Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha)

Abstract

Large-scale-even genome-wide-duplications have repeatedly been invoked as an explanation for major radiations. Teleosts, the most species-rich vertebrate clade, underwent a ''fish-specific genome duplication'' (FSGD) that is shared by most ray-finned fish lineages. We investigate here the Hox complement of the goldeye (Hiodon alosoides), a representative of Osteoglossomorpha, the most basal teleostean clade. An extensive PCR survey reveals that goldeye has at least eight Hox clusters, indicating a duplicated genome compared to basal actinopterygians. The possession of duplicated Hox clusters is uncoupled to species richness. The Hox system of the goldeye is substantially different from that of other teleost lineages, having retained several duplicates of Hox genes for which crown teleosts have lost at least one copy. A detailed analysis of the PCR fragments as well as full length sequences of two HoxA13 paralogs, and HoxA10 and HoxC4 genes places the duplication event close in time to the divergence of Osteoglossomorpha and crown teleosts. The data are consistent with-but do not conclusively prove-that Osteoglossomorpha shares the FSGD.

Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome

“…In total, there are 42 Hox genes ordered in the same transcriptional orientation throughout respective clusters, as well as two Evx paralogues associated with the HOXA and HOXD clusters. Based on our data and those of other taxa (22,23,26,(30)(31)(32)(33)(34), we constructed a more complete scenario of the evolutionary history of vertebrate HOX clusters (Fig. 1).…”

“…The zebrafish genome contains seven HOX clusters, with a remnant of the eighth cluster (HOXDb) having retained only a single microRNA (21). A recent PCR survey of the mooneye (Hiodon alosoides, Osteoglossomorpha) provides evidence for the survival of all eight HOX clusters in the aftermath of the WGD (22). Within the teleosts, some fishes such as the salmonids (salmons and trouts) have undergone yet an additional genome doubling event such that they possess twice as many HOX clusters as other teleosts (23).…”

“…Within the teleosts, some fishes such as the salmonids (salmons and trouts) have undergone yet an additional genome doubling event such that they possess twice as many HOX clusters as other teleosts (23). In contrast, basal ray-finned fishes such as bichir, gar, and bowfin do not appear to have undergone this extra WGD (22,(24)(25)(26). The effects of the extra HOX clusters within teleosts are still unclear; some authors have implicated that they may have contributed to the success (speciation) of the teleost fishes (16,20,27), although this is an ad hoc hypothesis especially when one considers that this increase in cluster number has been accompanied by increases in gene losses (28).…”

Whole-genome duplication in teleost fishes and its evolutionary consequences

“…Recently, duplicated Hox gene clusters were found in the two most basal extant groups of teleost fishes, the Elopomorpha (including eels and tarpons) (Guo et al, 2009;Henkel et al, 2012). and Osteoglossomorpha (including bony tongues and elephantfish) (Chambers et al, 2009). …”

Duplicated Gene Evolution Following Whole-Genome Duplication in Teleost Fish

“…Some Hox genes are specifically preserved in different teleosts, for example, HoxA1b has been identified thus far only in the Japanese eel (Guo et al 2010). At the cluster level, eight Hox clusters were retained in basal species such as the Japanese eel (Guo et al 2010) and the goldeye (Chambers et al 2009), whereas one Hox cluster (C or D) was lost respectively in the Otocephala (Amores et al 1998) and Euteleostei (Kurosawa et al 2006). Based on the phylogeny of teleosts, Guo et al (2010) Fig.…”