Skip to main content
SpringerLink
Log in

Analysis of a botryllid enriched-full-length cDNA library: insight into the evolution of spliced leader trans-splicing in tunicates

  • Original Article
  • Published:
Development Genes and Evolution Aims and scope Submit manuscript

Abstract

In some animals, mRNA may be modified after transcription by the addition of a 5′ spliced leader sequence. This is known as spliced leader (SL) trans-splicing, and is of uncertain function and evolutionary origin. Here, we report the identification of SL trans-splicing in the colonial ascidian Botryllus schlosseri. Combining our own expressed sequence tag (EST) data with additional data from GenBank, we identify the dominant spliced leader sequence and show it to be similar to that of other ascidians and to that of Oikopleura dioica, a basally diverging tunicate. Gene Ontology analysis of B. schlosseri ESTs with and without a 5′ spliced leader shows that genes encoding ribosomal proteins tend not to be trans-spliced, a character shared with the ascidian Ciona intestinalis. We also examine individual cases of genes that produce mRNAs that are SL trans-spliced in B. schlosseri but not in C. intestinalis. We conclude that SL trans-splicing evolved early in the tunicate lineage and shows stability over considerable evolutionary time. However, SL trans-splicing may be gained or lost in individual genes.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene Ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25(1):25–29

    Article  PubMed  CAS  Google Scholar 

  • Blumenthal T, Gleason KS (2003) Caenorhabditis elegans operons: form and function. Nat Rev Genet 4(2):112–120

    Article  PubMed  CAS  Google Scholar 

  • Bluthgen N, Brand K, Cajavec B, Swat M, Herzel H, Beule D (2005) Biological profiling of gene groups utilizing Gene Ontology. Genome Inform 16(1):106–115

    PubMed  Google Scholar 

  • Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25(2):288–289

    Article  PubMed  CAS  Google Scholar 

  • Chou HH, Holmes MH (2001) DNA sequence quality trimming and vector removal. Bioinformatics 17(12):1093–1104

    Article  PubMed  CAS  Google Scholar 

  • De Tomaso AW, Saito Y, Ishizuka KJ, Palmeri KJ, Weissman IL (1998) Mapping the genome of a model protochordate. I. A low resolution genetic map encompassing the fusion/histocompatibility (fu/hc) locus of Botryllus schlosseri. Genetics 149(1):277–287

    PubMed  Google Scholar 

  • Delsuc F, Tsagkogeorga G, Lartillot N, Philippe H (2008) Additional molecular support for the new chordate phylogeny. Genesis 46(11):592–604

    Article  PubMed  Google Scholar 

  • Douris V, Telford MJ, Averof M (2010) Evidence for multiple independent origins of trans-splicing in Metazoa. Mol Biol Evol 27(3):684–693

    Article  PubMed  CAS  Google Scholar 

  • Ganot P, Kallesoe T, Reinhardt R, Chourrout D, Thompson EM (2004) Spliced-leader RNA trans splicing in a chordate, Oikopleura dioica, with a compact genome. Mol Cell Biol 24(17):7795–7805

    Article  PubMed  CAS  Google Scholar 

  • Gasparini F, Franchi N, Spolaore B, Ballarin L (2008) Novel rhamnose-binding lectins from the colonial ascidian Botryllus schlosseri. Dev Comp Immunol 32(10):1177–1191

    Article  PubMed  CAS  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/nt. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Hastings KE (2005) SL trans-splicing: easy come or easy go? Trends Genet 21(4):240–247

    Article  PubMed  CAS  Google Scholar 

  • Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9(4):286–298

    Article  PubMed  CAS  Google Scholar 

  • Krause M, Hirsh D (1987) A trans-spliced leader sequence on actin mRNA in C. elegans. Cell 49(6):753–761

    Article  PubMed  CAS  Google Scholar 

  • Marletaz F, Gilles A, Caubit X, Perez Y, Dossat C, Samain S, Gyapay G, Wincker P, Le Parco Y (2008) Chaetognath transcriptome reveals ancestral and unique features among bilaterians. Genome Biol 9(6):R94

    Article  PubMed  Google Scholar 

  • Matsumoto J, Dewar K, Wasserscheid J, Wiley GB, Macmil SL, Roe BA, Zeller RW, Satou Y, Hastings KE (2010) High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: alternative expression modes and gene function correlates. Genome Res 20(5):636–645

    Article  PubMed  CAS  Google Scholar 

  • McCarthy FM, Wang N, Magee GB, Nanduri B, Lawrence ML, Camon EB, Barrell DG, Hill DP, Dolan ME, Williams WP, Luthe DS, Bridges SM, Burgess SC (2006) AgBase: a functional genomics resource for agriculture. BMC Genomics 7:229

    Article  PubMed  Google Scholar 

  • Milhausen M, Nelson RG, Sather S, Selkirk M, Agabian N (1984) Identification of a small RNA containing the trypanosome spliced leader: a donor of shared 5′ sequences of trypanosomatid mRNAs? Cell 38(3):721–729

