TIGR Annotation 5.0 - Pseudogenes and transposons - clarification

Dear Colleagues



Our previous announcement about the gene content of TIGR annotation
5.0, we failed to point out a change in our approach towards
annotating transposons. We also, inadvertently lumped transposons and
other pseudogenes together with the result that the apparent number
of protein-coding genes in this latest annotation is decreased from
previous releases. The following paragraph attempts to clarify the
situation.



"Transposons and pseudogenes were the last categories of genes to be
addressed by the re-annotation progress. Many ORFs were originally
annotated as being similar to transposons or transposon-related
proteins. However, the majority of these regions are degenerate so
that it is difficult or impossible to model ORFs across their entire
extent although shorter ORFs may be contained within the boundaries
of transposon similarity. Thus the legacy annotation for
transposon-related sequences consisted of a mixture of genes and
pseudogenes, only some of which were annotated as transposon-related.
In the latest release (5.0), we have provided a uniform annotation of
all transposon-related sequences by searching the entire genome
against a curated database of transposons sequences and automatically
applying the corresponding Tn family annotation. The majority of such
sequences are degenerate and clearly pseudogenes. We have not
attempted to discriminate between possible complete ORFs and
pseudogenes in this (transposon) category. There are 2,424 loci
annotated as transposons in the current release and (in contrast to
all previous releases) these are no longer included in the count of
"protein coding genes" nor in that dataset.

In addition to transposon-related sequences, there are approximately
500 "genuine" pseudogenes that are clearly related to genes of
identifiable function. Finally, there are ~ 850 pseudogenes that are
similar to proteins from Arabidopsis or other species that have no
known function and may represent degenerate ORFs of hypothetical
proteins yet to be characterized or to proteins from either of the
above categories. Users should note also that the naming of these
pseudogenes has not been subjected to the same set of uniform
curation standards that we applied to the full set of non-pseudogenes
and thus contains a mixture of TIGR and legacy annotation."



Please feel free to comment or write with questions.



Best wishes



Chris Town

_________________________________

Chris Town

Associate Investigator

The Institute for Genomic Research

9712 Medical Center Drive

Rockville, MD 20850



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