RNA-seq-based genome reannotation of dermatophyte

38 Dermatophytes are the most common agents of superficial mycoses in humans and 39 animals. The aim of the present investigation was to systematically identify the 40 extracellular, possibly secreted, proteins that are putative virulence factors and antigenic 41 molecules of dermatophytes. A complete gene expression profile of Arthroderma 42 benhamiae was obtained during infection of its natural host (guinea pig) using RNA-seq 43 technology. This profile was completed with those of the fungus cultivated in vitro in two 44 media containing keratin and soy meal protein as the sole source of nitrogen, and in 45 Sabouraud medium. More than 60% of transcripts deduced from RNA-seq data differ from 46 those previously deposited for A. benhamiae. Using these RNA-seq data along with an 47 automatic gene annotation procedure, followed by manual curation, we produced a new 48 annotation of the A. benhamiae genome. This annotation comprised 7405 CDSs, among 49 which only 2662 were identical to the currently available annotation, 383 were newly 50 identified, and 15 secreted proteins were manually corrected. The expression profile of 51 genes encoding proteins with a signal peptide in infected guinea pigs was found very 52 different from that during in vitro growth when using keratin as substrate. Especially, the 53 sets of the 12 most highly expressed genes encoding proteases with a signal sequence 54 only had the putative vacuolar aspartic protease gene PEP2 in common, during infection 55 and in keratin medium. The most upregulated gene encoding a secreted protease during 56 infection was that encoding subtilisin SUB6, which is a known major allergen in the related 57 dermatophyte Trichophyton rubrum. 58 59