WHOLE mRNA SEQUENCING AND TRANSCRIPTOME ASSEMBLY OF CANDIDA ALBICANS AND CANDIDA AFRICANA UNDER CHLAMYDOSPORE-INDUCING CONDITIONS

Candida albicans is the most common opportunistic pathogen causing severe fungal infection in humans, especially in immunocompromised patients. Crucial to its success as a pathogen is the substantial dynamism of its genome which readily undergoes genetic changes generating new strains. Candida africana is a low virulence biovariant of C. albicans possessing peculiar vaginal tropism. This particular strain is unable to form chlamydospores, structures whose biological function is still unknown. In this study we sequenced the whole mRNA and assembled the transcriptomes of a strong C. albicans chlamydospore-producing strain (GE1) and a natural chlamydospore-negative C. africana strain (CBS11016), under specific experimental conditions. Here we showed the assembly results obtained using two strategies: a de novo and a genome-guided approach using Trinity program (v2.2.0). The assembled transcriptomes were evaluated using BUSCO, QUAST and rnaQUAST. De novo transcriptomes were assembled in 10681 (C. albicans) and 9612 (C. africana) contigs (≥200bp) whereas the assemblies produced by genome-guided option consisted of 21656 and 19160 contigs (≥200bp), respectively. Quality analysis showed that the de novo approach produced more complete transcriptomes despite the availability of a good reference genome. In conclusion, this study provides general guidance for transcriptome assembly of RNA-Seq data from closely related Candida yeast and emphasize the efficacy of the de novo assembly also when a sequenced reference genome of reasonable quality exists.