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Biscotti MA, Canapa A, Forconi M, Barucca M. HoxandParaHoxgenes: A review on molluscs. Genesis 2014; 52:935-45. [DOI: 10.1002/dvg.22839] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 11/10/2014] [Accepted: 11/11/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
| | - Mariko Forconi
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
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Hadrys H, Simon S, Kaune B, Schmitt O, Schöner A, Jakob W, Schierwater B. Isolation of Hox cluster genes from insects reveals an accelerated sequence evolution rate. PLoS One 2012; 7:e34682. [PMID: 22685537 PMCID: PMC3369913 DOI: 10.1371/journal.pone.0034682] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 03/08/2012] [Indexed: 01/10/2023] Open
Abstract
Among gene families it is the Hox genes and among metazoan animals it is the insects (Hexapoda) that have attracted particular attention for studying the evolution of development. Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera). We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics. These new gene sequences provide a first step towards comparative Hox gene studies in insects. Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution.
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Affiliation(s)
- Heike Hadrys
- ITZ, Division of Ecology and Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany.
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Ikuta T. Evolution of invertebrate deuterostomes and Hox/ParaHox genes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2011; 9:77-96. [PMID: 21802045 PMCID: PMC5054439 DOI: 10.1016/s1672-0229(11)60011-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 03/21/2011] [Indexed: 11/10/2022]
Abstract
Transcription factors encoded by Antennapedia-class homeobox genes play crucial roles in controlling development of animals, and are often found clustered in animal genomes. The Hox and ParaHox gene clusters have been regarded as evolutionary sisters and evolved from a putative common ancestral gene complex, the ProtoHox cluster, prior to the divergence of the Cnidaria and Bilateria (bilaterally symmetrical animals). The Deuterostomia is a monophyletic group of animals that belongs to the Bilateria, and a sister group to the Protostomia. The deuterostomes include the vertebrates (to which we belong), invertebrate chordates, hemichordates, echinoderms and possibly xenoturbellids, as well as acoelomorphs. The studies of Hox and ParaHox genes provide insights into the origin and subsequent evolution of the bilaterian animals. Recently, it becomes apparent that among the Hox and ParaHox genes, there are significant variations in organization on the chromosome, expression pattern, and function. In this review, focusing on invertebrate deuterostomes, I first summarize recent findings about Hox and ParaHox genes. Next, citing unsolved issues, I try to provide clues that might allow us to reconstruct the common ancestor of deuterostomes, as well as understand the roles of Hox and ParaHox genes in the development and evolution of deuterostomes.
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Affiliation(s)
- Tetsuro Ikuta
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Uruma, Japan.
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Abstract
UNLABELLED A large number of genomes have been sequenced, allowing a range of comparative studies. Here, we present the eukaryotic Gene Order Browser with information on the order of protein and non-coding RNA (ncRNA) genes of 74 different eukaryotic species. The browser is able to display a gene of interest together with its genomic context in all species where that gene is present. Thereby, questions related to the evolution of gene organization and non-random gene order may be examined. The browser also provides access to data collected on pairs of adjacent genes that are evolutionarily conserved. AVAILABILITY eGOB as well as underlying data are freely available at http://egob.biomedicine.gu.se SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT tore.samuelsson@medkem.gu.se.
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Affiliation(s)
- Marcela Dávila López
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, SE-405 30 Göteborg, Sweden
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Abstract
Abstract The ParaHox genes comprise three Hox-related homeobox gene families, found throughout the animals. They were first discovered in the invertebrate chordate amphioxus, where they are tightly clustered. In this paper we carry out a comparative review of ParaHox gene cluster organization among the deuterostomes, and discuss how the recently published hagfish ParaHox clusters fit into current theories about the evolution of this group of genes.
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Affiliation(s)
- Rebecca F Furlong
- Department of Zoology, Oxford University, South Parks Road, Oxford OX13PS, UK.
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Osborne PW, Benoit G, Laudet V, Schubert M, Ferrier DE. Differential regulation of ParaHox genes by retinoic acid in the invertebrate chordate amphioxus (Branchiostoma floridae). Dev Biol 2009; 327:252-62. [DOI: 10.1016/j.ydbio.2008.11.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 11/19/2008] [Accepted: 11/19/2008] [Indexed: 02/04/2023]
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Flores MVC, Hall CJ, Davidson AJ, Singh PP, Mahagaonkar AA, Zon LI, Crosier KE, Crosier PS. Intestinal differentiation in zebrafish requires Cdx1b, a functional equivalent of mammalian Cdx2. Gastroenterology 2008; 135:1665-75. [PMID: 18804112 DOI: 10.1053/j.gastro.2008.07.024] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 07/09/2008] [Accepted: 07/17/2008] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The ParaHox transcription factor Cdx2 is an essential determinant of intestinal phenotype in mammals throughout development, influencing gut function, homeostasis, and epithelial barrier integrity. Cdx2 expression demarcates the zones of intestinal stem cell proliferation in the adult gut, with deregulated expression implicated in intestinal metaplasia and cancer. However, in vivo analysis of these prospective roles has been limited because inactivation of Cdx2 in mice leads to preimplantation embryonic lethality. We used the zebrafish, a valuable model for studying gut development, to generate a system to further understanding of the role of Cdx2 in normal intestinal function and in disease states. METHODS We isolated and characterized the zebrafish cdx1b ortholog and analyzed its function by antisense morpholino gene knockdown. RESULTS We showed that zebrafish Cdx1b replaces the role of Cdx2 in gut development. Evolutionary studies have indicated that the zebrafish cdx2 loci were lost following the genome-wide duplication event that occurred in teleosts. Zebrafish Cdx1b is expressed exclusively in the developing intestine during late embryogenesis and regulates intestinal cell proliferation and terminal differentiation. CONCLUSIONS This work established an in vivo system to explore further the activity of Cdx2 in the gut and its impact on processes such as inflammation and cancer.
