Evidence for a Hox14 paralog group in vertebrates

Powers, Thomas P.; Amemiya, Chris T.

doi:10.1016/j.cub.2004.02.015

Cited by 73 publications

(78 citation statements)

References 5 publications

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“…Very recently, a finding by Powers and Amemiya (2004) has strengthened the amphioxus data; the analyses of the HoxA cluster of the coelacanth and the HoxD cluster of the horn shark revealed in each case an additional 14th gene, A14 and D14, respectively. Furthermore, the HoxA cluster of the horn shark also has a pseudogene of a Hoxa14 gene.…”

Section: Introductionmentioning

confidence: 94%

“…The phylogenetic analyses of these new 14th genes do not resolve whether AmphiHox-14 is pro-ortologous of the vertebrate 14th genes, probably as another consequence of Posterior Flexibility. However, position in the cluster and sharing of an intron (Ferrier et al, 2000;Powers and Amemiya, 2004) argue in favour of the hypothesis that the single ancestral Vertebrate, Chordate, or Deuterostomian cluster contained 14 PGs.…”

Section: Introductionmentioning

confidence: 94%

“…Guess 2: cis or trans? Tandem duplication and the 'coupled' array of Hox and ParaHox clusters The Hox-like gene Evx is closely linked to the Hox clusters in vertebrates (Dush and Martin, 1992;Amores et al, 1998;Powers and Amemiya, 2004), and in a Cnidarian species (Miller and Miles, 1993). The most plausible hypothesis to explain the linkage is that the primordial Hox cluster, before the divergence of Cnidarians and Bilaterians, was already closely linked to Evx.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Hox, ParaHox, ProtoHox: facts and guesses

Garcia‐Fernàndez

2004

Heredity

124

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The Hox gene cluster has captivated the imagination of evolutionary and developmental biologists worldwide. In this review, the origin of the Hox and ParaHox gene clusters by duplication of a ProtoHox gene cluster, and the changes in their gene numbers in major Metazoan Transitions are reviewed critically. Re-evaluation of existing data and recent findings in Cnidarians, Acoels, and critical stages of vertebrate evolution suggest alternative scenarios for the origin, structure, and changes in Hox gene numbers in relevant events of Metazoan evolution. I discuss opposing views and propose that (i) the ProtoHox cluster had only two genes, and not four as commonly believed: a corollary is that the origin of Bilaterians was coincident with the invention of new Hox and ParaHox gene classes, which may have facilitated such a transition; (ii) the ProtoHox cluster duplication was a cis duplication event, rather than a trans duplication event, as previously suggested, and (iii) the ancestral vertebrate cluster possessed 14 Hox genes, and not the 13 generally assumed. These hypotheses could be verified or refuted in the near future, but they may help critical discussion of the evolution of the Hox/ParaHox family in the metazoan kingdom. Heredity (2005) 94, 145-152.

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Section: Introductionmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Hox, ParaHox, ProtoHox: facts and guesses

Garcia‐Fernàndez

2004

Heredity

124

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“…Again, a complete list is provided in the Appendix. For the Hox gene complements of cephalochordates, we refer to Ferrier et al (2000) for the ancestral state of the vertebrate Hox cluster before the genome duplications; see Powers and Amemiya (2004).…”

Section: Computational Analysismentioning

confidence: 99%

PCR survey of Xenoturbella bocki Hox genes

Fritzsch¹,

Böhme²,

Thorndyke³

et al. 2007

J Exp Zool Pt B

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Xenoturbella bocki has recently been identified as one of the most basal deuterostomes, although an even more basal phylogenetic position cannot be ruled out. Here we report on a polymerase chain reaction survey of partial Hox homeobox sequences of X. bocki. Surprisingly, we did not find evidence for more than five Hox genes, one clear labial/PG1 ortholog, one posterior gene most similar to the PG9/10 genes of Ambulacraria, and three central group genes whose precise assignment to a specific paralog group remains open. We furthermore report on a re-evaluation of the available published evidence of Hox genes in other basal deuterostomes.

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“…1. (The Hox-14 paralog group which has recently been discovered in shark and latimeria [17] has been lost in mammals). On clearly sees the "anterior" Hox genes 10, 11, 12 as well 13 and 14 of the Amphioxus cluster together rather than with the gnathostome paralog groups as one would have expected.…”

Section: Introductionmentioning

confidence: 99%

Gene phylogenies and protein–protein interactions: possible artifacts resulting from shared protein interaction partners

Campos

Oliveira

Wagner

et al. 2004

Journal of Theoretical Biology

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The study of gene families critically depends on the correct reconstruction of gene genealogies, as for instance in the case of transcription factor genes like Hox genes and Dlx gene families. Proteins belonging to the same family are likely to share some of the same protein interaction partners and may thus face a similar selective environment. This common selective environment can induce co-evolutionary pressures and thus can give rise to correlated rates and patterns of evolution among members of a gene family. In this study we simulate the evolution of a family of sequences which share a set of interaction partners. Depending on the amount of sequence dedicated to protein-protein interaction and the relative rate parameters of sequence evolution three outcomes are possible: if the fraction of the sequence dedicated to interaction with common co-factors is low and the time since divergence is small, the trees based on sequence information tend to be correct. If the time since gene duplication is long two possible outcomes are observed in our simulations. If the rate of evolution of the interaction partner is small compared to the rate of evolution of the focal protein family, the reconstructed trees tend towards star phylogenies. As the rate of evolution of the interaction partner approaches that of the focal protein family the reconstructed phylogenies tend to be incorrectly resolved. We conclude that the genealogies of gene families can be hard to estimate, in particular if the proteins interact with a conserved set of binding partners, as is likely the case for transcription factors.

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Evidence for a Hox14 paralog group in vertebrates

Cited by 73 publications

References 5 publications

Hox, ParaHox, ProtoHox: facts and guesses

Hox, ParaHox, ProtoHox: facts and guesses

PCR survey of Xenoturbella bocki Hox genes

Gene phylogenies and protein–protein interactions: possible artifacts resulting from shared protein interaction partners

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