Document Detail


A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry.
MedLine Citation:
PMID:  21795387     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Anopheles gambiae is a major mosquito vector responsible for malaria transmission, whose genome sequence was reported in 2002. Genome annotation is a continuing effort, and many of the approximately 13,000 genes listed in VectorBase for Anopheles gambiae are predictions that have still not been validated by any other method. To identify protein-coding genes of An. gambiae based on its genomic sequence, we carried out a deep proteomic analysis using high-resolution Fourier transform mass spectrometry for both precursor and fragment ions. Based on peptide evidence, we were able to support or correct more than 6000 gene annotations including 80 novel gene structures and about 500 translational start sites. An additional validation by RT-PCR and cDNA sequencing was successfully performed for 105 selected genes. Our proteogenomic analysis led to the identification of 2682 genome search-specific peptides. Numerous cases of encoded proteins were documented in regions annotated as intergenic, introns, or untranslated regions. Using a database created to contain potential splice sites, we also identified 35 novel splice junctions. This is a first report to annotate the An. gambiae genome using high-accuracy mass spectrometry data as a complementary technology for genome annotation.
Authors:
Raghothama Chaerkady; Dhanashree S Kelkar; Babylakshmi Muthusamy; Kumaran Kandasamy; Sutopa B Dwivedi; Nandini A Sahasrabuddhe; Min-Sik Kim; Santosh Renuse; Sneha M Pinto; Rakesh Sharma; Harsh Pawar; Nirujogi Raja Sekhar; Ajeet Kumar Mohanty; Derese Getnet; Yi Yang; Jun Zhong; Aditya P Dash; Robert M MacCallum; Bernard Delanghe; Godfree Mlambo; Ashwani Kumar; T S Keshava Prasad; Mobolaji Okulate; Nirbhay Kumar; Akhilesh Pandey
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't     Date:  2011-07-27
Journal Detail:
Title:  Genome research     Volume:  21     ISSN:  1549-5469     ISO Abbreviation:  Genome Res.     Publication Date:  2011 Nov 
Date Detail:
Created Date:  2011-11-02     Completed Date:  2012-03-05     Revised Date:  2013-06-28    
Medline Journal Info:
Nlm Unique ID:  9518021     Medline TA:  Genome Res     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1872-81     Citation Subset:  IM    
Affiliation:
McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland 21205, USA.
Data Bank Information
Bank Name/Acc. No.:
GENBANK/GO935137;  GO935138
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MeSH Terms
Descriptor/Qualifier:
Alternative Splicing
Animals
Anopheles gambiae / genetics*,  metabolism*
Chromosome Mapping
Codon, Initiator
Exons
Genes, Insect
Genomics
Introns
Mass Spectrometry
Molecular Sequence Annotation
Molecular Sequence Data
Open Reading Frames
Peptides / genetics
Proteomics
RNA Splice Sites
Reproducibility of Results
Untranslated Regions / genetics
Grant Support
ID/Acronym/Agency:
S10RR023025/RR/NCRR NIH HHS
Chemical
Reg. No./Substance:
0/Codon, Initiator; 0/Peptides; 0/RNA Splice Sites; 0/Untranslated Regions
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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