    Article  PubMed  CAS  Google Scholar 

  • Oren M, Paz G, Douek J, Rosner A, Fishelson Z, Goulet TL, Henckel K, Rinkevich B (2010) ‘Rejected’ vs. ‘rejecting’ transcriptomes in allogeneic challenged colonial urochordates. Mol Immunol 47(11–12):2083–2093

    Article  PubMed  CAS  Google Scholar 

  • Pouchkina-Stantcheva NN, Tunnacliffe A (2005) Spliced leader RNA-mediated trans-splicing in phylum Rotifera. Mol Biol Evol 22(6):1482–1489

    Article  PubMed  CAS  Google Scholar 

  • Rajkovic A, Davis RE, Simonsen JN, Rottman FM (1990) A spliced leader is present on a subset of mRNAs from the human parasite Schistosoma mansoni. Proc Natl Acad Sci USA 87(22):8879–8883

    Article  PubMed  CAS  Google Scholar 

  • Satou Y, Kawashima T, Shoguchi E, Nakayama A, Satoh N (2005) An integrated database of the ascidian, Ciona intestinalis: towards functional genomics. Zoolog Sci 22(8):837–843

    Article  PubMed  CAS  Google Scholar 

  • Satou Y, Hamaguchi M, Takeuchi K, Hastings KE, Satoh N (2006) Genomic overview of mRNA 5′-leader trans-splicing in the ascidian Ciona intestinalis. Nucleic Acids Res 34(11):3378–3388

    Article  PubMed  CAS  Google Scholar 

  • Satou Y, Mineta K, Ogasawara M, Sasakura Y, Shoguchi E, Ueno K, Yamada L, Matsumoto J, Wasserscheid J, Dewar K, Wiley GB, Macmil SL, Roe BA, Zeller RW, Hastings KE, Lemaire P, Lindquist E, Endo T, Hotta K, Inaba K (2008) Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations. Genome Biol 9(10):R152

    Article  PubMed  Google Scholar 

  • Seo HC, Kube M, Edvardsen RB, Jensen MF, Beck A, Spriet E, Gorsky G, Thompson EM, Lehrach H, Reinhardt R, Chourrout D (2001) Miniature genome in the marine chordate Oikopleura dioica. Science 294(5551):2506

    Article  PubMed  CAS  Google Scholar 

  • Stock DW, Quattro JM, Whitt GS, Powers DA (1997) Lactate dehydrogenase (LDH) gene duplication during chordate evolution: the cDNA sequence of the LDH of the tunicate Styela plicata. Mol Biol Evol 14(12):1273–1284

    PubMed  CAS  Google Scholar 

  • Stover NA, Steele RE (2001) Trans-spliced leader addition to mRNAs in a cnidarian. Proc Natl Acad Sci USA 98(10):5693–5698

    Article  PubMed  CAS  Google Scholar 

  • Sugahara Y, Carninci P, Itoh M, Shibata K, Konno H, Endo T, Muramatsu M, Hayashizaki Y (2001) Comparative evaluation of 5′-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries. Gene 263(1–2):93–102

    Article  PubMed  CAS  Google Scholar 

  • Tang Z, Choi JH, Hemmerich C, Sarangi A, Colbourne JK, Dong Q (2009) ESTPiper—a web-based analysis pipeline for expressed sequence tags. BMC Genomics 10:174

    Article  PubMed  Google Scholar 

  • Tessier LH, Keller M, Chan RL, Fournier R, Weil JH, Imbault P (1991) Short leader sequences may be transferred from small RNAs to pre-mature mRNAs by trans-splicing in Euglena. EMBO J 10(9):2621–2625

    PubMed  CAS  Google Scholar 

  • Vandenberghe AE, Meedel TH, Hastings KE (2001) mRNA 5′-leader trans-splicing in the chordates. Genes Dev 15(3):294–303

    Article  PubMed  CAS  Google Scholar 

  • Wellenreuther R, Schupp I, Poustka A, Wiemann S (2004) SMART amplification combined with cDNA size fractionation in order to obtain large full-length clones. BMC Genomics 5:36

    Article  PubMed  Google Scholar 

  • Yeats B, Matsumoto J, Mortimer SI, Shoguchi E, Satoh N, Hastings KE (2010) SL RNA genes of the ascidian tunicates Ciona intestinalis and Ciona savignyi. Zoolog Sci 27(2):171–180

    Article  PubMed  CAS  Google Scholar 

  • Yuasa HJ, Kawamura K, Yamamoto H, Takagi T (2002) The structural organization of ascidian Halocynthia roretzi troponin I genes. J Biochem 132(1):135–141

    PubMed  CAS  Google Scholar 

  • Zeng L, Swalla BJ (2005) Molecular phylogeny of the protochordates: chordate evolution. Can J Zool 83(1):24–33

