An
important objective for inferring the evolutionary history of gene
families is the determination of orthologies and paralogies. Lineage
specific paralog loss following whole genome duplication events can
cause anciently related homologs to appear in some assays as orthologs.
Conserved synteny -- the tendency of neighboring genes to retain their
relative positions and orders on chromosomes over evolutionary time --
can help resolve such errors. Several previous studies examined
genome-wide syntenic conservation to infer the contents of ancestral
chromosomes and provided insights into the architecture of ancestral
genomes, but did not provide methods or tools applicable to the study
of the evolution of individual gene families. We developed an automated
system to identify conserved syntenic regions in a primary genome using
as outgroup a genome that diverged from the investigated lineage before
a whole genome duplication event. The product of this automated
analysis, the Synteny Database, allows a user to examine fully or
partially assembled genomes. The Synteny Database is optimized for the
investigation of individual gene families in multiple lineages and can
detect chromosomal inversions and translocations as well as ohnologs
(paralogs derived by whole-genome duplication) gone missing. To
demonstrate the utility of the system, we present a case study of gene
family evolution, investigating the ARNTL gene family in the genomes of
Ciona intestinalis, amphioxus, zebrafish, and human.
-- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele@psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- it's hard to keep the animo from driftin' away nowadays