Integration of RNA-seq and proteomics data with genomics for improved genome annotation in Apicomplexan parasites

Natalie C. Silmon de Monerri, Louis M. Weiss

Research output: Contribution to journalComment/debate

4 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2557-2559
Number of pages3
JournalProteomics
Volume15
Issue number15
DOIs
StatePublished - Aug 1 2015

Keywords

  • Apicomplexa
  • Neospora
  • Proteogenomics
  • Protozoa
  • Toxoplasma

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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