title: A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis.
abstract: Genome-wide resources, such as collections of cDNA clones encoding for complete proteins (full-ORF clones), are crucial tools for studying the evolution of gene function and genetic interactions. Non-model organisms, in particular marine organisms, provide a rich source of functional diversity. Marine organism genomes are, however, frequently highly polymorphic and encode proteins that diverge significantly from those of well-annotated model genomes. The construction of full-ORF clone collections from non-model organisms is hindered by the difficulty of predicting accurately the N-terminal ends of proteins, and distinguishing recent paralogs from highly polymorphic alleles. We report a computational strategy that overcomes these difficulties, and allows for accurate gene level clustering of transcript data followed by the automated identification of full-ORFs with correct 5'- and 3'-ends. It is robust to polymorphism, includes paralog calling and does not require evolutionary proximity to well annotated model organisms. We developed this pipeline for the ascidian Ciona intestinalis, a highly polymorphic member of the divergent sister group of the vertebrates, emerging as a powerful model organism to study chordate gene function, Gene Regulatory Networks and molecular mechanisms underlying human pathologies. Using this pipeline we have generated the first full-ORF collection for a highly polymorphic marine invertebrate. It contains 19,163 full-ORF cDNA clones covering 60% of Ciona coding genes, and full-ORF orthologs for approximately half of curated human disease-associated genes.
authors.affiliation: Gurdon Institute, Cambridge University, Cambridge, United Kingdom. Electronic address: mike.gilchrist@crick.ac.uk.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Gilchrist
authors.affiliation: Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 6216), CNRS, Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France.
authors.forename: Daniel
authors.initials: D
authors.lastname: Sobral
authors.affiliation: Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 6216), CNRS, Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Khoueiry
authors.affiliation: Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 6216), CNRS, Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Daian
authors.affiliation: Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 6216), CNRS, Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France.
authors.forename: Batiste
authors.initials: B
authors.lastname: Laporte
authors.affiliation: The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
authors.forename: Ilya
authors.initials: I
authors.lastname: Patrushev
authors.affiliation: Montreal Neurological Institute and Departments of Neurology and Neurosurgery and Biology, McGill University, 3801 University Street, Montreal, Quebec, Canada H3A 2B4.
authors.forename: Jun
authors.initials: J
authors.lastname: Matsumoto
authors.affiliation: Montreal Neurological Institute and Departments of Neurology and Neurosurgery and Biology, McGill University, 3801 University Street, Montreal, Quebec, Canada H3A 2B4.
authors.forename: Ken
authors.initials: K
authors.lastname: Dewar
authors.affiliation: Montreal Neurological Institute and Departments of Neurology and Neurosurgery and Biology, McGill University, 3801 University Street, Montreal, Quebec, Canada H3A 2B4.
authors.forename: Kenneth E M
authors.initials: KE
authors.lastname: Hastings
authors.affiliation: Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Satou
authors.affiliation: Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 6216), CNRS, Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France. Electronic address: patrick.lemaire@crbm.cnrs.fr.
authors.forename: Patrick
authors.initials: P
authors.lastname: Lemaire
authors.affiliation: Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 6216), CNRS, Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France. Electronic address: ute.rothbaecher@uibk.ac.at.
authors.forename: Ute
authors.initials: U
authors.lastname: Rothbächer
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D002938:Ciona intestinalis / Q000235:genetics*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks / Q000235:genetics*; D020022:Genetic Predisposition to Disease; D006801:Humans; D005810:Multigene Family / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
keywords: Ascidians; Full-ORF; Functional genomics; Human disease; Prediction pipeline; Transcriptomics