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

Abstract

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.

Construction and comparison of three reference‐quality genome assemblies for soybean

“…A second assembly, Wm82.a2, was released by DOE‐JGI in 2014 and comprised 949 Mbp in 20 pseudomolecules, plus 29.3 Mbp in 1170 unanchored scaffolds (Song et al ., ). Additional ab initio (Salamov and Solovyev, ) soybean genome assemblies have been released recently: Zhonghuang 13 (Shen et al ., ); Enrei (Shimomura et al ., ); a perennial relative of soybean, Glycine latifolia (Liu et al ., ); draft assemblies for seven wild soybean accessions (Li et al ., ); and a high‐quality G. soja assembly for accession W05 (Xie et al ., ).…”

Identification of candidate genes for blackleg resistance in the new Brassica juncea canola

“…The distribution pattern of LRR-RLK in B. rapa, detected in this study, is consistent with the previous report (Rameneni et al, 2015). The uneven distribution of LRR-RLKs is not novel in plants genomes (Shiu and Bleecker 2001b), as has been demonstrated in other plant species recently, including S. lycopersicum (Wei et al, 2015), T. aestivum (Sharma et al, 2016a), two Glycine species (G. max and G. latifolia) (Liu et al, 2018;Zhou et al, 2016) and…”

“…As plant genome assemblies are increasingly available, genome-wide characterisation of resistance gene families has been performed in many plant species using various bioinformatics tools, such as the RGAugury pipeline (Li et al, 2016), MAST/MEME (Motif Alignment Search Tool/Multiple Em for Motif Elicitation) (Bailey et al, 2009(Bailey et al, , 2015, PRGdb (Sanseverino et al, 2012) and BLASTn and BLASTp (Altschul et al, 1997). Genome-wide analyses of the LRR-RLK subfamily have been reported in plants, including, but not limited to, five Rosaceae species (Sun et al, 2017), Glycine max (Zhou et al, 2016), Triticum aestivum (Sharma et al, 2016a), Glycine latifolia (Liu et al, 2018), two Citrus species (Magalhães et al, 2016) and Amborella trichopoda (Liu et al, 2016b). In addition to this the evolution and diversification of the LRR-RLK subfamily has been studied in various plant species, including flowering plants, algae and bryophytes (Fischer et al, 2016;Liu et al, 2017;Shiu and Bleecker 2001a).…”

De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia provides insight into secondary growth

“…Long terminal repeats (LTRs), short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs) are the most common TEs in the C. equisetifolia genome, and we annotated about 33% sequences as TEs (Table S6). Consistent with the percentage in other plant species (Liu et al ., ), the most abundant repeat elements were LTRs with the highest ratio of 23% of the total assembly, of which 35.6% and 42.8% of LTR is Gypsy and Copia , respectively. The ratios were ~2.32%, (DNA transposons), ~2.16% (LINEs), ~0.04% (SINEs), and ~0.0006 (other types) of the total assembly, respectively.…”