Abstract
Human and mouse genomes contain six ParaHox genes implicated in gut and neural patterning. In coelacanths and cartilaginous fish, an additional ParaHox gene exists—Pdx2—that dates back to the genome duplications in early vertebrate evolution. Here we examine the genomic arrangement and flanking genes of all ParaHox genes in coelacanths, to determine the full complement of these genes. We find that coelacanths have seven ParaHox genes in total, in four chromosomal locations, revealing that five gene losses occurred soon after vertebrate genome duplication. Comparison of intergenic sequences reveals that some Pdx1 regulatory regions associated with development of pancreatic islets are older than tetrapods, that Pdx1 and Pdx2 share few if any conserved non-coding elements, and that there is very high sequence conservation between coelacanth species.
Highlights
The ParaHox gene cluster, first described in the cephalochordate amphioxus (Brooke et al, '98), contains three tandemly arrayed homeobox genes (Gsx, Xlox, and Cdx) and dates to the base of the Bilateria (Ferrier and Minguillón, 2003) or earlier (Hui et al, 2008; Mendivil Ramos et al, 2012)
We find that coelacanths have seven ParaHox genes in total, in four chromosomal locations, revealing that five gene losses occurred soon after vertebrate genome duplication
We previously reported that coelacanths have retained an additional ParaHox gene (Pdx2) that has been independently lost in other bony vertebrate lineages (Mulley and Holland, 2010) and set out to discover whether they may have retained additional members of the Gsx, Xlox and Cdx gene families
Summary
The ParaHox gene cluster, first described in the cephalochordate amphioxus (Brooke et al, '98), contains three tandemly arrayed homeobox genes (Gsx, Xlox, and Cdx) and dates to the base of the Bilateria (Ferrier and Minguillón, 2003) or earlier (Hui et al, 2008; Mendivil Ramos et al, 2012). In coelacanths and cartilaginous fish, an additional ParaHox gene exists—Pdx2—that dates back to the genome duplications in early vertebrate evolution.
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