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:qucosa:14946 |
| Date | January 2016 |
| Creators | Velandia-Huerto, Cristian A., Gittenberger, Adriaan A., Brown, Federico D., Stadler, Peter F., Bermúdez-Santana, Clara I. |
| Contributors | Universidad Nacional de Colombia, Leiden University, GiMaRIS, Naturalis Biodiversity Center, Universidad de los Andes, Universidade de São Paulo, Universität Leipzig, Max-Planck-Institut für Mathematik in den Naturwissenschaften, Fraunhofer-Institut für Zelltherapie und Immunologie, Universität Wien, Center for non-coding RNA in Technology and Health, Santa Fe Institute |
| Publisher | BioMed Central |
| Source Sets | Hochschulschriftenserver (HSSS) der SLUB Dresden |
| Language | English |
| Detected Language | English |
| Type | doc-type:article, info:eu-repo/semantics/article, doc-type:Text |
| Source | BMC Genomics (2016) 17:691 DOI 10.1186/s12864-016-2934-5 |
| Rights | info:eu-repo/semantics/openAccess |
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