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Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate

The carpet sea squirt Didemnum vexillum
: Velandia-Huerto, C.A.; Gittenberger, A.A.; Brown, F.D.; Stadler, P.F.; Bermúdez-Santana, C.I.

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BMC genomics. Online journal 17 (2016), No.1, Art.691, 15 pp.
ISSN: 1471-2164
Journal Article, Electronic Publication
Fraunhofer IZI ()

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.