Premium
The amphioxus Hox cluster: characterization, comparative genomics, and evolution
Author(s) -
Amemiya Chris T.,
Prohaska Sonja J.,
HillForce Alicia,
Cook April,
Wasserscheid Jessica,
Ferrier David E.K.,
PascualAnaya Juan,
GarciaFernàndez Jordi,
Dewar Ken,
Stadler Peter F.
Publication year - 2008
Publication title -
journal of experimental zoology part b: molecular and developmental evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.823
H-Index - 63
eISSN - 1552-5015
pISSN - 1552-5007
DOI - 10.1002/jez.b.21213
Subject(s) - hox gene , chordate , biology , vertebrate , evolutionary biology , lineage (genetic) , genome , genetics , computational biology , gene , transcription factor
The amphioxus Hox cluster is often viewed as “archetypal” for the chordate lineage. Here, we present a descriptive account of the 448 kb region spanning the Hox cluster of the amphioxus Branchiostoma floridae from Hox14 to Hox1 . We provide complete coding sequences of all 14 previously described amphioxus sequences and give a detailed analysis of the conserved noncoding regulatory sequence elements. We find that the posterior part of the Hox cluster is so highly derived that even the complete genomic sequence is insufficient to decide whether the posterior Hox genes arose by independent duplications or whether they are true orthologs of the corresponding gnathostome paralog groups. In contrast, the anterior region is much better conserved. The amphioxus Hox cluster strongly excludes repetitive elements with the exception of two repeat islands in the posterior region. Repeat exclusion is also observed in gnathostomes, but not protostome Hox clusters. We thus hypothesize that the much shorter vertebrate Hox clusters are the result of extensive resolution of the redundancy of regulatory DNA after the genome duplications rather than the consequence of a selection pressure to remove nonfunctional sequence from the Hox cluster. J. Exp. Zool. (Mol. Dev. Evol.) 310B:465–477, 2008 . © 2008 Wiley‐Liss, Inc.