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Genome Res. 2017 Jan;27(1):133-144. doi: 10.1101/gr.201368.115. Epub 2016 Nov 15.

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

Author information

1
Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.
2
YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India.
3
NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka 560029, India.
4
National Institute of Malaria Research, Field Station, Goa 403001, India.
5
Department of Zoology, Goa University, Taleigao Plateau, Goa 403206, India.
6
Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India.
7
Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India.
8
School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India.
9
Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA.
10
Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA.
11
Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India.
12
Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, Karnataka 572103, India.
13
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
14
Department of Neurology, Johns Hopkins University, Baltimore, Maryland 21205, USA.
15
Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana 70112, USA.
16
Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
17
Center for Genomics and Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA.
18
Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
19
Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
20
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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.

PMID:
28003436
PMCID:
PMC5204337
DOI:
10.1101/gr.201368.115
[Indexed for MEDLINE]
Free PMC Article

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