Abstract
Synorth is a web resource for exploring and categorizing the syntenic relationships in gene regulatory blocks across multiple genomes.
Highlights
Genome Biology 2009, Volume 10, Issue 8, Article R86 Dong et al R86.2 are present in two copies per gamete
How we define the fate of a genomic regulatory block (GRB) is tied to the fate of its target gene(s): if the target gene survives in two copies, we consider that the GRB has survived in two copies ('1-to-2 scenario'); if, on the other hand, one copy of the target gene becomes inactivated, the highly conserved non-coding element (HCNE) on that locus lose the gene on which they act and, as such, become non-functional, are no longer under selection, and are subsequently lost
We describe Synorth ("Syntenic orthologs") [20], a web-based application consisting of: a genome locus browser where all reference genome genes and HCNE locations in any given synteny block are displayed in relation to orthologous loci across multiple vertebrate genomes, with a number of adjustable parameters; a table browser that lists the orthologous and syntenic relationships for each bystander-target pair in a GRB, for each teleost fish species relative to human as a reference tetrapod genome; and a tree browser in which all genes in the GRB are projected onto an ideal gene tree that assumes a whole genome duplication (WGD) event in teleost fish
Summary
Genome Biology 2009, Volume 10, Issue 8, Article R86 Dong et al R86.2 are present in two copies per gamete This duplicated genome content is highly redundant, so a WGD is followed by an extended evolutionary period during which one copy of most genes will become inactivated and disappear by neutral mutation - a process known as re-diploidization. Since each GRB (with the full set of target genes, bystander genes and HCNEs) is present in two copies following WGD, we say each has a 1-to-2 orthologous relationship with the ancestral (pre-WGD) genome. The 2R WGD took place at the root of jawed vertebrates This is the last WGD in the human lineage, and many GRBs and their target genes were duplicated on that occasion (examples of duplicates from that event that remain in two subfunctionalized copies to this day are SOX2/3, MEIS1/2, BARHL1/2, PAX4/6). The re-diploidization has not progressed far and the genomes of salmonid fish are still largely tetraploid [17]
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