Genomic Profiling of Virulence in the Soybean Cyst Nematode Using Single-Nematode Sequencing

Abstract

Soybean cyst nematode (SCN) is one of the most important diseases in soybean. Currently, the main management strategy relies on planting resistant cultivars. However, the overuse of a single resistance source has led to the selection of virulent SCN populations, although the mechanisms by which the nematode overcomes the resistance genes remain unknown. In this study, we used a nematode-adapted single-cell RNA-seq approach to identify SCN genes potentially involved in resistance breakdown in Peking and PI 88788 parental soybean lines. We established for the first time the full transcriptome of single SCN individuals allowing us to identify a list of putative virulence genes against both major SCN resistance sources. Our analysis identified 48 differentially expressed putative effectors (secreted proteins required for infection) alongside 40 effectors showing evidence of novel structural variants, and 11 effector genes containing phenotype-specific sequence polymorphisms. Additionally, a differential expression analysis revealed an interesting phenomenon of co-expressed gene regions with some containing putative effectors. The selection of virulent SCN individuals on Peking resulted in a profoundly altered transcriptome, especially for genes known to be involved in parasitism. Several sequence polymorphisms were also specific to these virulent nematodes and could potentially play a role in the acquisition of nematode virulence. On the other hand, the transcriptome of virulent individuals on PI 88788 was very similar to avirulent ones with the exception of a few genes, which suggest a distinct virulence strategy to Peking.

Comparative Genomics of two Inbred Lines of the Potato Cyst NematodeGlobodera rostochiensisreveals disparate Effector Family-specific Diversification Patterns

“…Since more than 50% of the called SNPs in Gr-Line19 are still heterozygous, it seems reasonable to assume that the measured heterozygosity levels provide a more realistic picture of the heterozygosity that is present in an individual. Which is in line with previous findings in the cyst nematode Heterodera glycines by Ste-Croix et al (2021), who described that individuals can have mixing levels of zygosity.…”

Comparative genomics of two inbred lines of the potato cyst nematode Globodera rostochiensis reveals disparate effector family-specific diversification patterns

“…Since more than 50 % of the called SNPs in Gr-Line19 are still heterozygous, it seems reasonable to assume that the measured heterozygosity levels provide a more realistic picture of the heterozygosity that is present in an individual. Which is in line with previous findings in the cyst nematode Heterodera glycines by Ste-Croix et al (2021) [44], who described that individuals can have mixing levels of zygosity.…”

Comparative Genomics of two Inbred Lines of the Potato Cyst Nematode Globodera rostochiensis reveals disparate Effector Family-specific Diversification Patterns

“…Since more than 50% of the called SNPs in Gr-Line19 are still heterozygous, it seems reasonable to assume that the currently measured heterozygosity levels provide a more realistic picture of the heterozygosity that is present in an individual. This observation is in line with previous ndings for the cyst nematode Heterodera glycines by Ste-Croix et al (2021) [34] showing that individuals from a single population can be homozygous or heterozygous vis-à-vis putative virulence genes.…”