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Christian Schmitt,
Peter Atkinson,
Erica Sodergren,
Qingsong Zhu,
Jennifer Hume,
Shalini N Jhangiani,
Mimi N Chandrabose,
Jim Beidler,
Michael Schoppmeier,
Selina Vattahil, [......],
Jeremy A Lynch,
Peer Bork,
Rodrigo Nunes da Fonseca,
Manuel Aranda,
Nico Posnien,
Riyue Bao,
Rolf Reuter,
Anke Beermann,
Nicola Berns,
Johannes B Schinko
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ABSTRACT: Homeobox genes encode a large superclass of transcription factors with widespread roles in animal development. Within chordates there are over 100 homeobox genes in the invertebrate cephalochordate amphioxus and over 200 in humans. Set against this general trend of increasing gene number in vertebrate evolution, some ancient homeobox genes that were present in the last common ancestor of chordates have been lost from vertebrates. Here, we describe the embryonic expression of four amphioxus descendants of these genes--AmphiNedxa, AmphiNedxb, AmphiMsxlx and AmphiNKx7. All four genes are expressed with a striking asymmetry about the left-right axis in the pharyngeal region of neurula embryos, mirroring the pronounced asymmetry of amphioxus embryogenesis. AmphiMsxlx and AmphiNKx7 are also transiently expressed in an anterior neural tube region destined to become the cerebral vesicle. These findings suggest significant rewiring of developmental gene regulatory networks occurred during chordate evolution, coincident with homeobox gene loss. We propose that loss of otherwise widely conserved genes is possible when these genes function in a confined role in development that is subsequently lost or significantly modified during evolution. In the case of these homeobox genes, we propose that this has occurred in relation to the evolution of the chordate pharynx and brain.
Proceedings of the Royal Society B: Biological Sciences 11/2010; 277(1699):3381-9. · 5.41 Impact Factor
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ABSTRACT: The homeobox genes comprise a large and diverse gene superfamily, many of which encode transcription factors with pivotal roles in the embryonic development of animals. We searched the assembled draft genome sequence of an amphioxus, Branchiostoma floridae, for genes possessing homeobox sequences. Phylogenetic analysis was used to divide these into gene families and classes. The 133 amphioxus homeobox genes comprise 60 ANTP class genes, 29 PRD genes (excluding Pon and Pax1/9), nine TALE genes, seven POU genes, seven LIM genes, five ZF genes, four CUT genes, four HNF genes, three SINE genes, one CERS gene, one PROS gene, and three unclassified genes. Ten of the 11 homeobox gene classes are less diverse in amphioxus than humans, as a result of gene duplication on the vertebrate lineage. Amphioxus possesses at least one member for all of the 96 homeobox gene families inferred to be present in the common ancestor of chordates, including representatives of the Msxlx, Bari, Abox, Nk7, Ro, and Repo gene families that have been lost from tunicates and vertebrates. We find duplication of several homeobox genes in the cephalochordate lineage (Mnx, Evx, Emx, Vent, Nk1, Nedx, Uncx, Lhx2/9, Hmbox, Pou3, and Irx) and several divergent genes that probably originated by extensive sequence divergence (Hx, Ankx, Lcx, Acut, Atale, Azfh, Ahbx, Muxa, Muxb, Aprd1-6, and Ahnf). The analysis reveals not only the repertoire of amphioxus homeobox genes but also gives insight into the evolution of chordate homeobox genes.
Archiv für Entwickelungsmechanik der Organismen 10/2008; 218(11-12):579-90. · 1.77 Impact Factor
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Linda Z Holland,
Ricard Albalat,
Kaoru Azumi,
Elia Benito-Gutiérrez,
Matthew J Blow,
Marianne Bronner-Fraser,
Frederic Brunet, Thomas Butts,
Simona Candiani,
Larry J Dishaw, [......],
Fumiko Yoshizaki,
Jr-Kai Yu,
Qing Zhang,
Christian M Zmasek,
Pieter J de Jong,
Kazutoyo Osoegawa,
Nicholas H Putnam,
Daniel S Rokhsar,
Noriyuki Satoh,
Peter W H Holland
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ABSTRACT: Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates--a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.
Genome Research 08/2008; 18(7):1100-11. · 13.61 Impact Factor
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ABSTRACT: Comparison of whole genome sequences of representative animals enables reconstruction of the ancestral bilaterian genome: the starting point from which most extant animal lineages evolved. The Hox gene cluster patterns the anterior-posterior axis of bilaterians. Here we show that this cluster was embedded within a larger homeobox gene cluster, the Super-Hox cluster, in the ancestral bilaterian. This Super-Hox cluster contained at least eight genes alongside the core Hox genes ('EuHox' genes).
