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. 2019 Nov;19(6):1637-1646.
doi: 10.1111/1755-0998.13068. Epub 2019 Sep 9.

Chromosome-level reference genome of X12, a highly virulent race of the soybean cyst nematode Heterodera glycines

Yun Lian  1 , He Wei  1 , Jinshe Wang  1 , Chenfang Lei  1 , Haichao Li  1 , Jinying Li  1 , Yongkang Wu  1 , Shufeng Wang  1 , Hui Zhang  1 , Tingfeng Wang  1 , Pei Du  1 , Jianqiu Guo  2 , Weiguo Lu  1
Affiliations

Chromosome-level reference genome of X12, a highly virulent race of the soybean cyst nematode Heterodera glycines

Yun Lian et al. Mol Ecol Resour. 2019 Nov.

Abstract

Soybean cyst nematode (SCN, Heterodera glycines) is a major pest of soybean that is spreading across major soybean production regions worldwide. Increased SCN virulence has recently been observed in both the United States and China. However, no study has reported a genome assembly for H. glycines at the chromosome scale. Herein, the first chromosome-level reference genome of X12, an unusual SCN race with high infection ability, is presented. Using whole-genome shotgun (WGS) sequencing, Pacific Biosciences (PacBio) sequencing, Illumina paired-end sequencing, 10X Genomics linked reads and high-throughput chromatin conformation capture (Hi-C) genome scaffolding techniques, a 141.01-megabase (Mb) assembled genome was obtained with scaffold and contig N50 sizes of 16.27 Mb and 330.54 kilobases (kb), respectively. The assembly showed high integrity and quality, with over 90% of Illumina reads mapped to the genome. The assembly quality was evaluated using Core Eukaryotic Genes Mapping Approach and Benchmarking Universal Single-Copy Orthologs. A total of 11,882 genes were predicted using de novo, homolog and RNAseq data generated from eggs, second-stage juveniles (J2), third-stage juveniles (J3) and fourth-stage juveniles (J4) of X12, and 79.0% of homologous sequences were annotated in the genome. These high-quality X12 genome data will provide valuable resources for research in a broad range of areas, including fundamental nematode biology, SCN-plant interactions and co-evolution, and also contribute to the development of technology for overall SCN management.

Keywords: Heterodera glycines; Soybean cyst nematode; X12; chromosome scale; evolution; genome assembly.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
The combination of cysts on soybean roots (a) and micrograph of Heterodera glycines (soybean cyst nematode) second‐stage juvenile (J2) (b) [Colour figure can be viewed at http://wileyonlinelibrary.com]
Figure 2
Figure 2
Chromatin conformation capture‐based improved assembly Heterodera glycines genome. (a) Postclustering heat map showing the density of Hi‐C interactions between scaffolds from the proximity‐guided assembly. (b) Statistics of the completeness of the hybrid de novo assembly of X12 race genome. Listed are the assembled genome of ~141 Mb with scaffold and contig N50 size of 16.27 Mb and 330.54 Kb. Also listed in the table are the size and number of N60, N70, N80 and N90 of contigs and scaffolds. (c) Clustering of scaffolds using Hi‐C data into pseudochromosome‐scale scaffolds. Listed are the 258 scaffolds of total length ~12 Mb used for clustering. Also listed in the table are the cluster numbers, the number of contigs and the reference length of contigs [Colour figure can be viewed at http://wileyonlinelibrary.com]
Figure 3
Figure 3
The genome characteristics of Heterodera glycines. Circos plot showing the genomic features. 1u = 40 kb, small scale means 5u and large scale means 25u. From outer to inner circles: Track a: nine chromosomes of the genome; Track b: gene distribution in nine chromosomes; Track c: GC content distribution in nine chromosomes; Track d: LTR distribution in nine chromosomes; Track e: LINE distribution in nine chromosomes; Track f: SINE distribution in nine chromosomes; Track g: tRNA located on chromosomes; Track h: miRNA located on chromosomes; Track i: snRNA located on chromosomes; Track j: rRNA located on chromosomes [Colour figure can be viewed at http://wileyonlinelibrary.com]
Figure 4
Figure 4
Observation of the chromosome of Heterodera glycines in meiosis under fluorescence microscope with 450–490 nm excitation light (2n = 18) [Colour figure can be viewed at http://wileyonlinelibrary.com]
Figure 5
Figure 5
Phylogenetic relationships of species related to Heterodera glycines. Phylogenetic tree of the single‐copy gene families coexistent in the 12 species representing the relatedness of each species. Red box surrounded denotes the sequenced species H. glycines. Node labels represent node ages [Colour figure can be viewed at http://wileyonlinelibrary.com]
See this image and copyright information in PMC

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