Speaker: Dr. Richard D. Hayes, Molecular Biology Institute, University of California at Los Angeles
Time: 1:00-2:00pm, Wednesday, June 3rd, 2009
Place: 321 Stanley Hall
Abstract:
Trichomonas vaginalis is one of the most prevalent non-viral sexually
transmitted infectious parasitic protists in the world, with over 200 million
new cases of infection every year. T. vaginalis colonizes the human
urogenital tract, where it remains extracellular and causes lesions in vaginal
epithelia, leading to symptoms in infected women ranging from inflammatory
disease, infertility and pregnancy complications, to predisposition to HIV
infection and cervical cancer. Genome sequencing of a laboratory strain of
T. vaginalis was completed in April 2005 by The Institute for Genome
Research. The current version 1.0 of the genome annotation was produced by a
completely automated process that ultimately produced a set of nearly 60,000
putative gene models, most consisting of single exons. In a majority of cases,
existing molecular biology and biochemistry evidence, sequence homology, or
enzymatic domain homology matches were not correctly incorporated into these
annotations, resulting in more than 80% of predicted genes receiving the
annotation “conserved hypothetical protein”. Based on comparison to the
genomes of other divergent, unicellular parasites, a high percentage of
hypothetical proteins with insignificant similarity to proteins present in
other organisms is expected; however, 80% is unusually high. To begin the
process of validating the current annotation, peptide data from several
proteomics investigations of T. vaginalis were modeled against the
current genome annotation as sources of gene expression evidence. The results
presented include strong predictions for instances where sequencing or assembly
errors have contributed to annotation errors: incorrectly predicted start
codons leading to exon boundary errors, and frameshift errors resulting in the
annotation of single genes as two truncated genes in close proximity. All data
will become public by its incorporation in the current genome website, http://trichdb.org, to facilitate continued
analysis by the full T. vaginalis research community.
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