Evidence that inconsistent gene prediction can mislead analysis of algal genomes

Abstract

Comparative algal genomics often relies on predicted gene models from de novo assembled genomes. However, the artifacts introduced by different gene-prediction approaches, and their impact on comparative genomic analysis, remain poorly understood. Here, using available genome data from six dinoflagellate species in Symbiodiniaceae, we identified potential methodological biases in the published gene models that were predicted using different approaches. We developed and applied a comprehensive customized workflow to predict genes from these genomes. The observed variation among predicted gene models resulting from our workflow agreed with current understanding of phylogenetic relationships among these taxa, whereas those published earlier were largely biased by the distinct approaches used in each instance. Importantly, these biases mislead the inference of homologous gene families and synteny among genomes, thus impacting biological interpretation of these data. Our results demonstrate that a consistent gene-prediction approach is critical for comparative genomics, particularly for non-model algal genomes.