Genome annotation in the presence of insertional RNA editing.
BACKGROUND
Insertional RNA editing renders gene prediction very difficult compared to organisms without such RNA editing. A case in point is the mitochondrial genome of Physarum polycephalum in which only about one-third of the number of genes that are to be expected given its length are annotated. Thus, gene prediction methods that explicitly take into account insertional editing are needed for successful annotation of such genomes.


RESULTS
We annotate the mitochondrial genome of P.polycephalum using several different approaches for gene prediction in organisms with insertional RNA editing. We computationally validate our annotations by comparing the results from different methods against each other and as proof of concept experimentally validate two of the newly predicted genes. We more than double the number of annotated putative genes in this organism and find several intriguing candidate genes that are not expected in a mitochondrial genome.


BACKGROUND
The C source code of the programs described here are available upon request from the corresponding author.
Beargie
Christina
C
COSI, 333 West Broad Street, Columbus, OH 43215, USA.
Liu
Tsunglin
T
Corriveau
Mark
M
Lee
Ha Youn
HY
Gott
Jonatha
J
Bundschuh
Ralf
R
D000818:Animals; D054629:Genome, Mitochondrial / Q000235:genetics; D018503:Genome, Protozoan / Q000235:genetics*; D016839:Physarum polycephalum / Q000235:genetics*; D017393:RNA Editing / Q000235:genetics*