Regional sequence expansion or collapse in heterozygous genome assemblies.

ABSTRACT: High levels of heterozygosity present a unique genome assembly challenge and can adversely impact downstream analyses, yet is common in sequencing datasets obtained from non-model organisms. Here we show that by re-assembling a heterozygous dataset with variant parameters and different assembly algorithms, we are able to generate assemblies whose protein annotations are statistically enriched for specific gene ontology categories. While total assembly length was not significantly affected by assembly methodologies tested, the assemblies generated varied widely in fragmentation level and we show local assembly collapse or expansion underlying the enrichment or depletion of specific protein functional groups. We show that these statistically significant deviations in gene ontology groups can

SUBMITTER: Asalone KC 

PROVIDER: S-EPMC7423139 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature