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A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences
Tonia S Schwartz1, Hongseok Tae, Youngik Yang
1Ecology, Evolution and Organismal Biology Department, Iowa State University, Ames, IA 50011, USA.
BMC Genomics
|December 9, 2010
Summary
This study developed the first large-scale reptile transcriptome for the western terrestrial garter snake (Thamnophis elegans), identifying sex-specific genes and genetic variations to aid evolutionary studies.
Area of Science:
- Genomics
- Evolutionary Biology
- Herpetology
Background:
- Reptiles offer insights into metabolism, physiology, and development due to their diversity and adaptations.
- Limited molecular resources for ectothermic reptiles hinder research on traits like metabolic plasticity and longevity.
Purpose of the Study:
- To create a molecular resource for an ectothermic reptile.
- To identify sex-specific transcripts and genes of evolutionary interest in Thamnophis elegans.
Main Methods:
- Generated a sex-specific transcriptome using massively parallel sequencing (454 GS-FLX Titanium) from 7 tissue types across 35 snakes.
- Assembled sequence reads and annotated contigs using homology, clustering, and ORF predictions.
- Utilized graph-clustering to identify divergent alleles, gene duplications, and alternative splicing; identified SNPs and INDELs.
Main Results:
- Produced 1.24 million sequence reads, assembled into 96,379 contigs, with over 34% annotated.
- Estimated ~13,000 known and >66,000 novel protein-coding genes.
- Identified 190 sex-specific genes (84 female, 106 male), 95,295 SNPs, and 31,651 INDELs.
Conclusions:
- This is the first large-scale, multi-organ transcriptome for an ectothermic reptile, significantly expanding snake EST data.
- Identified genes under evolutionary selection and sex-specific transcripts.
- This resource facilitates gene expression, comparative genomics, and molecular-level studies of evolutionarily important traits.
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