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

Authors: LIU, QIONG - University Of Illinois; CHANG, SUNGYUL - Korea Institute Of Science And Technology; Hartman, Glen; Domier, Leslie

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/22/2018
Publication Date: 4/19/2018
Citation: Liu, Q., Chang, S., Hartman, G.L., Domier, L.L. 2018. Assembly and annotation of a draft genome sequence for Glycine latifolia, a perennial wild relative of soybean. Plant Journal. 91:71-85.

Interpretive Summary: Like most cultivated crops, soybean has a relatively narrow genetic base, while its wild perennial relatives are more genetically diverse and can display desirable traits not present in cultivated soybean. For example, no sources of complete resistance to Sclerotinia stem rot have been identified in soybean. However, high levels of resistance have been observed in some accessions of Glycine latifolia, a wild perennial relative of soybean. In addition, accessions of G. latifolia show resistance to drought, alfalfa mosaic virus, soybean rust and sudden death syndrome. To identify genes that condition these agronomically valuable traits, we assembled and annotated the genome sequence of an accession of G. latifolia with resistance to Sclerotinia stem rot. The annotation of the G. latifolia genome identified 64,692 genes. About 1% of the genes were predicted to be involved in disease resistance or responses to biotic and abiotic stresses. The whole genome sequence and annotation of G. latifolia provides a valuable source of alternative alleles and novel genes that are lacking in soybean germplasm. The results will be of interest to scientists who are interested in utilizing the genes from genetically diverse wild soybean species for soybean improvement.

Technical Abstract: Glycine latifolia (Benth.) Newell & Hymowitz (2n=40), one of the 26 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. To assess the continuity of this assembly, we observed high copy numbers of putative centromere-specific tandem repeats in consecutive blocks within predicted pericentromeric regions on several pseudomolecules. Annotation of the assembled genome yielded 64,692 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 (TNL) genes in G. latifolia. The G. latifolia genome was also predicted to contain genes encoding 367 LRR-receptor-like kinases (RLK), a family of proteins involved in basal defense responses and responses to abiotic stress. The whole 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.