Targeting Ascomycota genomes: what and how big?

Gap analysis of the available genomic data (i.e. identifying taxonomic groups with no representative genome assemblies) is a fundamental first step to design effective sampling strategies for whole genome sequencing (WGS) initiatives. We identified the significant holes that remain in genomic resources of the Ascomycota -the largest fungal phylum including many species of medicinal, ecological and/or economic significance -in order to prioritise WGS efforts towards reconstructing the Ascomycota tree of life. In doing so, we additionally looked at the existing genome size data for ascomycetes, given the importance of knowing the size of the genome to ensure sufficient sequencing coverage and assess the completeness and quality of genome assemblies. We found that 50 % of the ascomycete orders have no representative genome assembly and over 75 % have no reliably measured genome size data. We propose that integrating routine cytometric genome size measurements into WGS and genome assembly pipelines will provide both a valuable assembly quality metric and contribute data for addressing fundamental evolutionary questions. (c) 2021 The Authors. Published by Elsevier Ltd on behalf of British Mycological Society. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/ 4.0/).

Automated summary

By conducting a gap analysis of Ascomycota genomic data, significant deficiencies were identified, leading to a proposal to integrate genome size measurements into WGS and genome assembly pipelines for improving assembly quality and addressing evolutionary questions.