Evolution of Hox gene clusters in gnathostomes: insights from a survey of a shark (Scyliorhinus canicula) transcriptome.
It is now well established that there were four Hox gene clusters in the genome of the last common ancestor of extant gnathostomes. To better understand the evolution of the organization and expression of these genomic regions, we have studied the Hox gene clusters of a shark (Scyliorhinus canicula). We sequenced 225,580 expressed sequence tags from several embryonic cDNA libraries. Blast searches identified corresponding transcripts to almost all the HoxA, HoxB, and HoxD cluster genes. No HoxC transcript was identified, suggesting that this cluster is absent or highly degenerate. Using Hox gene sequences as probes, we selected and sequenced seven clones from a bacterial artificial chromosome library covering the complete region of the three gene clusters. Mapping of cDNAs to these genomic sequences showed extensive alternative splicing and untranslated exon sharing between neighboring Hox genes. Homologous noncoding exons could not be identified in transcripts from other species using sequence similarity. However, by comparing conserved noncoding sequences upstream of these exons in different species, we were able to identify homology between some exons. Some alternative splicing variants are probably very ancient and were already coded for by the ancestral Hox gene cluster. We also identified several transcripts that do not code for Hox proteins, are probably not translated, and all but one are in the reverse orientation to the Hox genes. This survey of the transcriptome of the Hox gene clusters of a shark shows that the high complexity observed in mammals is a gnathostome ancestral feature.
Oulion
Silvan
S
Laboratoire Evolution, Génomes et Spéciation, UPR 9034 Centre National de la Recherche Scientifique and Université Paris Diderot-Paris 7, 91198 Gif sur Yvette, France.
Debiais-Thibaud
Mélanie
M
d'Aubenton-Carafa
Yves
Y
Thermes
Claude
C
Da Silva
Corinne
C
Bernard-Samain
Sylvie
S
Gavory
Frédéric
F
Wincker
Patrick
P
Mazan
Sylvie
S
Casane
Didier
D
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D005091:Exons; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D015723:Gene Library; D005801:Genes, Homeobox; D018398:Homeodomain Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D012754:Sharks / Q000235:genetics*
D018398:Homeodomain Proteins; C088144:HoxA protein