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

Abstract

Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome 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 1196 scaffolds and 868 protein-coding gene models. This proteogenomic 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. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted “noncoding 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.

Multi-Omics Driven Assembly and Annotation of the Sandalwood (Santalum album) Genome

“…Proteome data helped us to delineate these predicted lncRNAs to be potential coding transcripts that serve as novel genes. These findings are not unprecedented, as mass spectrometry-based evidence for the coding potential of several noncoding RNAs have been reported (Kim et al, 2014;Prasad et al, 2017).…”

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“…Recent work has described the improvement and correction of genome annotations using high resolution mass spectrometry. 22 While this is beyond the scope of this study, we can develop metrics related to the quality of match of Figure 3A) PSMs matched to all databases described. B) Identified PSMs match 58,309 protein sequences that can be reduced to 17,269 unique protein groups.…”

The Cannabis Multi-Omics Draft Map Project

“…Recent work has described the improvement and correction of genome annotations using high resolution mass spectrometry. 31 While this is beyond the scope of this study, we can develop metrics related to the quality of match of genomic data using high coverage proteomics. An UpSetR graph 32 is shown in Figure 3 that shows the unique protein identifications and matches to the various genomic databases both unique and conserved.…”