseolus vulgaris (Guo et al, 2007) and Vigna radiata (Tangphatsornruang et al, 2010), infA in almost all rosid species (Millen et al, 2001), rpl32 in the Populus genus (Okumura et al, 2006;Steane, 2005), rps16 in Medicago truncatula (Saski et al, 2005), P. vulgaris (Guo et al, 2007), Cicer arietinum (Jansen et al, 2008), V. radiata (Tangphatsornruang et al, 2010), and the Populus genus (Okumura et al, 2006;Steane, 2005)). It is also possible that genes that have been transferred or substituted recently in evolution remain in the chloroplast genome as remnants when gene transfer or substitution has occurred.…”

Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species

“…For instance ycf15, a non-functional gene in other plants (10,22,12) is also present in G. thurberi. The other example is infA, most mobile gene between chloroplast and nuclear genome, that codes for a translation initial factor 1 (29,30,31).…”

“…Therefore and In addition to phylogenetic analysis based on plastidic genomes, it is imperative to understand the chloroplast genome in order to logically design our next generation transplastomics. Accordingly, chloroplast genomes of many species have been sequenced (7)(8)(9)(10)(11)(12)(13)(14).…”

Deep sequencing of Ptilidium (Ptilidiaceae) suggests evolutionary stasis in liverwort plastid genome structure

“…A similar approach is being followed in other labs around the world (e.g. Tangphatsornruang et al 2010, and provides a sound alternative in cases where pre-sequencing plastid enrichment is difficult or impossible.…”