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Assembly and annotation of a draft genome sequence for Glycine latifolia , a perennial wild relative of soybean
Author(s) -
Liu Qiong,
Chang Sungyul,
Hartman Glen L.,
Domier Leslie L.
Publication year - 2018
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13931
Subject(s) - biology , genetics , genome , gene , glycine soja , gene family , genome project , whole genome sequencing , tandem repeat , glycine , amino acid
Summary Glycine latifolia (Benth.) Newell & Hymowitz (2 n = 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.