Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

Abstract

The primary goal of whole genome sequencing efforts in any new organism is to provide accurate assembly and annotation of all protein-coding genes in the genome. Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. To this end, we provide a proof-of-concept for an analysis pipeline integrating experimental and computational workflows along with expert curation to greatly enhance genome assembly and annotation. We demonstrate a number of advantages of the proposed approach by analyzing the genome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1,196 scaffolds and 868 protein-coding gene models. This approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons and 76 events of joining of adjacent genes as a single gene. Incorporating proteomic evidence allowed us to change the designation of over 87 predicted 'non-coding RNAs' to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.