Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana

Katari, M.t S., Balija, V., Wilson, R. K., Martienssen, R. A., McCombie, W. R. (2005) Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. Genome Research, 15 (4). pp. 496-504. ISSN 10889051 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/15805491
DOI: 10.1101/gr.3239105

Abstract

Since the completion of the Arabidopsis thaliana genome sequence, there is an ongoing effort to annotate the genome as accurately as possible. Comparing genome sequences of related species complements the current annotation strategies by identifying genes and improving gene structure. A total of 595,321 Brassica oleracea shotgun reads were sequenced by TIGR (The Institute for Genome Research) and the collaboration of Washington University and Cold Spring Harbor. Vicogenta (a genome viewer based on GMOD and GBrowse) was created to view the current annotation and sequence alignments for Arabidopsis. Brassica reads were compared with the Arabidopsis genome and proteome databases using BLAST. Hypothetical genes and conserved unannotated regions on the short arm of chromosome 4 from Arabidopsis were experimentally verified using RT-PCR. We were able to improve the Arabidopsis annotation by identifying 25 genes that were missed, and confirming expression of 43 hypothetical genes in Arabidopsis. We were also able to detect conservation in genes whose transcription is normally suppressed due to methylation. We also examined how useful the O. sativa genome and ESTs from other species are, compared with Brassica, in improving the Arabidopsis annotation.

Item Type: Paper
Uncontrolled Keywords: Amino Acid Sequence Arabidopsis genetics Brassica genetics Chromosomes Plant Conserved Sequence Databases Expressed Sequence Tags Genes Plant Genome Plant Genomics methods Oryza sativa genetics Reverse Transcriptase Polymerase Chain Reaction Sequence Homology Amino Acid Species Specificity GMOD and GBrowse
Subjects: bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > computers > computer software
CSHL Authors:
Communities: CSHL labs > Martienssen lab
CSHL labs > McCombie lab
Depositing User: CSHL Librarian
Date Deposited: 10 Jan 2012 19:32
Last Modified: 11 Apr 2013 19:53
PMCID: PMC1074364
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22617

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