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Affiliation(s)
- Maria Vega C Flores
- Department of Molecular Medicine & Pathology, School of Medical Sciences, The University of Auckland, Auckland, New Zealand
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Lehmann J, Stadler PF, Prohaska SJ. SynBlast: assisting the analysis of conserved synteny information. BMC Bioinformatics 2008; 9:351. [PMID: 18721485 PMCID: PMC2543028 DOI: 10.1186/1471-2105-9-351] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 08/24/2008] [Indexed: 01/06/2023] Open
Abstract
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. Results Here we present the SynBlast pipeline that is designed to construct and evaluate local synteny information. SynBlast uses the genomic region around a focal reference gene to retrieve candidates for homologous regions from a collection of target genomes and ranks them in accord with the available evidence for homology. The pipeline is intended as a tool to aid high quality manual annotation in particular in those cases where automatic procedures fail. We demonstrate how SynBlast is applied to retrieving orthologous and paralogous clusters using the vertebrate Hox and ParaHox clusters as examples. Software The SynBlast package written in Perl is available under the GNU General Public License at .
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Affiliation(s)
- Jörg Lehmann
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
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Affiliation(s)
- Jeroen Bussmann
- Hubrecht Laboratory (NIOB-KNAW NIOB), Utrecht, The Netherlands
| | - Nathan Lawson
- University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Leonard Zon
- Harvard Medical School and Children's Hospital Pediatrics, Cambridge, Massachusetts, United States of America
| | | | - Zebrafish Nomenclature Committee
- Marc Ekker, Center for Advanced Research in Environmental Genomics, University of Ottawa, Ontario, Canada; Mary Mullins, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America; John Postlethwait, Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America; Monte Westerfield, Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
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Siegel N, Hoegg S, Salzburger W, Braasch I, Meyer A. Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications. BMC Genomics 2007; 8:312. [PMID: 17822543 PMCID: PMC2020491 DOI: 10.1186/1471-2164-8-312] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Accepted: 09/06/2007] [Indexed: 11/23/2022] Open
Abstract
Background The evolutionary lineage leading to the teleost fish underwent a whole genome duplication termed FSGD or 3R in addition to two prior genome duplications that took place earlier during vertebrate evolution (termed 1R and 2R). Resulting from the FSGD, additional copies of genes are present in fish, compared to tetrapods whose lineage did not experience the 3R genome duplication. Interestingly, we find that ParaHox genes do not differ in number in extant teleost fishes despite their additional genome duplication from the genomic situation in mammals, but they are distributed over twice as many paralogous regions in fish genomes. Results We determined the DNA sequence of the entire ParaHox C1 paralogon in the East African cichlid fish Astatotilapia burtoni, and compared it to orthologous regions in other vertebrate genomes as well as to the paralogous vertebrate ParaHox D paralogons. Evolutionary relationships among genes from these four chromosomal regions were studied with several phylogenetic algorithms. We provide evidence that the genes of the ParaHox C paralogous cluster are duplicated in teleosts, just as it had been shown previously for the D paralogon genes. Overall, however, synteny and cluster integrity seems to be less conserved in ParaHox gene clusters than in Hox gene clusters. Comparative analyses of non-coding sequences uncovered conserved, possibly co-regulatory elements, which are likely to contain promoter motives of the genes belonging to the ParaHox paralogons. Conclusion There seems to be strong stabilizing selection for gene order as well as gene orientation in the ParaHox C paralogon, since with a few exceptions, only the lengths of the introns and intergenic regions differ between the distantly related species examined. The high degree of evolutionary conservation of this gene cluster's architecture in particular – but possibly clusters of genes more generally – might be linked to the presence of promoter, enhancer or inhibitor motifs that serve to regulate more than just one gene. Therefore, deletions, inversions or relocations of individual genes could destroy the regulation of the clustered genes in this region. The existence of such a regulation network might explain the evolutionary conservation of gene order and orientation over the course of hundreds of millions of years of vertebrate evolution. Another possible explanation for the highly conserved gene order might be the existence of a regulator not located immediately next to its corresponding gene but further away since a relocation or inversion would possibly interrupt this interaction. Different ParaHox clusters were found to have experienced differential gene loss in teleosts. Yet the complete set of these homeobox genes was maintained, albeit distributed over almost twice the number of chromosomes. Selection due to dosage effects and/or stoichiometric disturbance might act more strongly to maintain a modal number of homeobox genes (and possibly transcription factors more generally) per genome, yet permit the accumulation of other (non regulatory) genes associated with these homeobox gene clusters.
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Affiliation(s)
- Nicol Siegel
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Simone Hoegg
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Walter Salzburger
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Ecology and Evolution (DEE), University of Lausanne UNIL Sorge, Le Biophore, Lausanne, Switzerland
| | - Ingo Braasch
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
- Physiological Chemistry I, Biozentrum, University of Würzburg, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
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Mulley JF, Chiu CH, Holland PWH. Breakup of a homeobox cluster after genome duplication in teleosts. Proc Natl Acad Sci U S A 2006; 103:10369-10372. [PMID: 16801555 PMCID: PMC1502464 DOI: 10.1073/pnas.0600341103] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- John F Mulley
- *Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom; and
| | - Chi-Hua Chiu
- Rutgers University, Department of Genetics, Life Sciences Building, Piscataway, NJ 08854
| | - Peter W H Holland
- *Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom; and
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