Background: 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. Results: 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. Conclusions: 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.
| Identifer | oai:union.ndltd.org:DRESDEN/oai:qucosa.de:bsz:15-qucosa-209604 |
| Date | 05 September 2016 |
| Creators | Velandia-Huerto, Cristian A., Gittenberger, Adriaan A., Brown, Federico D., Stadler, Peter F., Bermúdez-Santana, Clara I. |
| Contributors | Universidad Nacional de Colombia, Biology Department, Leiden University, Institute of Biology, GiMaRIS,, Naturalis Biodiversity Center,, Universidad de los Andes, Departamento de Ciencias Biológicas, Universidade de São Paulo, Departamento de Zoologia, Universidade de São Paulo, Centro de Biologia Marinha, Universität Leipzig, Fakultät für Mathematik und Informatik, Universität Leipzig, Interdisziplinäres Zentrum für Bioinformatik, Max-Planck-Institut für Mathematik in den Naturwissenschaften,, Fraunhofer-Institut für Zelltherapie und Immunologie,, Universität Wien, Fakultät für Chemie, Center for non-coding RNA in Technology and Health,, Santa Fe Institute,, BioMed Central, |
| Publisher | Universitätsbibliothek Leipzig |
| Source Sets | Hochschulschriftenserver (HSSS) der SLUB Dresden |
| Language | English |
| Detected Language | English |
| Type | doc-type:article |
| Format | application/pdf |
| Source | BMC Genomics (2016) 17:691 DOI 10.1186/s12864-016-2934-5 |
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