A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis

• Published in: Developmental biology Vol. 404; no. 2; pp. 149 - 163
• Main Authors: Gilchrist, Michael J., Sobral, Daniel, Khoueiry, Pierre, Daian, Fabrice, Laporte, Batiste, Patrushev, Ilya, Matsumoto, Jun, Dewar, Ken, Hastings, Kenneth E.M., Satou, Yutaka, Lemaire, Patrick, Rothbächer, Ute
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 15.08.2015; Elsevier
• Subjects: Algorithms; Animals; Ascidians; Base Sequence; BASIC BIOLOGICAL SCIENCES; Biological Evolution; Ciona intestinalis - genetics; Evolution, Molecular; Full-ORF; Functional genomics; Gene Expression Profiling; Gene Regulatory Networks - genetics; Genetic Predisposition to Disease; Human disease; Humans; Multigene Family - genetics; Open Reading Frames - genetics; Prediction pipeline; Sequence Alignment; Sequence Analysis, DNA; Transcriptomics; Human disease; Full-ORF; Transcriptomics; Ascidians; Functional genomics; Prediction pipeline
• ISSN: 0012-1606; 1095-564X
• DOI: 10.1016/j.ydbio.2015.05.014

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. [Display omitted] •Ascidians foster functional genomics by compact genomes and fixed cellular lineages.•A resource of 19.000 GATEWAY full ORF clones was generated for Ciona intestinalis.•Novel methods support automated finding of coding 5′ ends and paralog distinction.•The strategy is robust to polymorphism and poorly annotated genomes.•Half of human disease associated genes are covered by full ORF Ciona orthologs.