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  De novo assembly and vailidation of planaria transcriptome by massive parallel sequencing and shotgun proteomics

Adamidi, C., Wang, Y., Grün, D., Mastrobuoni, G., You, X., Tolle, D., et al. (2011). De novo assembly and vailidation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Research, 21, 1193-1120. doi:10.1101/gr.113779.110.

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 Creators:
Adamidi, Catherine1, Author
Wang, Yongbo1, Author
Grün, Dominic2, Author           
Mastrobuoni, Guido1, Author
You, Xintian1, Author
Tolle, Dominic1, Author
Dodt, Matthias1, Author
Mackowiak, Sebastian D.1, Author
Gogol-Doering, Andreas1, Author
Oenal, Pinar1, Author
Rybak, Agnieszka1, Author
Ross, Eric1, Author
Alvarado, Alejandro Sánchez1, Author
Kempa, Stefan1, Author
Dieterich, Christoph1, Author
Rajewsky, Nikolaus1, Author
Chen, Wei1, Author
Affiliations:
1External Organizations, ou_persistent22              
2Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_2243642              

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 Abstract: Freshwater planaria are a very attractive model system for stem cell biology, tissue homeostasis, and regeneration. The genome of the planarian Schmidtea mediterranea has recently been sequenced and is estimated to contain >20,000 protein-encoding genes. However, the characterization of its transcriptome is far from complete. Furthermore, not a single proteome of the entire phylum has been assayed on a genome-wide level. We devised an efficient sequencing strategy that allowed us to de novo assemble a major fraction of the S. mediterranea transcriptome. We then used independent assays and massive shotgun proteomics to validate the authenticity of transcripts. In total, our de novo assembly yielded 18,619 candidate transcripts with a mean length of 1118 nt after filtering. A total of 17,564 candidate transcripts could be mapped to 15,284 distinct loci on the current genome reference sequence. RACE confirmed complete or almost complete 5′ and 3′ ends for 22/24 transcripts. The frequencies of frame shifts, fusion, and fission events in the assembled transcripts were computationally estimated to be 4.2%–13%, 0%–3.7%, and 2.6%, respectively. Our shotgun proteomics produced 16,135 distinct peptides that validated 4200 transcripts (FDR ≤1%). The catalog of transcripts assembled in this study, together with the identified peptides, dramatically expands and refines planarian gene annotation, demonstrated by validation of several previously unknown transcripts with stem cell-dependent expression patterns. In addition, our robust transcriptome characterization pipeline could be applied to other organisms without genome assembly. All of our data, including homology annotation, are freely available at SmedGD, the S. mediterranea genome database.

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Language(s): eng - English
 Dates: 2011
 Publication Status: Issued
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1101/gr.113779.110
 Degree: -

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Title: Genome Research
Source Genre: Journal
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Publ. Info: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press
Pages: - Volume / Issue: 21 Sequence Number: - Start / End Page: 1193 - 1120 Identifier: ISSN: 1088-9051
CoNE: https://pure.mpg.de/cone/journals/resource/954926997202