Population differentiation and epidemic tracking of Bursaphelenchus xylophilus in China based on chromosome-level assembly and whole genome sequencing data.

Background Bursaphelenchus xylophilus, the pinewood nematode, kills millions of pine trees worldwide every year, and causes enormous economic and ecological losses. Despite extensive research on population variation, there is little understanding of the population-wide variation spectrum in China. Results We sequenced an inbred B. xylophilus strain using Pacbio+Illumina+Bionano+Hi-C and generated a chromosome-level assembly (AH1) with 6 chromosomes of 77.1 Mb (chromosome N50: 12 Mb). The AH1 assembly shows very high continuity, completeness and contains novel genes with potentially important functions compared with previous assemblies. Subsequently, we sequenced 181 strains from China and USA and found ~7.8 million SNPs. Analysis shows that the B. xylophilus population in China can be divided into geographically bounded subpopulations with severe cross infection and potential migrations. Besides, distribution of B. xylophilus is dominated by temperature zones while geographically associated SNPs are mainly located on adaptation related GPCR gene families, suggesting the nematode has been evolving to adapt to different temperatures. A machine learning based epidemic tracking method has been established to predict their geographical origins which can be applied to any other species. Conclusion Our study provides the community with the first high-quality chromosome-level assembly which includes a comprehensive catalogue of genetic variations. It provides insights into population structure and effective tracking method for this invasive species which facilitates future studies to address a variety of applied, genomic and evolutionary questions in the B. xylophilus as well as related species. This article is protected by copyright. All rights reserved.