Chromosome-Scale Genome Resource for Two Neopestalotiopsis spp. Isolates with Different Virulence in Strawberry (Fragaria × ananassa)

Abstract

Several Neopestalotiopsis spp. have been reported to affect strawberry worldwide. Here, we sequenced two isolates of Neopestalotiopsis 19-02 (high virulent) and 13-481 (moderate virulent) recovered from commercial strawberry fields in Florida and generated chromosome-scale assemblies using Oxford Nanopore Technologies and Illumina platforms. Each genome assembly for 19-02 and 13-481 contained putative telomere sequences at the 5’ and 3’ ends. By analyzing the collinearity of the two newly assembled genomes and verifying the conserved telomere sequence at the end of each chromosome, we confirmed that the genome of Neopestalotiopsis spp. consists of seven basic chromosomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis showed 98.5% of conserved core genes for both genome assemblies, 19-02 and 13-481. Phylogenetic analysis with internal transcribed spacer (ITS), beta-tubulin (β-tub), and translation elongation factor (tef1) regions obtained from the assemblies 19-02 and 13-481 demonstrated that the highly virulent isolate 19-02 is phylogenetically distinct from moderate virulent N. rosae 13-481. Comparative genome analysis of the high-quality reference genome assemblies provided in this study will facilitate the identification of genomic regions responsible for the different virulence of Neopestalotiopsis pathogen to strawberry.