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XB-ART-35901
BMC Genomics July 10, 2007; 8 118.

Exploring nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis.

Fierro AC , Thuret R , Coen L , Perron M , Demeneix BA , Wegnez M , Gyapay G , Weissenbach J , Wincker P , Mazabraud A , Pollet N .


Abstract
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. 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. 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.

PubMed ID: 17506875
PMC ID: PMC1890556
Article link: BMC Genomics


Species referenced: Xenopus laevis
Genes referenced: adgrl1 agap2 ahsg apoa1 arf3 armh4 arrb1 ass1 cacna2d1 ccdc136 cel.2 cela1.1 cntnap1 col5a3 cpb1 ctrb2 diras2 dmtn dnajb2 eif2a eif2ak3 epha8 fibcd1 frat1 frzb gnrh2 gps2 gria4 hba2 hbg2 kif1a klc1 krt12.1 krt78.7 laptm4b map2 map6 mogat2.1 myb myh8 myl3 ndufa6 nptx2 nrsn1 nrxn1 phyhip plp1 prickle2 rab40b rpl3l serpina3 slc7a7 stom tf tmem59l umodl1 ybx3


Article Images: [+] show captions
References [+] :
Adams, Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. 1995, Pubmed