Whole-genome sequencing and intensive analysis of the undomesticated soybean ( Glycine soja Sieb. and Zucc.) genome

Abstract

The genome of soybean ( Glycine max ), a commercially important crop, has recently been sequenced and is one of six crop species to have been sequenced. Here we report the genome sequence of G. soja , the undomesticated ancestor of G. max (in particular, G. soja var. IT182932). The 48.8-Gb Illumina Genome Analyzer (Illumina-GA) short DNA reads were aligned to the G. max reference genome and a consensus was determined for G. soja . This consensus sequence spanned 915.4 Mb, representing a coverage of 97.65% of the G. max published genome sequence and an average mapping depth of 43-fold. The nucleotide sequence of the G. soja genome, which contains 2.5 Mb of substituted bases and 406 kb of small insertions/deletions relative to G. max , is ∼0.31% different from that of G. max . In addition to the mapped 915.4-Mb consensus sequence, 32.4 Mb of large deletions and 8.3 Mb of novel sequence contigs in the G. soja genome were also detected. Nucleotide variants of G. soja versus G. max confirmed by Roche Genome Sequencer FLX sequencing showed a 99.99% concordance in single-nucleotide polymorphism and a 98.82% agreement in insertion/deletion calls on Illumina-GA reads. Data presented in this study suggest that the G. soja / G. max complex may be at least 0.27 million y old, appearing before the relatively recent event of domestication (6,000∼9,000 y ago). This suggests that soybean domestication is complicated and that more in-depth study of population genetics is needed. In any case, genome comparison of domesticated and undomesticated forms of soybean can facilitate its improvement.

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

“…IT182932) genome-specific sequences 15 as references. The mapping ratio of the wild soybean accessions to the G. soja specific sequences was higher than that of the cultivated soybeans, and the mapping ratio of the landraces was slightly higher than that of the improved cultivars ( Supplementary Fig.…”

“…Duplicated reads were filtered with the Picard package (picard.sourceforge.net, Version:1.87). Using BWA software, all the unmapped reads in the cultivated soybean (Williams 82) genome were mapped to 1,537 G. soja (IT182932)-specific sequences 15 , which were provided by Suk-Ha Lee, Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University. The BEDtools 49 (Version: 2.17.0) coverageBed program was used to compute the coverage of sequence alignments.…”

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

“…Of 1,978 genes affected in the G. soja accessions, 1,179 had CNV loss, 726 had CNV gain and 73 had both CNV loss and gain (Supplementary Tables 9 and 10). Gene Ontology (GO) analysis indicated that genes related to abiotic and biotic stress tolerance, such as resistance (R)-genes with nucleotide-binding site (NBS) or NBS-leucine-rich repeat (LRR) domains and transcription factors, were significantly (P < 0.01, chi-squared test) enriched in genes 4 . Our lower PAV discovery rate may be due to the use of more stringent filtering criteria, including the removal of unassembled sequences in G. max and putative microbial sequences.…”

“…Williams 82 (GmaxW82)) 2 , attempts have been made to characterize G. soja through genome resequencing [3][4][5] . However, resequencing is limited in terms of capturing many types of structural variation, especially for crop wild relatives, which are more genetically diverse than their domesticated counterparts.…”

“…De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits 1 0 4 6 VOLUME 32 NUMBER 10 OCTOBER 2014 nature biotechnology A r t i c l e s G. soja back to ~0.8 million years ago (mya), from a recent estimate of ~0.27 mya 4 . This work illustrates the value of de novo assemblies in building and characterizing large eukaryotic pan-genomes, and provides candidate genes for introgression into cultivated soybean for crop improvement.…”