title: The amphioxus Hox cluster: characterization, comparative genomics, and evolution.
abstract: 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.
authors: Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA.
authors: Chris T
authors: CT
authors: Amemiya
authors: Sonja J
authors: SJ
authors: Prohaska
authors: Alicia
authors: A
authors: Hill-Force
authors: April
authors: A
authors: Cook
authors: Jessica
authors: J
authors: Wasserscheid
authors: David E K
authors: DE
authors: Ferrier
authors: Juan
authors: J
authors: Pascual-Anaya
authors: Jordi
authors: J
authors: Garcia-Fernàndez
authors: Ken
authors: K
authors: Dewar
authors: Peter F
authors: PF
authors: Stadler
mesh_terms: D000818:Animals; D005075:Biological Evolution; D002816:Chordata, Nonvertebrate / Q000235:genetics*; D022201:Chromosomes, Artificial; D005801:Genes, Homeobox; D023281:Genomics; D005810:Multigene Family; D012091:Repetitive Sequences, Nucleic Acid