Genome sequence of the palaeopolyploid soybean

Abstract

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

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

“…After mapping against the soybean Williams 82 reference genome 9 , we identified 9,790,744 single-nucleotide polymorphisms (SNPs) and 876,799 indels (shorter than or equal to 6 bp) (Supplementary Table 2). In addition, the depth of sequencing data allowed us to identify a total of 1,614 copy number variations (CNVs) and 6,388 segmental deletions comprising 15.14 Mb and 73.6 Mb sequences, respectively.…”

“…Regarding the LD for overall genome, the r 2 value was calculated for individual chromosomes using SNPs from the corresponding chromosome with parameter-ld-window-r2 0-ld-window 99999-ld-window-kb 1000, and then the pairwise r 2 values were averaged across the whole genome. The chromosome arm and pericentromeric region boundaries for each chromosome were previously described 9 .…”

“…Mapping. Paired-end resequencing reads were mapped to the soybean Williams 82 reference genome 9 with BWA 47 (Version: 0.6.1-r104) using the default parameters. SAMtools 48 (Version: 0.1.18) software was used to convert mapping results into the BAM format and to filter the unmapped and non-unique reads.…”

“…SNP annotation was performed according to the soybean genome 9 (Williams 82 assembly v1, gene model set 1.1, internal identifier v189 accessed from Phytozome on June 2013) using the package ANNOVAR 51 (Version: 2013-08-23). Based on the genome annotation, SNPs were categorized in exonic regions (overlapping with a coding exon), splicing sites (within 2 bp of a splicing junction), 5′UTRs and 3′UTRs, intronic regions (overlapping with an intron), upstream and downstream regions (within a 1 kb region upstream or downstream from the transcription start site), and intergenic regions.…”

Ectopic phytocystatin expression increases nodule numbers and influences the responses of soybean (Glycine max) to nitrogen deficiency

“…The recent release of the complete soybean genome (Schmutz et al, 2010) and the RNAseq atlas of genes expressed in fourteen different soybean tissues (Severin et al, 2010) allows the accurate identification and characterisation of soybean cystatins, cysteine proteases and VPEs. The Phytozome database (www.phytozome.…”