General information

Glycine soja W05 is a Chinese wild soybean accession originally collected in Henan Province. It was used to generate a RI population for the identification of important QTLs and the causal gene of a major QTL for salt tolerance [Ref 1-3].

The Glycine soja W05 genome was generated from a combination of data set, including PacBio subreads, Illumina paired-end reads, Optical mapping molecules (Bionano) and Illumina Hi-C reads (Dovetail). The final assembly is 1013.2 Mb in length, with a contig N50 of 3.3 Mb. In total, 95.7% of sequences are anchored to 20 superscaffolds, corresponding to 20 soybean chromosomes [Ref 4].

Genes in W05 genome were annotated based on abundant expression data, including 234.7 Gb of Illumina RNA-seq reads collected from 31 samples at various development and physiological stages and 414,750 PacBio IsoSeq full length and non-chimeric transcripts. In total, 89,477 protein-coding transcripts were annotated for 55,539 gene loci in W05 genome [Ref 4].

Data Availability:

  • Data is also available in NCBI:
    BioProject: PRJNA486704
    Accession number: QZWG00000000

Citation:

  • For the use of the genomic data of W05, please cite the following:
    Xie, M. et al. A reference-grade wild soybean genome. Nat Biotech, submitted

Inquiry contact:

  • PI: Hon-Ming Lam (CUHK) (email: honming@cuhk.edu.hk)
  • PI: Ting-Fung Chan (CUHK) (email: tf.chan@cuhk.edu.hk)
  • Webmaster: Tin-Hang Wong (email: wongtinhang@cuhk.edu.hk)
  • Webmaster:  Xie Min (email: xiemin@link.cuhk.edu.hk)

References:

  1. Lam, H.M. et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42, 1053-U1041 (2010).
  2. Qi, X.P. et al. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun 5, 10.1038/ncomms5340 (2014).
  3. Li, M.W. et al. QTLs Regulating the Contents of Antioxidants, Phenolics, and Flavonoids in Soybean Seeds Share a Common Genomic Region. Front Plant Sci  7 (2016)
  4. Xie, M. et al. A reference-grade wild soybean genome. Nat Biotech, submitted

Funding:

  • Hong Kong Research Grants Council Area of Excellence Scheme (AoE/M‐403/16)