Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

Supplementary online materials belonging to the Genome Research manuscript "Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen" by de Jonge et al. (2013). The raw sequencing data and the <em>Verticillium dahliae</em> 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 <em>V. dahliae</em> 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. Repeatmasking was performed with the RepeatMasker using a de novo, RepeatModeler trained/generated, repeat library incorporating RECON, RepeatScout and the Tandem Repeat Finder (TRF). Gene models with alternative names depicted in the gff3 and fasta files important for the manuscript are: <em>XLOC_009059</em> - evm.TU.contig34339.15 <em>XLOC_008951</em> - evm.TU.contig1569.345 <em>Ave1</em> - evm.TU.contig45503.197 All other XLOC** gene models can be directly found. de Jonge R, Bolton MD, Kombrink A, van den Berg GCM, Yadeta KA, Thomma BPHJ. 2013. Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen. Genome Research <em>In press</em> doi:10.1101/gr.152660.112