Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum

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.

The genome of the "Sea Vomit" Didemnum vexillum

“…The new assembly also decreases the estimated genome size by about 25 Mb. While only about 15% of the contigs in our previous study [21] were longer than 1 kb, this threshold is now exceeded by almost 96% of the scaffolds in the new assembly and thus allows at least a comprehensive gene-level analysis. The newly analyzed nucleotide composition was consistent with our previous study [21].…”

“…Noncoding RNAs were annotated using a homologybased strategy combining blastn searches, HMM profiles, and covariance models (CMs) as described in [21] with some modifications detailed in Methods. Not counting tRNAs, we identified 2153 ncRNA loci corresponding to 271 distinct ncRNA families.…”

“…A search with tRNAscan-SE resulted in 18,343 predicted loci, including pseudogenes and undetermined isotype candidates. In addition we mapped the 206 families of ncR-NAs identified in a preliminary draft of the D. vexillum genome [21] to the current assembly (see Methods and Additional File 1). As in other genomes, in particular the pol-III transcribed RNAs including 5S rRNA, tRNAs, U6 RNA as well as the snRNAs transcribed by pol-II appear in multiples copies [31].…”

“…For colonial ascidians, the genome of Botryllus schlosseri has been assembled to 13 incomplete chromosomes (of the 16 chromosomes in total) [19], and a draft assembly comprising 1778 scaffolds has been reported for the related species Botrylloides leachii [20]. A very fragmented assembly of the "sea vomit" Didemnum vexillum was also recently sequenced by our group to analyze noncoding RNAs (ncRNAs) [21]. Here we report on a substantial improvement of this assembly.…”

Polymorphic adaptations in metazoans to establish and maintain photosymbioses

“…Among Ascidia the genome of the carpet sea squirt, Didemnum vexillum (Didemnidae), has been sequenced (Velandia‐Huerto et al, ). This non‐symbiotic species (Lin et al, ) is currently considered a highly successful invasive taxon (Bullard et al, ; Lengyel, Collie & Valentine, ; Locke & Carman, ; Stefaniak et al, ).…”