title: ncRNA orthologies in the vertebrate lineage.
abstract: Annotation of orthologous and paralogous genes is necessary for many aspects of evolutionary analysis. Methods to infer these homology relationships have traditionally focused on protein-coding genes and evolutionary models used by these methods normally assume the positions in the protein evolve independently. However, as our appreciation for the roles of non-coding RNA genes has increased, consistently annotated sets of orthologous and paralogous ncRNA genes are increasingly needed. At the same time, methods such as PHASE or RAxML have implemented substitution models that consider pairs of sites to enable proper modelling of the loops and other features of RNA secondary structure. Here, we present a comprehensive analysis pipeline for the automatic detection of orthologues and paralogues for ncRNA genes. We focus on gene families represented in Rfam and for which a specific covariance model is provided. For each family ncRNA genes found in all Ensembl species are aligned using Infernal, and several trees are built using different substitution models. In parallel, a genomic alignment that includes the ncRNA genes and their flanking sequence regions is built with PRANK. This alignment is used to create two additional phylogenetic trees using the neighbour-joining (NJ) and maximum-likelihood (ML) methods. The trees arising from both the ncRNA and genomic alignments are merged using TreeBeST, which reconciles them with the species tree in order to identify speciation and duplication events. The final tree is used to infer the orthologues and paralogues following Fitch's definition. We also determine gene gain and loss events for each family using CAFE. All data are accessible through the Ensembl Comparative Genomics ('Compara') API, on our FTP site and are fully integrated in the Ensembl genome browser, where they can be accessed in a user-friendly manner. Database URL: http://www.ensembl.org.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute mp@ebi.ac.uk.
authors.forename: Miguel
authors.initials: M
authors.lastname: Pignatelli
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute.
authors.forename: Albert J
authors.initials: AJ
authors.lastname: Vilella
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Muffato
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute.
authors.forename: Leo
authors.initials: L
authors.lastname: Gordon
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Simon
authors.initials: S
authors.lastname: White
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK mp@ebi.ac.uk.
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute UCL Cancer Institute, University College London, London WC1E 6BT, UK.
authors.forename: Javier
authors.initials: J
authors.lastname: Herrero
mesh_terms: D000465:Algorithms; D000818:Animals; D002938:Ciona intestinalis; D019295:Computational Biology / Q000379:methods*; D003532:Cyprinodontiformes; D019143:Evolution, Molecular; D014644:Genetic Variation; D016678:Genome; D023281:Genomics; D006801:Humans; D016013:Likelihood Functions; D051379:Mice; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D010802:Phylogeny; D022661:RNA, Untranslated / Q000235:genetics*; D051381:Rats; D014714:Vertebrates / Q000235:genetics*; D015027:Zebrafish
chemical_list: D022661:RNA, Untranslated