    Article  CAS  Google Scholar 

  • Zhang H, Hou Y, Miranda L, Campbell DA, Sturm NR, Gaasterland T, Lin S (2007) Spliced leader RNA trans-splicing in dinoflagellates. Proc Natl Acad Sci USA 104(11):4618–4623

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

The authors wish to thank Michael Kube, Richard Reinhardt and Sven Klages for the support in preparing the library during the NoE “Marine Genomics Europe” training course “Generation of cDNA Libraries by Primer Extension” (20 November–1 December, 2006) attended to one of us (FG) at the Max Planck Institute for Molecular Genetics, Berlin (Germany). We also thank two anonymous referees for their thoughtful comments. FG acknowledges the support of the Ministero della Università e Ricerca Scientifica e Tecnologica and the Università degli Studi di Padova. SMS acknowledges the support of the Royal Society and the British Council. The authors declare that the experiments comply with the current laws of the country in which they were performed. The authors declare that they have no conflict of interest. Additional data are available at http://www.fabiogasparini.org/Data/DGEsuppl/info.htm. (1) The 765 singleton clones and contigs derived from the assembled ESTs generated in this study; (2) accessions and sequences of the 4,477 B. schlosseri ESTs extracted from GenBank and used in this study; (3) dbEST and GenBank accession numbers of the 1,259 B. schlosseri ESTs generated in this study.

Author information

Authors and Affiliations

  1. Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy

    Fabio Gasparini

  2. Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK

    Sebastian M. Shimeld

Authors
  1. Fabio Gasparini
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sebastian M. Shimeld
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Fabio Gasparini.

Additional information

Communicated by H. Nishida

Electronic supplementary materials

Below is the link to the electronic supplementary material.

ESM 1

The 765 singleton clones and contigs derived from the assembled ESTs generated in this study are available at: http://www.fabiogasparini.org/Data/DGEsuppl/info.htm. (TXT 0 kb)

ESM 2

B. schlosseri ESTs available in GenBank on 13 Oct 2009 with putaitive SL sequences marked in blue or green, and additional possible contaminant sequences as described in the text in purple. This subset includes only those without internal variants (PDF 96 kb)

ESM 3

B. schlosseri ESTs available in GenBank on 13 Oct 2009 with putative SL sequences marked in green, additional possible contaminant sequences as described in the text in purple, and internal variants marked in black. This subset includes only those with internal variants (PDF 26 kb)

ESM 4

B. schlosseri singleton clones and contigs from assembled library with putative SL sequences. This is a subset of Online Resource 1. Each sequence is in Fasta format with only the first 40 nucleotides of 5' region shown (TXT 9 kb)

ESM 5

B. schlosseri ESTs generated in this study with putative SL sequences. Each EST is in Fasta format with only the first 40 nucleotides of the 5' region shown (TXT 13 kb)

ESM 6

GOSSIP output of statistical analysis of association between annotations from the Gene Ontology and groups of genes. Test group, non trans-spliced members; reference group, trans-spliced members. Results with FDR < 0.01 are highlighted (PDF 416 kb)

ESM 7

GOSSIP output of statistical analysis of association between annotations from the Gene Ontology and groups of genes. Test group, trans-spliced members; reference group, non trans-spliced members (PDF 296 kb)

ESM 8

GOanna2ga gene association file format of trans-spliced annotated sequences obtained by converting the GOanna Excel spreadsheet output with GO annotations (XLS 51 kb)

ESM 9

GOanna2ga gene association file format of non-trans-spliced annotated sequences obtained by converting the GOanna Excel spreadsheet output with GO annotations (XLS 149 kb)

ESM 10

AmiGO graphs of ontological hierarchies obtained with the eight GO terms (encircled in red) significantly over-represented in the non-trans-spliced cDNA assembled library subset (PNG 4732 kb)

ESM 11

B. schlosseri sequences matching C. intestinalis KH gene models for which cRAR has been calculated by Matsumoto et al. (2010). Columns G to M show characters of the KH gene model predicted to be orthologous to the B. schlosseri sequence. These have only been calculated for genes with cRAR < 0.05 (XLS 45 kb)

ESM 12

B. schlosseri sequences matching C. intestinalis KH gene models for which cRAR is not calculated but for which evidence of SL trans-splicing comes from the raw data of Matsumoto et al. (2010; XLS 28 kb)

ESM 13

B. schlosseri sequences matching C. intestinalis KH gene models that were not detected in the tailbud stage sequencing data of Matsumoto et al. (2010; XLS 24 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gasparini, F., Shimeld, S.M. Analysis of a botryllid enriched-full-length cDNA library: insight into the evolution of spliced leader trans-splicing in tunicates. Dev Genes Evol 220, 329–336 (2011). https://doi.org/10.1007/s00427-011-0351-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00427-011-0351-y

Keywords

Search

Navigation