Title: Fungal genome assembly and annotation: B. bassiana case study
Abstract: Fungi are cosmopolitan organisms which colonize a variety of environments. Members from this taxonomic group aid combatting crop pests of worldwide importance. This capability of broad “conquering” is directly linked to the fungi’s ability to produce a mixture of enzymes and molecules, usually encoded by a cluster of genes. The entomopathogenic fungi B. bassiana has a worldwide distribution and therefore has been well studied for pest management; nonetheless more efforts are required to increase its potential from an industrialized point of view, especially in the tropics. We studied eight B. bassiana genomes from Neotropical origin to complete its genome assembly as a first approach to exploit its biopesticide capacity. Despite shown utility, in Latin-American countries, budget might be a restrictive factor to produce both long and short read sequence data but should not avert to fulfill the assembly task. We implemented a bioinformatic pipeline which demonstrated suitability for short-read data only, which consisted of QC validation, genome completeness, gene-calling and further functional annotation. An important tool to accomplish this pipeline was MeDuSa which aids in the contigs ordering and orientation. From comparative genomics we determined our final assemblies had similar genome metrics as B. bassiana 2860 and 8028 reference genomes and determined differences in the presence of virulent associated genes within our isolates which grouped mostly in single copy orthogroups. Our proven pipeline demonstrated the importance of both, having bioinformatic abilities and access to HPC facilities to handle genomic data and boost the current knowledge of neotropical fungal diversity.
Bio: Stefany Solano-González is an associate professor at the School of Biological Sciences, National University of Costa Rica (UNA), where she coordinates the Applied Bioinformatics Laboratory (https://www.biologia.una.ac.cr/index.php/conozcanos-labap). She holds a B.Sc. on Biology with emphasis on Biotechnology from UNA and a Ph.D. on Biological Sciences, from the Institute of Integrative Biology at the University of Liverpool, UK. She has teaching experience in undergraduate and postgraduate university programs. During her work experience she has conducted research projects related to genetic analysis, fungal secondary metabolites, bioinformatics and comparative genomics, on which she has published research article. Currently she is studying biosurfactant production from Costarrican mangrove isolated fungi, to manipulate and exploit this type of molecules.