Research article
Transcriptome characterization via 454 pyrosequencing of the annelid Pristina leidyi, an emerging model for studying the evolution of regeneration
1 Department of Biology, University of Maryland, College Park, MD, 20742, USA
2 Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
3 Current address: Department of Biology, Indiana University, Bloomington, IN, 47401, USA
BMC Genomics 2012, 13:287 doi:10.1186/1471-2164-13-287
Published: 29 June 2012Additional files
Additional file 1:
Genome sizes of five naid species. Genome sizes of five species of naid worms, including P. leidyi, were estimated using the Feulgen image analysis densitometry method.
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Additional file 2:
PCR assay for metabolic activity in dried Spirulina food. To assess the possibility of dried Spirulina (used as P. leidyi food) contributing to the cDNA library, we used PCR to detect the large subunit of rubisco (rbcL) and c-phycocyanin (cpc) of Spirulina (Arthrospira platensis). No PCR bands were detectable for either gene in negative water controls (lane 1) while strong bands were detected when cDNA from live Spirulina cultures was used as template (lane 2). Neither Spirulina gene could be detected by PCR in the P. leidyi cDNA (lane 3), though PCR of a positive control gene (Pl-α-tubulin) produced strong bands using the same template (lane 4).
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Additional file 3:
Gene Ontology Molecular Function and Cellular Component designations of isotigs. Representative isotigs were subjected to Gene Ontology (GO) analysis using Blast2GO. Categories are level 2 (A) Molecular Function and (B) Cellular Component designations. Proportion on the y-axis was calculated from the total number of representative isotigs that were annotated with GO terms (11,140).
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Additional file 4:
Nucleotide alignments for isogroups 08478 and 03233. Nucleotide alignment of isotigs from (A) isogroup08478, a putative piwi-like gene, and (B) isogroup03233, a putative frizzled gene. Alignments are diagrammed in Figure 5.
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Additional file 5:
Primer sequences. Primer sequences used for cDNA synthesis, 454 adaptors, PCR detection of Spirulina metabolic activity, qPCR of cDNA normalization efficiency, PCR validation of transcript assemblies, and synthesis of in situ hybridization probes are provided. All primer sequences are listed 5’→ 3’.
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