Trends in Genetics 07/2008; 24(6):259-62. · 10.06 Impact Factor
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Nicholas H Putnam, Thomas Butts,
David E K Ferrier,
Rebecca F Furlong,
Uffe Hellsten,
Takeshi Kawashima,
Marc Robinson-Rechavi,
Eiichi Shoguchi,
Astrid Terry,
Jr-Kai Yu, [......],
Tatjana Sauka-Spengler,
Jeremy Schmutz,
Tadasu Shin-I,
Atsushi Toyoda,
Marianne Bronner-Fraser,
Asao Fujiyama,
Linda Z Holland,
Peter W H Holland,
Nori Satoh,
Daniel S Rokhsar
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ABSTRACT: Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.
Nature 07/2008; 453(7198):1064-71. · 36.28 Impact Factor
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Nicholas H. Putnam, Thomas Butts,
David E. K. Ferrier,
Rebecca F. Furlong,
Uffe Hellsten,
Takeshi Kawashima,
Marc Robinson-Rechavi,
Eiichi Shoguchi,
Astrid Terry,
Jr-Kai Yu, [......],
Tatjana Sauka-Spengler,
Jeremy Schmutz,
Tadasu Shin-I,
Atsushi Toyoda,
Marianne Bronner-Fraser,
Asao Fujiyama,
Linda Z. Holland,
Peter W. H. Holland,
Nori Satoh,
Daniel S. Rokhsar
[show abstract]
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ABSTRACT: Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.
Nature 06/2008; 453(7198):1064-1071. · 36.28 Impact Factor
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Stephen Richards,
Richard A Gibbs,
George M Weinstock,
Susan J Brown,
Robin Denell,
Richard W Beeman,
Richard Gibbs,
Gregor Bucher,
Markus Friedrich,
Cornelis J P Grimmelikhuijzen, [......],
Joachim Schachtner,
Peter Verleyen,
Florian Raible,
Kimberly K O Walden,
Sergio Angeli,
Sylvain Forêt,
Stefan Schuetz,
Ryszard Maleszka,
Sherry C Miller,
Daniela Grossmann
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ABSTRACT: Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
Nature 05/2008; 452(7190):949-55. · 36.28 Impact Factor
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Stephen Richards,
Richard A. Gibbs,
George M. Weinstock,
Susan J. Brown,
Robin Denell,
Richard W. Beeman,
Richard Gibbs,
Gregor Bucher,
Markus Friedrich,
Cornelis J. P. Grimmelikhuijzen, [......],
Joachim Schachtner,
Peter Verleyen,
Florian Raible,
Kimberly K. O. Walden,
Sergio Angeli,
Sylvain For|[ecirc]|t,
Stefan Schuetz,
Ryszard Maleszka,
Sherry C. Miller,
Daniela Grossmann
[show abstract]
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ABSTRACT: Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell–cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
Nature 03/2008; 452(7190):949-955. · 36.28 Impact Factor
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Nicholas H. Putnam, Thomas Butts,
David E. K. Ferrier,
Rebecca F. Furlong,
Uffe Hellsten,
Takeshi Kawashima,
Marc Robinson-Rechavi,
Eiichi Shoguchi,
Astrid Terry,
Jr-Kai Yu, [......],
Tatjana Sauka-Spengler,
Jeremy Schmutz,
Tadasu Shin-I,
Atsushi Toyoda,
Marianne Bronner-Fraser,
Asao Fujiyama,
Linda Z. Holland,
Peter W. H. Holland,
Nori Satoh,
Daniel S. Rokhsar
Nature. 01/2008; 453:1064-1071.
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ABSTRACT: Comparison of whole genome sequences of representative animals enables reconstruction of the ancestral bilaterian genome: the starting point from which most extant animal lineages evolved. The Hox gene cluster patterns the anterior–posterior axis of bilaterians. Here we show that this cluster was embedded within a larger homeobox gene cluster, the Super-Hox cluster, in the ancestral bilaterian. This Super-Hox cluster contained at least eight genes alongside the core Hox genes (‘EuHox’ genes).
Trends in Genetics.
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ABSTRACT: The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Comparative study of homeobox genes, both within and between species, requires an evolutionary-based classification. HomeoDB was designed and implemented as a manually curated database to collect and present homeobox genes in an evolutionarily structured way, allowing genes, gene families and gene classes to be compared between species more readily than was possible previously. In its first release, HomeoDB includes all homeobox genes from human, amphioxus (Branchiostoma floridae) and fruitfly (Drosophila melanogaster); additional species can be added. HomeoDB is freely accessible at (http://homeodb.cbi.pku.edu.cn).
Evolution & Development 10(5):516-8. · 2.47 Impact Factor
