Insights from draft genomes of Heterodera species isolated from field soil samples.

Background: The nematode phylum includes many species key to soil food webs with trophic behaviours extending from feeding on microbes to macrofauna and plant roots. Among these, the plant parasitic cyst nematodes retain their eggs in protective cysts prolonging their survival under harsh conditions. These nematodes, including those from the genus Heterodera, cause significant economic losses in agricultural systems. Understanding of nematode diversity and ecology has expanded through application of genomic research, however, for Heterodera species there are very few available whole genome sequences. Sequencing and assembling Heterodera genomes is challenging due to various technical limitations imposed by the biology of Heterodera. Overcoming these limitations is essential for comprehensive insights into Heterodera parasitic interactions with plants, population studies, and for Australian biosecurity implications.

Results: We hereby present draft genomes of six species of which Heterodera australis, H. humuli, H. mani and H. trifolii are presently recorded in Australia and two species, H. avenae and H. filipjevi, currently absent from Australia. The draft genomes were sequenced from genomic DNA isolated from 50 cysts each using an Illumina NovaSeq short read sequencing platform. The data revealed disparity in sequencing yield between species. What was previously identified as H. avenae in Australia using morphological traits is now confirmed as H. australis and may have consequences for wheat breeding programs in Australia that are breeding for resistance to H. avenae. A multigene phylogeny placed the sequenced species into taxonomic phylogenetic perspective. Genomic comparisons within the Avenae species group revealed orthologous gene clusters within the species, emphasising the shared and unique features of the group. The data also revealed the presence of a Wolbachia species, a putative bacterial endosymbiont from Heterodera humuli short read sequencing data.

Conclusion: Genomic research holds immense significance for agriculture, for understanding pest species diversity and the development of effective management strategies. This study provides insight into Heterodera, cyst nematode genomics and the associated symbionts and this work will serve as a baseline for further genomic analyses in this economically important nematode group.