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Comparison and Characterisation of Mutation Calling from Whole Exome and RNA Sequencing Data for Liver and Muscle Tissue in Lactating Holstein Cows Divergent for Fertility

Bruce Moran, Stephen T. Butler, Christopher J. Creevey
doi: https://doi.org/10.1101/101733
Bruce Moran
*Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8, Ireland.
†Teagasc, Animal and Grassland Research and Innovation Centre, Grange, Meath, C15 PW93, Ireland.
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Stephen T. Butler
‡Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Cork, P61 C997, Ireland.
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Christopher J. Creevey
†Teagasc, Animal and Grassland Research and Innovation Centre, Grange, Meath, C15 PW93, Ireland.
§Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3FL, Wales.
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Abstract

Whole exome sequencing has had low uptake in livestock species, despite allowing accurate analysis of single nucleotide variant (SNV) mutations. Transcriptomic data in the form of RNA sequencing has been generated for many livestock species and also represents a source of mutational information. However, there is little information on the accuracy of using this data for the identification of SNVs. We generated a bovine exome capture design and used it to sequence and call mutations from a lactating dairy cow model genetically divergent for fertility (Fert+, n=8; Fert-, n=8). We compared mutations called from liver and muscle transcriptomes from the same animals. Our exome capture demonstrated 99.1% coverage of the exome design of 56.7MB, whereas transcriptomes covered 55 and 46.5% of the exome, or 24.4 and 20.7MB, in liver and muscle respectively after filtering. We found that specificity of SNVs in the transcriptome data is approximately 75% following basic hard-filtering, and could be increased to above 80% by increasing the minimum threshold of reads covering SNVs, but this effect was negated in more highly covered SNVs. RNA-DNA differences, SNVs found in transcriptome but not exome, were discovered and shown to have significantly increased levels of transition mutations in both tissues. Functional annotation of non-synonymous SNVs specific to the high and low fertility phenotypes identified immune response-related genes, supporting previous work that has identified differential expression in the same genes. Publically available RNAseq data may be analysed in a similar way to further increase the utility of this resource.

Summary The exome and transcriptome both relate to the same protein-coding regions of the genome. There has been sparse research on characterising mutations in RNA and DNA within the same individuals. Here we characterise the similarities in our Holstein dairy cow animal model. We offer practical and biological results indicating that RNA sequencing is a useful proxy of exome sequencing, itself shown to be applicable to this livestock species using a previously untested commercial application. This potentially unlocks public RNA sequencing data for further analysis, also indicating that RNA-DNA differences may associate with transcriptomic divergence.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted January 20, 2017.
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Comparison and Characterisation of Mutation Calling from Whole Exome and RNA Sequencing Data for Liver and Muscle Tissue in Lactating Holstein Cows Divergent for Fertility
Bruce Moran, Stephen T. Butler, Christopher J. Creevey
bioRxiv 101733; doi: https://doi.org/10.1101/101733
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Comparison and Characterisation of Mutation Calling from Whole Exome and RNA Sequencing Data for Liver and Muscle Tissue in Lactating Holstein Cows Divergent for Fertility
Bruce Moran, Stephen T. Butler, Christopher J. Creevey
bioRxiv 101733; doi: https://doi.org/10.1101/101733

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