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

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.

Metabolomics as an Emerging Tool for the Study of Plant–Pathogen Interactions

“…Diseases caused by soybean cyst nematodes are estimated to cause an 11% annual loss of soybean yield in the United States [16]. The damage by soybean cyst nematode-Heterodera schachtii, which is present around the world in most producing regions [160]-led to a deficit of over 136 million bushels in 2013 [16], and represents over one billion US dollar losses each year [161,162]. The use of resistant cultivars as the main management practice is challenged by the ability of the nematodes to rapidly adaptation to overcome it [163].…”

Speciation and adaptive evolution reshape antioxidant enzymatic system diversity across the phylum Nematoda

“…To determine whether the single cluster CAT of rootknot nematodes is lineage-specific, we analyzed other plant-parasitic nematodes [43][44][45][46], including five other root-knot nematodes. Three to eleven CATs were encoded in the draft genomes of root-knot nematodes.…”

A chromosomal assembly of the soybean cyst nematode genome

“…However, this increased genome size may be due to the incorporation of repetitive haplotigs, an assumption supported by the inflation of repeats (61.4 Mb) compared to the previous TN10 H. glycines draft (42.1 Mb). Still, total repeat content (38.9%) is within the published range (34-47.7%) [40,41], and yet maintains a lower repeat content than the X12 assembly (67.3 Mb) (Supplementary Table 1).…”

“…The H. glycines genome assembly comprises 2,109 contigs, all of which were incorporated into the expected 9 pseudomolecule scaffolds using the Juicer pipeline, in agreement with cytological observations [41,94]. The genome size of the new assembly is 157,982,452 bp, within the expected range for this clade of species (Table 1).…”

“…Understanding the totality of effector proteins in the nematode genome and how they manipulate the host will shed light on this molecular interplay, inspiring the development of novel mechanisms to defend plants from these important pests. To accomplish this goal for the soybean cyst nematode, two annotated genome assemblies were published from two different nematode strains: a partially virulent TN10 line [40] and a highly virulent X12 line [41]. Here we improve upon the current genomes by reassembling the TN10 PacBio reads and scaffolding with Chicago and Hi-C reads to obtain the highest quality plant-parasitic nematode genome assembly to date with nine complete pseudomolecule chromosomes and zero unscaffolded contigs.…”