Identical genomic organization of two hemichordate hox clusters.
Genomic comparisons of chordates, hemichordates, and echinoderms can inform hypotheses for the evolution of these strikingly different phyla from the last common deuterostome ancestor. Because hox genes play pivotal developmental roles in bilaterian animals, we analyzed the Hox complexes of two hemichordate genomes. We find that Saccoglossus kowalevskii and Ptychodera flava both possess 12-gene clusters, with mir10 between hox4 and hox5, in 550 kb and 452 kb intervals, respectively. Genes hox1-hox9/10 of the clusters are in the same genomic order and transcriptional orientation as their orthologs in chordates, with hox1 at the 3' end of the cluster. At the 5' end, each cluster contains three posterior genes specific to Ambulacraria (the hemichordate-echinoderm clade), two forming an inverted terminal pair. In contrast, the echinoderm Strongylocentrotus purpuratus contains a 588 kb cluster of 11 orthologs of the hemichordate genes, ordered differently, plausibly reflecting rearrangements of an ancestral hemichordate-like ambulacrarian cluster. Hox clusters of vertebrates and the basal chordate amphioxus have similar organization to the hemichordate cluster, but with different posterior genes. These results provide genomic evidence for a well-ordered complex in the deuterostome ancestor for the hox1-hox9/10 region, with the number and kind of posterior genes still to be elucidated.
Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA.
Robert
R
Freeman
Tetsuro
T
Ikuta
Michael
M
Wu
Ryo
R
Koyanagi
Takeshi
T
Kawashima
Kunifumi
K
Tagawa
Tom
T
Humphreys
Guang-Chen
GC
Fang
Asao
A
Fujiyama
Hidetoshi
H
Saiga
Christopher
C
Lowe
Kim
K
Worley
Jerry
J
Jenkins
Jeremy
J
Schmutz
Marc
M
Kirschner
Daniel
D
Rokhsar
Nori
N
Satoh
John
J
Gerhart
D000818:Animals; D005075:Biological Evolution; D002816:Chordata, Nonvertebrate / Q000235:genetics*; D005801:Genes, Homeobox; D016678:Genome; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D014158:Transcription, Genetic