Molecular evolution of the HoxA cluster in the three major gnathostome lineages

Abstract

The duplication of Hox clusters and their maintenance in a lineage has a prominent but little understood role in chordate evolution. Here we examined how Hox cluster duplication may influence changes in cluster architecture and patterns of noncoding sequence evolution. We sequenced the entire duplicated HoxAa and HoxAb clusters of zebrafish (Danio rerio) and extended the 5 (posterior) part of the HoxM (HoxA-like) cluster of horn shark (Heterodontus francisci) containing the hoxa11 and hoxa13 orthologs as well as intergenic and flanking noncoding sequences. The duplicated HoxA clusters in zebrafish each house considerably fewer genes and are dramatically shorter than the single HoxA clusters of human and horn shark. We compared the intergenic sequences of the HoxA clusters of human, horn shark, zebrafish (Aa, Ab), and striped bass and found extensive conservation of noncoding sequence motifs, i.e., phylogenetic footprints, between the human and horn shark, representing two of the three gnathostome lineages. These are putative cis-regulatory elements that may play a role in the regulation of the ancestral HoxA cluster. In contrast, homologous regions of the duplicated HoxAa and HoxAb clusters of zebrafish and the HoxA cluster of striped bass revealed a striking loss of conservation of these putative cisregulatory sequences in the 3 (anterior) segment of the cluster, where zebrafish only retains single representatives of group 1, 3, 4, and 5 (HoxAa) and group 2 (HoxAb) genes and in the 5 part of the clusters, where zebrafish retains two copies of the group 13, 11, and 9 genes, i.e., AbdB-like genes. In analyzing patterns of cis-sequence evolution in the 5 part of the clusters, we explicitly looked for evidence of complementary loss of conserved noncoding sequences, as predicted by the duplication-degeneration-complementation model in which genetic redundancy after gene duplication is resolved because of the fixation of complementary degenerative mutations. Our data did not yield evidence supporting this prediction. We conclude that changes in the pattern of cis-sequence conservation after Hox cluster duplication are more consistent with being the outcome of adaptive modification rather than passive mechanisms that erode redundancy created by the duplication event. These results support the view that genome duplications may provide a mechanism whereby master control genes undergo radical modifications conducive to major alterations in body plan. Such genomic revolutions may contribute significantly to the evolutionary process.H ox genes encode transcription factors that control pattern formation along the anterior-posterior axis (1). Hox genes are organized in clusters produced by a series of tandem duplications of progenitor gene(s) long before the protostomedeuterostome split (2). Although cluster organization has been maintained in both protostome (e.g., Drosophila) and deuterostome (e.g., human) lineages, the number of Hox clusters varies. To date, all protostome lineages have a single Hox cluster (3-8).The numb...

Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications

“…With this model we show that the number of PFC retained is less than what is expected from structural causes in all examined cases. This supports the idea that Hox cluster duplication can facilitate the evolution of development [22,9].…”

“…In some case one might want to argue that two or several cliques in close proximity should only be counted as a single PFC. For example, in [9] footprints are merged into the same PFC if they are separated by less than 100nt. Since we are interested in relative abundances here this distinction is not important for our conclusions.…”

“…The reason is that at least in this case there appear to be substantial changes in the regulatory patterns that do not necessarily conform with established phylogenetic relationships: In [9], for example, it has been reported that -quite unexpectedly -the footprint pattern of the horn shark Heterodontus francisci has much more in common with the pattern in Homo sapiens than with other fish species (Morone saxatilis and Danio rerio). We therefore drop the maximum parsimony assumption for the evolution of regulatory sequences in large gene clusters and instead adopt a stepwise procedure that first extracts potentially conserved regions from pairwise sequence comparisons and passes these candidates through a series of filtering steps.…”

“…This approach was successful to identify the regulatory elements in many cases, see e.g. [18,23,29,9,6] and the review [11]. In a related approach, the rVISTA tool uses pairwise alignments of orthologous regions to determine the significance of putative transcription factor binding sites found by comparison with a database of binding motifs [19].…”

“…The purpose of the study [9] was to assess the effect of Hox cluster duplication on the structure and function of Hox genes. The qualitative results in [9] suggested that cluster duplication leads to a massive loss of non-coding sequence conservation, which could be indicative of extensive modifications in the function of Hox genes. If this is the case one would expect to find a similar degree of loss of conservation in other teleost Hox clusters.…”