title: Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum.
abstract: The colonial ascidian Didemnum vexillum, sea carpet squirt, is not only a key marine organism to study morphological ancestral patterns of chordates evolution but it is also of great ecological importance due to its status as a major invasive species. Non-coding RNAs, in particular microRNAs (miRNAs), are important regulatory genes that impact development and environmental adaptation. Beyond miRNAs, not much in known about tunicate ncRNAs.
  
  
  
  We provide here a comprehensive homology-based annotation of non-coding RNAs in the recently sequenced genome of D. vexillum. To this end we employed a combination of several computational approaches, including blast searches with a wide range of parameters, and secondary structured centered survey with infernal. The resulting candidate set was curated extensively to produce a high-quality ncRNA annotation of the first draft of the D. vexillum genome. It comprises 57 miRNA families, 4 families of ribosomal RNAs, 22 isoacceptor classes of tRNAs (of which more than 72 % of loci are pseudogenes), 13 snRNAs, 12 snoRNAs, and 1 other RNA family. Additionally, 21 families of mitochondrial tRNAs and 2 of mitochondrial ribosomal RNAs and 1 long non-coding RNA.
  
  
  
  The comprehensive annotation of the D. vexillum non-coding RNAs provides a starting point towards a better understanding of the restructuring of the small RNA system in ascidians. Furthermore it provides a valuable research for efforts to establish detailed non-coding RNA annotations for other recently published and recently sequences in tunicate genomes.
authors: Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C, Colombia. cavelandiah@unal.edu.co.
authors: Cristian A
authors: CA
authors: Velandia-Huerto
authors: Institute of Biology, Leiden University, Leiden, P.O. Box 9505, 2300 RA, Netherlands.|GiMaRIS, BioScience Park Leiden, J.H. Oortweg 21, 2333 CH, Leiden, Netherlands.|Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands.
authors: Adriaan A
authors: AA
authors: Gittenberger
authors: Laboratorio de Biología del Desarrollo Evolutiva, Departamento de Ciencias Biológicas, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá, Colombia.|Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, Rua do Matão, Tr. 14 no. 101, São Paulo SP, Brazil.|Centro de Biologia Marinha, Universidade de São Paulo, Rod. Manuel Hypólito do Rego km. 131.5, Praia do Cabelo Gordo, São Sebastião, Brazil.
authors: Federico D
authors: FD
authors: Brown
authors: Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.|Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, D-04103, Germany.|Fraunhofer Institut for Cell Therapy and Immunology, Perlickstraße 1, Leipzig, D-04103, Germany.|Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna, A-1090, Austria.|Center for non-coding RNA in Technology and Health, Grønegårdsvej 3, Frederiksberg C, DK-1870, Denmark.|Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501, USA.
authors: Peter F
authors: 0000-0002-5016-5191
authors: PF
authors: Stadler
authors: Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C, Colombia.
authors: Clara I
authors: CI
authors: Bermúdez-Santana
mesh_terms: D000818:Animals; D059001:Aquatic Organisms / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D008386:Marine Biology; D035683:MicroRNAs / Q000145:classification / Q000235:genetics; D058977:Molecular Sequence Annotation; D062085:RNA, Long Noncoding; D012342:RNA, Small Nuclear / Q000145:classification / Q000235:genetics; D020537:RNA, Small Nucleolar / Q000145:classification / Q000235:genetics; D022661:RNA, Untranslated / Q000145:classification / Q000235:genetics*; D014561:Urochordata / Q000235:genetics
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012342:RNA, Small Nuclear; D020537:RNA, Small Nucleolar; D022661:RNA, Untranslated
keywords: Didemnum vexillum; Genome annotation; Tunicata; microRNAs