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Integration of RNA‐seq and proteomics data with genomics for improved genome annotation in Apicomplexan parasites
Author(s) -
Silmon de Monerri Natalie C.,
Weiss Louis M.
Publication year - 2015
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201500253
Subject(s) - proteogenomics , proteomics , gene annotation , biology , computational biology , genome , genomics , genome project , annotation , gene prediction , gene , genetics
While high quality genomic sequence data is available for many pathogenic organisms, the corresponding gene annotations are often plagued with inaccuracies that can hinder research that utilizes such genomic data. Experimental validation of gene models is clearly crucial in improving such gene annotations; the field of proteogenomics is an emerging area of research wherein proteomic data is applied to testing and improving genetic models. Krishna et al. [ Proteomics 2015, 15 , 2618–2628] investigated whether incorporation of RNA‐seq data into proteogenomics analyses can contribute significantly to validation studies of genome annotation, in two important parasitic organisms Toxoplasma gondii and Neospora caninum . They applied a systematic approach to combine new and previously published proteomics data from T. gondii and N. caninum with transcriptomics data, leading to substantially improved gene models for these organisms. This study illustrates the importance of incorporating experimental data from both proteomics and RNA‐seq studies into routine genome annotation protocols.