Assembly and annotation of a draft genome sequence for Glycine latifolia, a perennial wild relative of soybean

• Published in: The Plant journal : for cell and molecular biology Vol. 95; no. 1; pp. 71 - 85
• Main Authors: Liu, Qiong, Chang, Sungyul, Hartman, Glen L., Domier, Leslie L.
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.07.2018
• Subjects: 10X Genomics; abiotic stress; Agronomy; alleles; Annotations; Assembly; Binding sites; Chromium; Comparative analysis; cost effectiveness; diploidy; disease resistance; Filtration; Gene families; Gene mapping; Genes; Genetic diversity; genetic variation; genome assembly; genome sequence; Genomes; Glycine latifolia; Glycine max; Glycine tomentella; Kinases; Legumes; Leucine; loci; NBS-LRR gene; Nucleotide sequence; phosphotransferases (kinases); Proteins; soybean; Soybeans; tandem repeat sequences; wild perennial relative; wild relatives; soybean; genome sequence; wild perennial relative; disease resistance; 10X Genomics; Glycine latifolia
• ISSN: 0960-7412; 1365-313X; 1365-313X
• DOI: 10.1111/tpj.13931

Summary Glycine latifolia (Benth.) Newell & Hymowitz (2n = 40), one of the 27 wild perennial relatives of soybean, possesses genetic diversity and agronomically favorable traits that are lacking in soybean. Here, we report the 939‐Mb draft genome assembly of G. latifolia (PI 559298) using exclusively linked‐reads sequenced from a single Chromium library. We organized scaffolds into 20 chromosome‐scale pseudomolecules utilizing two genetic maps and the Glycine max (L.) Merr. genome sequence. High copy numbers of putative 91‐bp centromere‐specific tandem repeats were observed in consecutive blocks within predicted pericentromeric regions on several pseudomolecules. No 92‐bp putative centromeric repeats, which are abundant in G. max, were detected in G. latifolia or Glycine tomentella. Annotation of the assembled genome and subsequent filtering yielded a high confidence gene set of 54 475 protein‐coding loci. In comparative analysis with five legume species, genes related to defense responses were significantly overrepresented in Glycine‐specific orthologous gene families. A total of 304 putative nucleotide‐binding site (NBS)‐leucine‐rich‐repeat (LRR) genes were identified in this genome assembly. Different from other legume species, we observed a scarcity of TIR‐NBS‐LRR genes in G. latifolia. The G. latifolia genome was also predicted to contain genes encoding 367 LRR‐receptor‐like kinases, a family of proteins involved in basal defense responses and responses to abiotic stress. The genome sequence and annotation of G. latifolia provides a valuable source of alternative alleles and novel genes to facilitate soybean improvement. This study also highlights the efficacy and cost‐effectiveness of the application of Chromium linked‐reads in diploid plant genome de novo assembly. Significance statement Glycine latifolia, a perennial wild relative of soybean, contains genetic diversity that is lacking in the soybean genome due to domestication and long‐term improvement processes. This study reports the draft genome assembly and annotation of G. latifolia, which will serve as an essential genetic source to enhance soybean agronomic performance and documents the application of Chromium linked‐reads in diploid plant genome de novo assembly.