Xenopus tropicalis is an anuran amphibian species used as model in vertebrate comparative genomics. It provides the same advantages as Xenopus laevis but is diploid and has a smaller genome of 1.7 Gbp. Therefore X. tropicalis is more amenable to systematic transcriptome surveys. We initiated a large-scale partial cDNA sequencing project to provide a functional genomics resource on genes expressed in the nervous system during early embryogenesis and metamorphosis in X. tropicalis. A gene index was defined and analysed after the collection of over 48,785 high quality sequences. Partial cDNA sequences were obtained from an embryonic head and retina library (30,272 sequences) and from a metamorphic brain and spinal cord library (27,602 sequences). These ESTs are estimated to represent 9,693 transcripts derived from an estimated 6,000 genes. An estimated 46% of these cDNA sequences contain their start codon. Further annotation included Gene Ontology functional classification, InterPro domain analysis, alternative splicing and non-coding RNA identification. Gene expression profiles were derived from EST counts and used to define transcripts specific to metamorphic stages of development. Moreover, these ESTs allowed identification of a set of 225 polymorphic microsatellites that can be used as genetic markers. These cDNA sequences permit in silico cloning of numerous genes and will facilitate studies aimed at deciphering the roles of cognate genes expressed in the nervous system during neural development and metamorphosis. The genomic resources developed to study X. tropicalis biology will accelerate exploration of amphibian physiology and genetics.
Deep Dive into Exploring nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis.
Xenopus tropicalis is an anuran amphibian species used as model in vertebrate comparative genomics. It provides the same advantages as Xenopus laevis but is diploid and has a smaller genome of 1.7 Gbp. Therefore X. tropicalis is more amenable to systematic transcriptome surveys. We initiated a large-scale partial cDNA sequencing project to provide a functional genomics resource on genes expressed in the nervous system during early embryogenesis and metamorphosis in X. tropicalis. A gene index was defined and analysed after the collection of over 48,785 high quality sequences. Partial cDNA sequences were obtained from an embryonic head and retina library (30,272 sequences) and from a metamorphic brain and spinal cord library (27,602 sequences). These ESTs are estimated to represent 9,693 transcripts derived from an estimated 6,000 genes. An estimated 46% of these cDNA sequences contain their start codon. Further annotation included Gene Ontology functional classification, InterPro domai
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BMC Genomics
Open Access
Research article
Exploring nervous system transcriptomes during embryogenesis
and metamorphosis in Xenopus tropicalis using EST analysis
Ana C Fierro*1,2,5, Raphaël Thuret1,2, Laurent Coen3, Muriel Perron1,2,
Barbara A Demeneix3, Maurice Wegnez1,2, Gabor Gyapay4,
Jean Weissenbach4, Patrick Wincker4, André Mazabraud1,2 and
Nicolas Pollet*1,2,5
Address: 1CNRS UMR 8080, F-91405 Orsay, France, 2Univ Paris Sud, F-91405 Orsay, France, 3CNRS UMR 5166, Evolution des Régulations
Endocriniennes, USM 501, Département Régulations, Développement et Diversité Moléculaire, Muséum National d'Histoire Naturelle, 7 rue
Cuvier, 75231 Paris Cedex 5, France, 4Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France and 5Programme
d'Épigénomique, Univ Evry, Tour Évry 2, 10è étage, 523 Terrasses de l'Agora, 91034 Evry cedex, France
Email: Ana C Fierro* - carolina.fierro@gmail.com; Raphaël Thuret - raphael.thuret@u-psud.fr; Laurent Coen - coen@mnhn.fr;
Muriel Perron - muriel.perron@u-psud.fr; Barbara A Demeneix - demeneix@mnhn.fr; Maurice Wegnez - maurice.wegnez@u-psud.fr;
Gabor Gyapay - gabor@genoscope.cns.fr; Jean Weissenbach - jsbach@genoscope.cns.fr; Patrick Wincker - pwincker@genoscope.cns.fr;
André Mazabraud - andre.mazabraud@u-psud.fr; Nicolas Pollet* - Nicolas.Pollet@u-psud.fr
* Corresponding authors
Abstract
Background: The western African clawed frog Xenopus tropicalis is an anuran amphibian species now used
as model in vertebrate comparative genomics. It provides the same advantages as Xenopus laevis but is
diploid and has a smaller genome of 1.7 Gbp. Therefore X. tropicalis is more amenable to systematic
transcriptome surveys. We initiated a large-scale partial cDNA sequencing project to provide a functional
genomics resource on genes expressed in the nervous system during early embryogenesis and
metamorphosis in X. tropicalis.
Results: A gene index was defined and analysed after the collection of over 48,785 high quality sequences.
These partial cDNA sequences were obtained from an embryonic head and retina library (30,272
sequences) and from a metamorphic brain and spinal cord library (27,602 sequences). These ESTs are
estimated to represent 9,693 transcripts derived from an estimated 6,000 genes. Comparison of these
cDNA sequences with protein databases indicates that 46% contain their start codon. Further annotation
included Gene Ontology functional classification, InterPro domain analysis, alternative splicing and non-
coding RNA identification. Gene expression profiles were derived from EST counts and used to define
transcripts specific to metamorphic stages of development. Moreover, these ESTs allowed identification
of a set of 225 polymorphic microsatellites that can be used as genetic markers.
Conclusion: These cDNA sequences permit in silico cloning of numerous genes and will facilitate studies
aimed at deciphering the roles of cognate genes expressed in the nervous system during neural
development and metamorphosis. The genomic resources developed to study X. tropicalis biology will
accelerate exploration of amphibian physiology and genetics. In particular, the model will facilitate analysis
of key questions related to anuran embryogenesis and metamorphosis and its associated regulatory
processes.
Published: 16 May 2007
BMC Genomics 2007, 8:118
doi:10.1186/1471-2164-8-118
Received: 17 November 2006
Accepted: 16 May 2007
This article is available from: http://www.biomedcentral.com/1471-2164/8/118
© 2007 Fierro et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
BMC Genomics 2007, 8:118
http://www.biomedcentral.com/1471-2164/8/118
Page 2 of 13
(page number not for citation purposes)
Background
Xenopus tropicalis is now an anuran amphibian reference
genome for vertebrate comparative genomics. It presents
the same advantages as Xenopus laevis but has a smaller
genome of 1.7 Gbp and a shorter generation time [1].
Moreover, while X. laevis is an allotetraploid derived from
an allopolyploidization event, X. tropicalis is diploid [2,3].
Even though phylogenetic studies indicate that 30 to 50
MY evolution separate the two species [3,4], it has been
shown that most methods and resources developed for X.
laevis can be readily applied to X. tropicalis [5]. Thus, the
genome of X. tropicalis was selected to explore amphibian
genome
characteristics
by
whole-genome
shotgun
sequencing [6].
Working on X. laevis constitutes a challenge when dealing
with large-scale transcriptomics, such as microarrays
experiments or systematic cDNA sequencing. This is
because some X. laevis genes are present as diploids, while
others form pairs of paralogs (al
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