Abstract
The nematode Ditylenchus destructor comprises multiple haplotypes with distinct host preferences, while the genetic basis remains unclear. We generate three genomes (Haplotypes A, B, and C) using hybrid assembly and conduct comparative analysis with two published Haplotype A genomes. Integrating haplotype-resolved phylogeny, whole-genome alignments, functional annotation, orthogroup profiling, and secretome analysis shows Haplotypes B and C are more similar to each other than to Haplotype A. We identify several key genomic differences that may underlie host adaptation: Haplotype A features expanded chemosensory GPCR repertoires and GH31 glycoside hydrolases. Haplotype B possesses an abundance of cytochrome P450 domain proteins and secretory pectate lyases. Haplotype C harbors more genes encoding NADPH reductases, oxidoreductases, ABC transporters, secreted animal haem peroxidases, C-type lectins, and Astacins. We propose that these genomic variations facilitate the nematode’s adaptation to different host plants. Collectively, our findings establish a genomic framework for understanding host adaptation in D. destructor.
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Data availability
The draft genome assemblies of Ditylenchus destructor isolates GSAUP (Haplotype C), BazhouSP (Haplotype A), and DdB (Haplotype B) have been deposited in GenBank (accessions JAKKQA000000000.1 and JAKKPZ000000000.1) and Genome Warehouse (accession GWHGEIJ00000000.1), respectively. The corresponding BioProjects are PRJNA800207 (GSAUP and BazhouSP) and PRJCA041684 (DdB). The Illumina sequencing data of BazhouSP, DdB, and GSAUP, and the Oxford Nanopore sequencing data of DdB have been deposited in the Genome Sequence Archive (https://ngdc.cncb.ac.cn/gsa/browse/CRA038505). PacBio raw sequencing data for BazhouSP and GSAUP have been deposited in the Open Science Framework (https://doi.org/10.17605/OSF.IO/4T7GR). RNA-seq data for BazhouSP, DdB, and GSAUP are available in the Genome Sequence Archive (https://ngdc.cncb.ac.cn/gsa/browse/CRA038639). Numerical source data for graphs and charts can be found in Supplementary Data 1–7 (https://doi.org/10.5281/zenodo.18540296). All other data are available from the corresponding author on reasonable request.
Code availability
The pipeline for removing contaminant sequences from nematode genomes is available at https://github.com/wangjy-ll/remove-contaminant-sequences.
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Acknowledgements
We thank Professor Xinyue Cheng from Beijing Normal University for the help and support in this research. This work was supported by grants from the National Key R&D Program of China (2023YFD1400400), the Hainan Provincial Sanya Yazhou Bay Science and Technology Innovation Joint Project (ZDYF2025GXJS140), and the Regional Collaborative Innovation Project of Gansu Academy of Agricultural Sciences (2024GAAS04).
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B.X. and R.L. conceived and designed the research. Z.Z., R.L., and J.W. performed the data analysis and interpretation. H.L., H.Z., and N.L. prepared the experimental materials and carried out the sequencing. Z.Z. wrote the manuscript, R.L. and B.X. revised it. All authors read and approved the manuscript.
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Zhao, Z., Zhang, H., Wang, J. et al. Comparative genomics of different haplotypes in Ditylenchus destructor provides insights into their host preferences. Commun Biol (2026). https://doi.org/10.1038/s42003-026-09851-0
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DOI: https://doi.org/10.1038/s42003-026-09851-0
