Evolution of the vertebrate parahox clusters

Prohaska, Sonja J.; Stadler, Peter F.

doi:10.1002/jez.b.21099

Cited by 12 publications

(11 citation statements)

References 27 publications

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“…We find that Tetraodon possesses two chromosomal regions homologous to human 13q12.1 (the location of the human ParaHox cluster), but each contains only a single ParaHox gene: the gsh1 or the pdx1 gene, respectively. Contrary to an earlier report (12), both copies of cdx2 are lost, but this may be compensated for by two copies of cdx1 on other chromosomes (Figs. 1, 7, 11, and 12).…”

Section: Resultscontrasting

confidence: 97%

Breakup of a homeobox cluster after genome duplication in teleosts

Mulley

Chiu

Holland

2006

Proc. Natl. Acad. Sci. U.S.A.

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Several families of homeobox genes are arranged in genomic clusters in metazoan genomes, including the Hox, ParaHox, NK, Rhox, and Iroquois gene clusters. The selective pressures responsible for maintenance of these gene clusters are poorly understood. The ParaHox gene cluster is evolutionarily conserved between amphioxus and human but is fragmented in teleost fishes. We show that two basal ray-finned fish, Polypterus and Amia, each possess an intact ParaHox cluster; this implies that the selective pressure maintaining clustering was lost after whole-genome duplication in teleosts. Cluster breakup is because of gene loss, not transposition or inversion, and the total number of ParaHox genes is the same in teleosts, human, mouse, and frog. We propose that this homeobox gene cluster is held together in chordates by the existence of interdigitated control regions that could be separated after locus duplication in the teleost fish.Amia ͉ gene cluster ͉ genome evolution ͉ ParaHox ͉ Polypterus

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Section: Resultscontrasting

confidence: 97%

Breakup of a homeobox cluster after genome duplication in teleosts

Mulley

Chiu

Holland

2006

Proc. Natl. Acad. Sci. U.S.A.

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“…The significant variations in number, sequence and regulation affecting Hox and ParaHox genes, as well as in their expression patterns, are responsible for body plan evolution and diversification (Amores et al, 1998;Duboule, 2007;Fr€ obius and Seaver, 2006;Gellon and McGinnis, 1998;Hui et al, 2008Hui et al, , 2009Lemmons and McGinnis, 2006;Prohaska and Stadler, 2006;Wagner et al, 2003). The comprehension of the evolutionary history of the Hox cluster genes is pivotal for understanding the evolution of bilaterian body architecture, the link between genetic and morphological complexity, and issues on metazoan phylogeny (de Rosa et al, 1999).…”

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confidence: 99%

Hox and ParaHox genes: A review on molluscs

Biscotti

Canapa

Forconi

et al. 2014

Genesis

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Summary: Hox and ParaHox genes are involved in patterning the anterior-posterior body axis in metazoans during embryo development. Body plan evolution and diversification are affected by variations in the number and sequence of Hox and ParaHox genes, as well as by their expression patterns. For this reason Hox and ParaHox gene investigation in the phylum Mollusca is of great interest, as this is one of the most important taxa of protostomes, characterized by a high morphological diversity. The comparison of the works reviewed here indicates that species of molluscs, belonging to different classes, share a similar composition of Hox and ParaHox genes. Therefore evidence suggests that the wide morphological diversity of this taxon could be ascribed to differences in Hox gene interactions and expressions and changes in the Hox downstream genes rather than to Hox cluster composition. Moreover the data available on Hox and ParaHox genes in molluscs compared with those of other Lophotrochozoa shed light on the complex and controversial evolutionary histories that these genes have undergone within protostomes. genesis 52:935-945, 2014. V C 2014Wiley Periodicals, Inc.Key words: Hox genes; ParaHox genes; molluscs; ProtoHox cluster HOX AND PARAHOX GENES: EVOLUTIONARY HYPOTHESESBoth Hox and ParaHox genes belong to the ANTP homeobox gene class, which also includes the NK genes, the NK-related genes, the Dlx genes, and many more (Holland, 2013). It has been hypothesized that the ancestor genes of the current ANTP class were originally arranged in a single cluster called "Megacluster" (Garcıa-Fernandez, 2005a;Holland, 2013).The comparison of Hox and ParaHox gene number is interesting in order to reconstruct the evolutionary history of these gene families. In this regard the increase in sequenced genomes is providing significant data concerning the Hox and ParaHox gene complement in several organisms.Considering the early appearance of NK genes during evolution and their genomic proximity to the Hox genes in some species (Larroux et al., 2007), Holland (2013 proposed the ProtoHox cluster as originating from a ProtoNK cluster. Given the lack of Hox and ParaHox genes in basal metazoans, such as the demosponge Amphimedon queenslandica (Larroux et al., 2007) and the lobate ctenophore Mnemiopsis leidyi, it has been hypothesized (Ryan et al., 2010) that the ProtoHox gene/cluster could have arisen after the divergence of Porifera and Ctenophora from ParaHoxozoa (Placozoa, Cnidaria, and Bilateria). However, the phylogenetic relationships among basal metazoans are still

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“…Knowledge about the number of paralogous Cdx genes and their assignment to paralogous groups is a good starting point for such a reconstruction. Two studies based on publicly available genome sequences arrived at different scenarios for the history of this particular ParaHox gene in teleost fishes [ 40 , 41 ]. While Prohaska et al [ 40 ] proposed the existence of a Cdx2 gene copy (at least for fugu and tetraodon), Mulley et al [ 41 ] concluded that both copies of Cdx2 were lost and suggested that this loss was compensated by two copies of Cdx1 .…”

Section: Resultsmentioning

confidence: 99%

“…Two studies based on publicly available genome sequences arrived at different scenarios for the history of this particular ParaHox gene in teleost fishes [ 40 , 41 ]. While Prohaska et al [ 40 ] proposed the existence of a Cdx2 gene copy (at least for fugu and tetraodon), Mulley et al [ 41 ] concluded that both copies of Cdx2 were lost and suggested that this loss was compensated by two copies of Cdx1 . A more recent analysis that uses additional sequence data [ 42 ] settles the discrepancy in favor of [ 41 ], supporting the retention of two Cdx1 genes in cichlids.…”

Section: Resultsmentioning

confidence: 99%

“…The query with human ParaHoxB yields only poorly conserved synteny information. This can be due to the reorganization of this locus when it got translocated to the mammalian sex chromosome X, see [ 40 , 43 ] for details. Nevertheless, we obtain sufficient information from the linkage of the Cdx loci with chic1 to see that zebrafish has one Cdx4 locus, DrB1 (Chr.14).…”

Section: Resultsmentioning

confidence: 99%

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SynBlast: Assisting the analysis of conserved synteny information

2008

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Motivation: In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene loss events inherently limit the accuracy of orthology detection based on sequence similarity alone. Fully automated methods for orthology annotation do exist but often fail to identify individual members in cases of large gene families, or to distinguish missing data from traceable gene losses. This situation can be improved in many cases by including conserved synteny information.

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Evolution of the vertebrate parahox clusters

Cited by 12 publications

References 27 publications

Breakup of a homeobox cluster after genome duplication in teleosts

Breakup of a homeobox cluster after genome duplication in teleosts

Hox and ParaHox genes: A review on molluscs

SynBlast: Assisting the analysis of conserved synteny information

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