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De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)
Jared Mamrot1,2, Roxane Legaie3, Stacey J Ellery1,2
1The Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Australia.
Scientific Reports
|August 23, 2017
Summary
Researchers generated a draft transcriptome for the Common spiny mouse (Acomys cahirinus), providing a key genetic resource. This study details the spiny mouse transcriptome, aiding research into unique mammalian traits like scar-free healing.
Area of Science:
- Genomics
- Mammalian Physiology
- Comparative Transcriptomics
Background:
- Spiny mice (Acomys) exhibit rare mammalian traits such as menstruation and scar-free wound healing.
- These unique physiological characteristics make spiny mice valuable models for human disease research.
- Limited genetic information is currently available for the Acomys genus, hindering further investigation.
Purpose of the Study:
- To generate a draft transcriptome for the Common spiny mouse (Acomys cahirinus).
- To establish a comprehensive gene catalogue for Acomys.
- To provide a foundational genetic resource for studying unique spiny mouse physiology.
Main Methods:
- RNA sequencing of 15 organ types from male and female Acomys cahirinus.
- De novo transcriptome assembly using Trinity, SOAPdenovo-Trans, and Oases.
- Meta-assembly of non-redundant transcripts using the EvidentialGene tr2aacds pipeline.
Main Results:
- Generated 451 million 150 bp paired-end reads (92.4 Gbp) from Illumina sequencing.
- Created 50 single-kmer assemblies and a merged meta-assembly.
- Established the largest gene catalogue to date for Acomys cahirinus.
Conclusions:
- This study provides the first detailed characterization of the Acomys cahirinus transcriptome.
- The EvidentialGene tr2aacds pipeline is validated for augmenting mammalian transcriptome assembly.
- The generated transcriptome serves as a crucial resource for future research on Acomys physiology.
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