XB-FEAT-6485520

nomenclature changes

November 1st, 2018.

The orthology and homology of the bix gene family (brachyury-inducible homeobox genes) has been reassessed. Following nomenclature guidelines, the following changes have been made to the naming system for the Xenopus bix genes.

Previously, only bix1-bix4 were named, and with latest genome annotation, it was clear that the first 3 loci are tandem duplication of the same orthologue, and as such should be named bix1, genes 1, 2 and 3. In addition, X. tropicalis has 3 additional bix genes, before acbd3. These bix genes are named in order, from left to right, bix1 genes 4, 5 and 6.

The earlier names are now recorded as synonyms on the Xenbase gene pages.

The order of the genes ( and flanking genes) on chromosome 5 for X. tropicalis, X. laevis.L and X. laevis.S are shown below. (# indicates newly annotated bix gene; < and > symbols indicate directionality).

previous annotation:

X. tropicalis" : lin9>; mixer>; mix1>; <bix#: bix#>; bix#>; bix#>; bix#>; bix#>; acbd3>

X. laevis.L : lin9>; mixer>; mix1>; <bix3; bix#>; bix1>; acbd3>

X. laevis.S: lin9>; mixer>; mix1>; <bix#; bix2>; bix4>; acbd3>

new nomenclature

X. tropicalis : lin9>; mixer>; mix1>; <bix1.1: bix1.2> ; bix1.3>; bix1.4>; bix1.5>; bix1.6>; acbd3>

X. laevis.L: lin9>; mixer>; mix1>; <bix1.1; bix1.2>; bix1.3>; acbd3>

X. laevis.S: lin9>; mixer>; mix1>; <bix1.1; bix1.2>; bix1.3>; acbd3>

synonyms:

bix3 is now bix1.1

bix2 is now bix1.2

bix1 and bix4 are now bix 1.3

New gene pages for X. tropicalis genes bix1.4, bix1.5 and bix 1.6 are currently being constructed.