Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian

BMC Genomics

Database

Allyson L Byrd¹  Tristan J Lubinski²  Derek J Stefanik²  Brian R Granger³  John R Finnerty⁴  Adam M Reitzel⁵  Lukas DeFilippo⁶  Allison Lorenc⁶ 

[1] Bioinformatics Program, Boston University, 24 Cummington Mall, 02215, Boston, MA, USA;Department of Biology, Boston University, 5 Cummington Mall, 02215, Boston, MA, USA;Department of Biology, Boston University, 5 Cummington Mall, 02215, Boston, MA, USA;Bioinformatics Program, Boston University, 24 Cummington Mall, 02215, Boston, MA, USA;Department of Biology, Boston University, 5 Cummington Mall, 02215, Boston, MA, USA;Bioinformatics Program, Boston University, 24 Cummington Mall, 02215, Boston, MA, USA;Marine Program, Boston University, 5 Cummington Street, 02215, Boston, MA, USA;Department of Biology, University of North Carolina at Charlotte, 28223, Charlotte, NC, USA;Marine Program, Boston University, 5 Cummington Street, 02215, Boston, MA, USA;

关键词: Gene Ontology;    Enzyme Commission;    Transcriptome Assembly;    Enzyme Commission Number;    Sock Gene;   

DOI  :  10.1186/1471-2164-15-71

 received in 2013-07-18, accepted in 2013-12-11,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundThe lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. Additionally, E. lineata is confamilial with the model cnidarian Nematostella vectensis, providing an opportunity for comparative genomic, molecular and organismal studies.DescriptionWe generated a reference transcriptome for E. lineata via high-throughput sequencing of RNA isolated from five developmental stages (parasite; parasite-to-larva transition; larva; larva-to-adult transition; adult). The transcriptome comprises 90,440 contigs assembled from >15 billion nucleotides of DNA sequence. Using a molecular clock approach, we estimated the divergence between E. lineata and N. vectensis at 215–364 million years ago. Based on gene ontology and metabolic pathway analyses and gene family surveys (bHLH-PAS, deiodinases, Fox genes, LIM homeodomains, minicollagens, nuclear receptors, Sox genes, and Wnts), the transcriptome of E. lineata is comparable in depth and completeness to N. vectensis. Analyses of protein motifs and revealed extensive conservation between the proteins of these two edwardsiid anemones, although we show the NF-κB protein of E. lineata reflects the ancestral structure, while the NF-κB protein of N. vectensis has undergone a split that separates the DNA-binding domain from the inhibitory domain. All contigs have been deposited in a public database (EdwardsiellaBase), where they may be searched according to contig ID, gene ontology, protein family motif (Pfam), enzyme commission number, and BLAST. The alignment of the raw reads to the contigs can also be visualized via JBrowse.ConclusionsThe transcriptomic data and database described here provide a platform for studying the evolutionary developmental genomics of a derived parasitic life cycle. In addition, these data from E. lineata will aid in the interpretation of evolutionary novelties in gene sequence or structure that have been reported for the model cnidarian N. vectensis (e.g., the split NF-κB locus). Finally, we include custom computational tools to facilitate the annotation of a transcriptome based on high-throughput sequencing data obtained from a “non-model system.”

【 授权许可】

Unknown   
© Stefanik et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.