A comprehensive reference transcriptome resource for the common house spider Parasteatoda tepidariorum

PLoS One. 2014 Aug 13;9(8):e104885. doi: 10.1371/journal.pone.0104885. eCollection 2014.

Abstract

Parasteatoda tepidariorum is an increasingly popular model for the study of spider development and the evolution of development more broadly. However, fully understanding the regulation and evolution of P. tepidariorum development in comparison to other animals requires a genomic perspective. Although research on P. tepidariorum has provided major new insights, gene analysis to date has been limited to candidate gene approaches. Furthermore, the few available EST collections are based on embryonic transcripts, which have not been systematically annotated and are unlikely to contain transcripts specific to post-embryonic stages of development. We therefore generated cDNA from pooled embryos representing all described embryonic stages, as well as post-embryonic stages including nymphs, larvae and adults, and using Illumina HiSeq technology obtained a total of 625,076,514 100-bp paired end reads. We combined these data with 24,360 ESTs available in GenBank, and 1,040,006 reads newly generated from 454 pyrosequencing of a mixed-stage embryo cDNA library. The combined sequence data were assembled using a custom de novo assembly strategy designed to optimize assembly product length, number of predicted transcripts, and proportion of raw reads incorporated into the assembly. The de novo assembly generated 446,427 contigs with an N50 of 1,875 bp. These sequences obtained 62,799 unique BLAST hits against the NCBI non-redundant protein data base, including putative orthologs to 8,917 Drosophila melanogaster genes based on best reciprocal BLAST hit identity compared with the D. melanogaster proteome. Finally, we explored the utility of the transcriptome for RNA-Seq studies, and showed that this resource can be used as a mapping scaffold to detect differential gene expression in different cDNA libraries. This resource will therefore provide a platform for future genomic, gene expression and functional approaches using P. tepidariorum.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Base Composition
  • Base Sequence
  • Computational Biology
  • Expressed Sequence Tags
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Developmental / genetics*
  • Gene Expression Regulation, Developmental / physiology
  • Gene Library
  • Life Cycle Stages / genetics*
  • Life Cycle Stages / physiology
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Sequence Analysis, DNA
  • Signal Transduction / genetics*
  • Signal Transduction / physiology
  • Species Specificity
  • Spiders / genetics*
  • Spiders / metabolism*
  • Transcriptome / genetics*

Associated data

  • BioProject/PRJNA253975
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Grant support

MH was funded by the European Union via the Marie Curie RTN ZOONET (MRTN-CT-2004-005624) to WGMD. The work of NMP is supported by the Deutsche Forschungsgemeinschaft (DFG; grant numbers PR 1109/1-1 and PR 1109/6-1 to NMP). Additional financial backing to NMP has been received from the Göttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences (GGNB), the Göttingen Centre for Molecular Biosciences (GZMB), and the University of Göttingen (GAU). The work of NP is partially supported by the Volkswagen foundation (85 983). The work of CGE and VZ is funded by Harvard Stem Cell Institute Seed Grant SG-0057-10-00 to CGE, Ellison Medical Foundation New Scholar Award AG-NS-07010-10 to CGE and National Science Foundation (NSF) Grants IOS-0817678 and IOS-1257217 to GCE. The work of EES is supported by DFG fellowship SCHW 1557/1-1 to EES. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.