The amphioxus Hox cluster: deuterostome posterior flexibility andHox14

Abstract

The amphioxus (Branchiostoma floridae) Hox cluster is a model for the ancestral vertebrate cluster, prior to the hypothesized genome-wide duplications that may have facilitated the evolution of the vertebrate body plan. Here we describe the posterior (5') genes of the amphioxus cluster, and report the isolation of four new homeobox genes. Vertebrates possess 13 types of Hox gene (paralogy groups), but we show that amphioxus possesses more than 13 Hox genes. Amphioxus is now the first animal in which a Hox14 gene has been found. Our mapping and phylogenetic analysis of amphioxus "Posterior Class" Hox genes reveals that these genes are evolving at a faster rate in deuterostomes than in protostomes, a phenomenon we term Posterior Flexibility.

PCR survey of Xenoturbella bocki Hox genes

“…Again, a complete list is provided in the Appendix. For the Hox gene complements of cephalochordates, we refer to Ferrier et al (2000) for the ancestral state of the vertebrate Hox cluster before the genome duplications; see Powers and Amemiya (2004).…”

Organization of Hox genes in ascidians: Present, past, and future

“…The cluster organization of Hox genes has been investigated in a variety of chordates: larvacean (Seo et al, 2004), amphioxus (Garcia-Fernandez and Holland, 1994;Ferrier et al, 2000), lamprey (Force et al, 2002;Irvine et al, 2002), horn shark (Kim et al, 2000;Chiu et al, 2002), coelacanth (Koh et al, 2003), ray-fin fish, bichir (Chiu et al, 2004), zebrafish (Amores et al, 1998;Chiu et al, 2002), medaka (Misof and Wagner, 1996), cichlid (Malaga-Trillo and Meyer, 2001), puffer fish (Aparicio et al, 1997), newt (Belleville et al, 1992), mouse (Duboule and Dolle, 1989), and human (Acampora et al, 1989). Nonchordate Hox clusters have been reported with Drosophila (Lewis, 1978;Von Allmen et al, 1996), mosquito (Devenport et al, 2000;Powers et al, 2000), red flour beetle (Brown et al, 2002), silk moth (Ueno et al, 1992), a grasshopper (Ferrier and Akam, 1996), nematode, Caenorhabditis elegans (Wang et al, 1993;Van Auken et al, 2000), ribbon worm (Kmita-Cunisse et al, 1998), and sea urchin (Popodi et al, 1996;Martinez et al, 1999).…”

Gene phylogenies and protein–protein interactions: possible artifacts resulting from shared protein interaction partners

“…the human and the Amphioxus Hox genes we therefore expect that (1) the up to four human Hox genes of each of the 14 paralog groups cluster together, (2) these subtrees cluster together with the corresponding Amphioxus Hox genes, and (3) the "top" of the tree above these subtrees reflects the history by which the ancestral chordate Hox cluster came about through a history of duplications from a single "Ur-Hox" gene. While this pattern is presented by the anterior and (mostly) the middle group Hox genes, the posterior genes Hox-9 through Hox13 surprisingly show a different pattern, as described in [4], see Fig. 1.…”

“…For example, the Hox genes from paralog groups PG1 through PG10 gain DNA binding affinity through cooperative binding with the protein Pbx1 [11], while the socalled posterior Hox genes HoxA9, HoxA10, HoxA11, HoxA13, and HoxD12 all interact with Meis1 [19]. The work presented here was motivated by the analysis of the Hox genes of the Amphioxus (Branchiostoma floridae) [4]. Hox genes code for homeodomain containing transcription factors which are homologous to the genes in the Drosophila homeotic gene clusters [12].…”

“…Another possibility is that the rate of evolution of posterior genes is higher than that of anterior genes and thus obscures the phylogenetic signal, a hypothesis called posterior flexibility [4]. An alternative explanation is that the reconstructed gene tree in Fig.…”