The chordate ancestor possessed a single copy of the Brachyury gene for notochord acquisition

Background: The T-box family transcription-factor gene, Brachyury, has two expression domains with discretefunctions during animal embryogenesis. The primary domain, associated with the blastopore, is shared by mostmetazoans, while the secondary domain, involved in the notochord, is specific to chordates. In most animals,Brachyury is present in a single copy, but in cephalochordates, the most basal of the chordates, the gene is presentin two copies, suggesting allotment of the two domains to each of the duplicates.Results: In order to clarify whether Brachyury duplication occurred in the common ancestor of chordates afterwhich one of duplicates was lost in the urochordate and vertebrate lineages, we estimated phylogeneticrelationships of Brachyury genes and examined the synteny of a Brachyury-containing genomic region ofdeuterostomes with decoded genomes. The monophyletic origin of tandemly arranged Brachyury genes ofcephalochordates indicates that the tandem duplication occurred in the cephalochordate lineage, but not in thechordate ancestor.Conclusions: Our results thus suggest that, in the common ancestor of chordates, a single copy of Brachyuryacquired two expression domains and that the duplication was not involved in the acquisition of the notochord.However, in relation to regulatory mechanisms, both possibilities—namely a single copy with two domains andtwo copies with different domains—should be considered in future studies of Brachyury