Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex <i>Soja</i> Population Structure and Deep Introgression

<div><p>Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus <i>Soja</i> population in the <i>Glycine</i> genus. In this study, a semi-wild soybean line (Maliaodou) and a wild line (Lanxi 1) collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1) no independent phylogenetic branch covering all 10 semi-wild lines was observed in the <i>Soja</i> phylogenetic tree; (2) besides two distinct subpopulations of wild and cultivated soybean in the <i>Soja</i> population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3) high heterozygous rates (0.19–0.49) were observed in several semi-wild lines; and (4) over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex <i>Soja</i> population structure.</p></div

Summary of selective sweep analysis.

<p>Distribution of <i>Z</i>-transformed average pooled heterozygosity (<i>H_p</i>) in semi-wild (top) and cultivated soybeans (bottom), respectively. The negative end of the <i>Z</i>(<i>H_p</i>) distribution plotted along soybean autosomes 1–20 are shown. A dashed horizontal line indicates the cut-off (<i>Z</i><–4) used for extracting outliers.</p

Phylogenetic relationships among STB03, BTS02, and 30 <i>Echinochloa</i> accessions based on the nucleotide sequences of <i>trn</i>T-L-F region of the chloroplast genome.

<p>See the study by Yamaguchi <i>et al.</i> (2005) for code numbers of the 30 accessions <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113657#pone.0113657-Aoki1" target="_blank">[12]</a>. The tree was constructed using NJ method. Bootstrap values with less than 50 are not shown.</p

Genomic variations between the semi-wild genome Maliaodou and the reference genome Williams 82.

<p>Circles from outside: 20 chromosomes labeled with different colors; in the blue bars, each white vertical line presents a >10 kb un-mapped region in the reference genome; green and purple vertical lines present the intra-chromosomal translocations and inversion events, respectively. Distribution of the SNP density of the Maliaodou is labeled with grey lines.</p

Divergence time of the genus <i>Echinochloa</i>.

<p>Divergence time was estimated using BEAST based on the complete chloroplast genomes of six species (<i>E. oryzicola</i>, <i>E. crus-galli</i>, <i>P. virgatum</i>, <i>S. bicolor</i>, <i>Z. mays</i>, and <i>O. sativa</i>). The numbers showed at nodes indicate divergence time.</p

Phylogenetic tree and population structure of wild, semi-wild, and cultivated soybeans.

<p>(a) A neighbor-joining phylogenetic tree constructed using SNP data. Cultivated, semi-wild, and wild soybeans are labeled with green, red, and blue lines, respectively. (b) Bayesian clustering (STRUCTURE, <i>K</i> = 3) of soybean accessions were grouped based on their species. Cultivated lines were designated with ‘C’ as prefix while wild lines were with ‘W’ as prefix except IT182932 (Korean) and Lanxi 1 (this study). Semi-wild lines were titled with ‘Z’ as prefix except Maliaodou.</p

Visualization of alignments of chloroplast genome sequences.

<p>The sequence identity was plotted with the <i>E.oryzicola</i> chloroplast genome as the reference. Sequence identity with 50%–100% is shown. Exonic regions and conserved non-coding sequences (CNS) are colored in blue and red, respectively.</p

Phenotypes of cultivated, semi-wild and wild soybeans used in the present study.

<p>Seed weight (per 100 seeds) and plant architecture are shown.</p

<i>Echinochloa</i> Chloroplast Genomes: Insights into the Evolution and Taxonomic Identification of Two Weedy Species

<div><p>The genus <i>Echinochloa</i> (Poaceae) includes numerous problematic weeds that cause the reduction of crop yield worldwide. To date, DNA sequence information is still limited in the genus <i>Echinochloa</i>. In this study, we completed the entire chloroplast genomes of two <i>Echinochloa</i> species (<i>Echinochloa oryzicola</i> and <i>Echinochloa crus-galli</i>) based on high-throughput sequencing data from their fresh green leaves. The two <i>Echinochloa</i> chloroplast genomes are 139,891 and 139,800 base pairs in length, respectively, and contain 131 protein-coding genes, 79 indels and 466 substitutions helpful for discrimination of the two species. The divergence between the genus <i>Echinochloa</i> and <i>Panicum</i> occurred about 21.6 million years ago, whereas the divergence between <i>E. oryzicola</i> and <i>E. crus-galli</i> chloroplast genes occurred about 3.3 million years ago. The two reported <i>Echinochloa</i> chloroplast genome sequences contribute to better understanding of the diversification of this genus.</p></div