Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

The raw sequencing data and the Verticillium dahliae strain JR2 assembly are deposited at the NCBI under BioProject accessions PRJNA169154 and PRJNA175765 (APFD00000000) respectively. The whole genome assembly plus annotation (proteins and repetitive elements) are deposited here at figshare.

This is version 1.5 of the JR2 V. dahliae assembly. Protein-coding gene annotation was performed using a combinatorial approach with the EvidenceModeler, implementing (trained) ab initio gene finders Augustus, GenemarkES and GlimmerHMM, protein alignments (by AAT) and transcript alignments (by combining RNA-Seq, genome-assisted Trinity and PASA). Ultimately, gene models were improved (to add UTR and alternative splicing) by PASA again and further updated by limited manual curation.