Comparative analysis of complete plastid genomes from wild soybean (Glycine soja) and nine other Glycine species

Abstract

The plastid genomes of different plant species exhibit significant variation, thereby providing valuable markers for exploring evolutionary relationships and population genetics. Glycine soja (wild soybean) is recognized as the wild ancestor of cultivated soybean (G. max), representing a valuable genetic resource for soybean breeding programmes. In the present study, the complete plastid genome of G. soja was sequenced using Illumina paired-end sequencing and then compared it for the first time with previously reported plastid genome sequences from nine other Glycine species. The G. soja plastid genome was 152,224 bp in length and possessed a typical quadripartite structure, consisting of a pair of inverted repeats (IRa/IRb; 25,574 bp) separated by small (178,963 bp) and large (83,181 bp) single-copy regions, with a 51-kb inversion in the large single-copy region. The genome encoded 134 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 39 transfer RNA genes, and possessed 204 randomly distributed microsatellites, including 15 forward, 25 tandem, and 34 palindromic repeats. Whole-plastid genome comparisons revealed an overall high degree of sequence similarity between G. max and G. gracilis and some divergence in the intergenic spacers of other species. Greater numbers of indels and SNP substitutions were observed compared with G. cyrtoloba. The sequence of the accD gene from G. soja was highly divergent from those of the other species except for G. max and G. gracilis. Phylogenomic analyses of the complete plastid genomes and 76 shared genes yielded an identical topology and indicated that G. soja is closely related to G. max and G. gracilis. The complete G. soja genome sequenced in the present study is a valuable resource for investigating the population and evolutionary genetics of Glycine species and can be used to identify related species.

Expanded inverted repeat region with large scale inversion in the first complete plastid genome sequence of Plantago ovata

“…Though gene content and organisation in P. ovata plastome found to be similar with other species in Plantaginaceae, however, the genome size and IRs of P. ovata was markedly different from P. media and P. maritima 25 . Similar to P. media and P. maritima, P. ovata plastome www.nature.com/scientificreports www.nature.com/scientificreports/ exhibited a higher level of sequence and structural divergence as well as showed some rearrangements in its plastome in comparison with those for typical angiosperms plastomes [25][26][27] . We observed a similar number of intron-containing protein-coding genes with 7 tRNA genes (with an exception of ycf3 and clpP which contained two introns) in P. media plastome 25 .…”

“…In synergy with other angiosperms, rps12 gene was unevenly divided with its 5′ terminal exon located in the LSC region, whereas the 3′ terminal exon and intron were located in the IRb region and also duplicated in the IRa region 29,30 . The trnK-UUU had the longest intron (2,434 bp) 26,31 . According to a previous study, introns play a vital role in gene expression regulation; improve exogenous gene expression and transformational efficiency 32 .…”

“…The plastome of P. ovata showed a high divergence level in non-coding and intergenic spacer regions (atpH-atpI, rpoC1-rpoC2, ycf1-rps15, accD-psaI, psaA-ycf3, and trnL-rrn5) as opposed to the coding regions (Fig. 2) 26,39,43 . However, some divergent protein-coding genes (accD, clpP, ndhA, ndhF, rpl16, petD, matK, rpl16, ycf2, ycf1, and rpl2) were also detected in P. ovata plastome.…”

Korean Wild Soybeans (Glycine soja Sieb & Zucc.): Geographic Distribution and Germplasm Conservation

“…A comparative and in-depth genome resequencing of G. soja chloroplast genomes could enhance our understanding of the domestication process of G. max, as well as of the traits regulated by the plastid genome. Up until now, only limited knowledge of these aspects is available [115,116]. types, respectively [32].…”

Análise comparativa de regiões microssintênicas entre >i<Passiflora edulis>/i< e as Malpighiales >i<Populus trichocarpa>/i< e >i<Manihot esculenta>/i<

“…Permitem também localizar regiões codificadores de proteínas e identificar segmentos conservados, possibilitando o estudo dos padrões evolutivos de espécies relacionadas [22,[26][27][28][29]. Pesquisas em genômica comparativa foram reportadas em diversas espécies vegetais, por exemplo, as realizadas entre Brassica oleracea e Arabidopsis thaliana [30], Zea mays e A. thaliana [31], Fragaria e outras espécies do clado das Rosideas [32], Solanum lycopersicum e S. tuberosum [33], Oryza sativa e Ananas comosus [34], Glycine soja e outras 9 espécies de Glicine [35], Saccharum officinarum e S. spontaneum [36], entre outras.…”