Open Access Highly Accessed Research article

A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences

Tonia S Schwartz12, Hongseok Tae3, Youngik Yang4, Keithanne Mockaitis3, John L Van Hemert2, Stephen R Proulx15, Jeong-Hyeon Choi3* and Anne M Bronikowski1*

Author Affiliations

1 Ecology, Evolution and Organismal Biology Department, Iowa State University, Ames, IA 50011, USA

2 BCBlab, Iowa State University, Ames, IA 50011, USA

3 The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA

4 School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA

5 Ecology, Evolution and Marine Biology Department, University of California, Santa Barbara, Santa Barbara, CA 93106-9620, USA

For all author emails, please log on.

BMC Genomics 2010, 11:694  doi:10.1186/1471-2164-11-694

Published: 7 December 2010

Additional files

Additional file 1:

Table containing details of the samples used for the sex-specific RNA pools. Tissue samples of the same type were pooled across individuals (either laboratory or field born animals) for total RNA extraction. Extracted pools of RNA were quantified and the quality checked on the Bioanalyzer. Equal amounts of RNA from each tissue type were pooled by sex.

Format: DOC Size: 46KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 2:

Graphs illustrating the size distribution of the reads for each sex. Length (bp) distribution of reads obtained with the 454 GS-FLX Titanium sequencing. Read number (N) and length (L) in base pairs. A) Female run. B) Male runs.

Format: DOC Size: 107KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 3:

Description of NEWBLER assembly and graph-clustering procedure.

Format: PDF Size: 142KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Pie graphs of GO assignments. GO slim (level 1, Biological Processes) assignments for all the sequences with annotation, broken down by class of sequences: male singletons, male contigs, both contigs (containing male and female reads), female contigs, female singletons.

Format: DOC Size: 55KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 5:

Snake transcripts mapped to coding and non-coding regions of the Anolis lizard draft genome (AnoCar1.0). A 2007 Excel file (.xlsx) providing details where the snake transcripts mapped to the Anolis draft genome. See the ReadME tab for description of columns.

Format: XLS Size: 9.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Clustering based on homology and contig-graphs. A) Distribution of the number of contigs in a HomoloGene accession, and B) the number of HomoloGene accessions that a contig is assigned to, both at e-value = 1e-20. C) Distribution of the number of contigs belonging to a graph-cluster.

Format: DOC Size: 183KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 7:

Details of variants. A 2007 Excel file (.xlsx) providing details for the variants (SNPs and INDELs). See the ReadME tab for description of columns.

Format: XLSX Size: 8MB Download file

Open Data

Additional file 8:

Contigs of interest. A 2007 Excel file (.xlsx) containing the sequences of interest including those that are sex-specific, that have homology to the chicken Z chromosome, those in the 1st percentile of TS/TV ratios, hose in the top 99th percentile of Ka/Ks ratios, and those, in the top 99th percentile of variability (number of variants per bp). See the ReadME tab for description of columns.

Format: XLSX Size: 196KB Download file

Open Data

Additional file 9:

Sex-specific enrichment of GO terms (level 2, Biological Processes) assigned to the 190 sex-specific sequences. The * indicates the significant over-enrichment of sequences involved in biosynthetic processes in the female-specific sequences (Fisher's Exact Test, FDR <0.006, p-value < 0.0002).

Format: DOC Size: 42KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data