Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni

Abstract

BackgroundTeleost fish have seven paralogous clusters of Hox genes stemming from two complete genome duplications early in vertebrate evolution, and an additional genome duplication during the evolution of ray-finned fish, followed by the secondary loss of one cluster. Gene duplications on the one hand, and the evolution of regulatory sequences on the other, are thought to be among the most important mechanisms for the evolution of new gene functions. Cichlid fish, the largest family of vertebrates with about 2500 species, are famous examples of speciation and morphological diversity. Since this diversity could be based on regulatory changes, we chose to study the coding as well as putative regulatory regions of their Hox clusters within a comparative genomic framework.ResultsWe sequenced and characterized all seven Hox clusters of Astatotilapia burtoni, a haplochromine cichlid fish. Comparative analyses with data from other teleost fish such as zebrafish, two species of pufferfish, stickleback and medaka were performed. We traced losses of genes and microRNAs of Hox clusters, the medaka lineage seems to have lost more microRNAs than the other fish lineages. We found that each teleost genome studied so far has a unique set of Hox genes. The hoxb7a gene was lost independently several times during teleost evolution, the most recent event being within the radiation of East African cichlid fish. The conserved non-coding sequences (CNS) encompass a surprisingly large part of the clusters, especially in the HoxAa, HoxCa, and HoxDa clusters. Across all clusters, we observe a trend towards an increased content of CNS towards the anterior end.ConclusionThe gene content of Hox clusters in teleost fishes is more variable than expected, with each species studied so far having a different set. Although the highest loss rate of Hox genes occurred immediately after whole genome duplications, our analyses showed that gene loss continued and is still ongoing in all teleost lineages. Along with the gene content, the CNS content also varies across clusters. The excess of CNS at the anterior end of clusters could imply a stronger conservation of anterior expression patters than those towards more posterior areas of the embryo.

Embryonic Development and Skeletogenesis of the Pharyngeal Jaw Apparatus in the Cichlid Nile Tilapia (Oreochromis niloticus)

“…Primers for Hox genes were designed based on published Oreochromis niloticus (Nile tilapia) cDNA sequences (Santini and Bernardi, 2005), or genomic Astatotilapia burtoni sequences (Hoegg et al, 2007). Primers for fli-1, pea-3 and dlx2a were designed based on genomic sequence comparisons of each gene between Gasterosteus aculeatus (three-spined stickleback), Takifugu rubripes, Oryzias latipes (japanese medaka), and Danio rerio (zebrafish).…”

“…Although expression of hoxa3a and hoxa4a has not been reported in zebrafish, recent evidence from conditional deletion of the mouse Hoxa cluster in NC cells suggests that Hoxa cluster genes have a primary role in the biology of skeletogenic NC cells in mice (Minoux et al, 2009). Because all PG1 to PG8 genes, except for hoxa2b, have been lost from the teleostean hoxab cluster (Hoegg et al, 2007), it is likely that functions carried by the ancestral osteichthyan hoxa cluster were mostly inherited by the teleostean hoxaa cluster. Studies of zebrafish hoxa3a and a4a expression are needed to explore this possibility, and functional studies in zebrafish and tilapia will tell whether genes of the hoxaa cluster have a dominant role in specifying the PJA skeleton.…”

“…Interestingly, hoxd4b, one of the only two members of the tilapia hoxdb cluster and which co-ortholog was lost in zebrafish (Hoegg et al, 2007), is robustly expressed in PA5 alone, also with strong dorsal expression. Studies of zebrafish hoxd3a and d4a are necessary to determine how divergent pharyngeal expression is between zebrafish and tilapia hoxda genes, and thus predict whether they played a role in PJA evolution.…”

Elephant shark ( Callorhinchus milii ) provides insights into the evolution of Hox gene clusters in gnathostomes

“…In vertebrates, Hox cluster genes also exhibit temporal collinearity; that is, genes located in the 3Ј-end of the cluster are expressed early during development, whereas genes in the 5Ј-end are expressed later (2). Recent comparative studies of Hox clusters in model genomes have shown that Hox clusters have experienced repeated molecular changes, including fragmentation, cluster duplication, gene loss, coding-sequence divergence, and cisregulatory element evolution (3)(4)(5)(6)(7). Because of their critical role in defining the identities of body segments, Hox genes are believed to have played a key role in driving the morphologic diversification of animals (8)(9)(10) and thus are of particular interest in understanding the genetic basis of morphologic diversity of metazoans.…”

“…Whereas a duplicate HoxD cluster is lost in zebrafish, acanthopterygians such as fugu, medaka, and cichlids have lost a duplicate HoxC cluster. In addition, several Hox genes have experienced lineagespecific secondary losses resulting in each of these teleosts possessing a unique set of Hox genes (5,15). In contrast to these teleosts, Atlantic salmon contains as many as 13 Hox clusters owing to an additional genome duplication in a salmonid ancestor (16).…”