Hox cluster genomics in the horn shark, Heterodontus francisci

Abstract

Reconstructing the evolutionary history of Hox cluster origins will lead to insights into the developmental and evolutionary significance of Hox gene clusters in vertebrate phylogeny and to their role in the origins of various vertebrate body plans. We have isolated two Hox clusters from the horn shark, Heterodontus francisci. These have been sequenced and compared with one another and with other chordate Hox clusters. The results show that one of the horn shark clusters (HoxM) is orthologous to the mammalian HoxA cluster and shows a structural similarity to the amphioxus cluster, whereas the other shark cluster (HoxN) is orthologous to the mammalian HoxD cluster based on cluster organization and a comparison with noncoding and Hox genecoding sequences. The persistence of an identifiable HoxA cluster over an 800-million-year divergence time demonstrates that the Hox gene clusters are highly integrated and structured genetic entities. The data presented herein identify many noncoding sequence motifs conserved over 800 million years that may function as genetic control motifs essential to the developmental process.T he Hox gene clusters, first described in Drosophila as the Antenapedia and Bithorax clusters, control pattern formation along the anterior-posterior axis in bilateral animals (1). There is a single Hox gene cluster in all invertebrate species reported to date (2-5). In contrast, multiple Hox clusters have been reported in all vertebrate species examined (6-9). Reconstructing the evolutionary history of vertebrate Hox cluster duplication is necessary to identify orthologous clusters in different vertebrate species, to establish phylogenetic relationships among and between clades, and to elucidate the role of Hox cluster duplication in the vertebrate radiation.We have isolated two genomic clones containing Hox clusters from the primitive horn shark, Heterodontus francisci. One (Het1) is 81.2 kilobases (kb) in length, and the other (Het2) is 98.8 kb. Both have been sequenced completely and compared inter se and with other vertebrate Hox sequences. The Heterodontus Hox cluster data reported herein provide definitive map positions for the Hox genes within the shark clusters as well as extensive sequence information in coding and noncoding domains. Materials and MethodsGenomic DNA Sequencing. Nucleotide sequences were primarily determined by using the shotgun method, and unsequenced gaps were filled by the primer walking method (10). Two distinct dye termination kits (dRhodamine terminator cycle sequencing kit and BigDye terminator cycle sequencing kit, Perkin-Elmer) were used and analyzed by a 377 PRISM DNA sequencer (Perkin-Elmer). Regions covered with only one shotgun clone were resequenced with the other dye termination kit. The entire sequencing region was ensured by covering at least one highly reliable reading (Ͻ550-nucleotides-long from a sequencing primer). For regions covered by unidirectional readings or covered by less than three readings, all the sequence trace patterns were inspected to elimina...

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).…”

“…In hagfish, seven distinct nucleotide sequences of paralogous subgroup 9 have been identified through polymerase chain reaction (PCR) analysis, suggesting that the hagfish lineage may have undergone another independent Hox gene duplication . In the horn shark, two Hox clusters have been described (Kim et al, 2000), but the accurate cluster number is unknown. Nevertheless, with all Hox genes of higher chordates examined for both organization and expression so far, spatial-temporal colinearity is exhibited.…”

The duplication of the Hox gene clusters in teleost fishes*1

“…The four cluster situation is retained in the sarcopterygian lineage (data are available for a number of mammalia, Xenopus tropicalis, and both known coelacanth species [28,4], in basal actinopterygians (bichir Polypterus senegalus [9]), and (presumably) also in condrichtya (horn shark, Heterodontus francisci [27]). Higher ray-finned fishes, however, have 6 or 7 Hox clusters that arose by means of duplication from the ancestral gnathostome clusters [3].…”

Timing and mechanism of ancient vertebrate genome duplications – the adventure of a hypothesis

“…Two of them are homologous to mammalian Hox clusters, which also supports the hypothesis that at least one Hox-cluster duplication occurred in the ancestor of gnathostomes and agnathans. The two Hox clusters isolated so far from cartilaginous fish [62] are homologous to the mammalian HoxA and HoxD [63], placing the second '2R' duplication before the divergence of cartilagenous fish. TRENDS in Genetics Figure 3.…”

“…Bichir (Polypterus senegalus) has one HoxA cluster, whereas all other teleosts have two, which have undergone 3R [78]. The existence of one HoxA and one HoxD cluster (which implies that HoxB and HoxC should be present) in shark (Heterodontus francisci) places the 2R duplication before the emergence of cartilaginous fish [62]. For information on the number of Hox clusters in other species, see the following references: lamprey (Petromyzon marinus) [53,54], hagfish (Eptatretus stoutii) [61], zebrafish (Danio rerio) [50], pufferfish (S. nephalus) [51], medaka (Oryzia latipes) [52], Ciona (Ciona intestinalis) [79], coelocanth (Latimeria menadoensis) [80], amphioxus (Branchiostoma floridae) [3].…”