Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2934-5) contains supplementary material, which is available to authorized users.
Highlights
The colonial ascidian Didemnum vexillum, sea carpet squirt, is a key marine organism to study morphological ancestral patterns of chordates evolution but it is of great ecological importance due to its status as a major invasive species
Preliminary draft of the genome assembly of D. vexillum Sequencing data utilized for this first de novo assembly was derived from one experiment of generation sequencing described in the Methods
The preliminary draft genome assembly of D. vexillum comprises 542.3 Mb of sequence distributed across 882 106 unscaffolded contigs with N50 size of 918 nt (Additional file 1: Figure S2)
Summary
The colonial ascidian Didemnum vexillum, sea carpet squirt, is a key marine organism to study morphological ancestral patterns of chordates evolution but it is of great ecological importance due to its status as a major invasive species. Gene expression patterns and regulatory networks of developmental processes are generally conserved among tunicates and vertebrates, substantial change has been reported for cisregulatory regions, which differ considerably even among closely related species [13, 14]. It is not known whether the rapid rate of evolution and mutational change observed for cis-regulatory regions in the non-coding regions of tunicate genomes is related to the rapid rate of loss of tunicate miRNAs, as well as to fast evolution of other ncRNAs
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