First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data

F. Genova, M. Longeri, L. A. Lyons, A. Bagnato, Barbara Gandolfi, Danielle Aberdein, Paulo C. Alves, Gregory S. Barsh, Holly C. Beale, Tomas F. Bergström, Adam R. Boyko, Jeffrey A. Brockman, Marta G. Castelhano, Patricia P. Chan, Brian W. Davis, Ottmar Distl, Nicholas H. Dodman, N. Matthew Ellinwood, Jonathan E. Fogle, Oliver P. FormanDorian J. Garrick, Jens Häggström, Christopher R. Helps, Marjo K. Hytönen, Daniel M. Ibrahim, Maria Kaukonen, Christopher B. Kaelin, Emilie Leclerc, Teri L. Lear, Tosso Leeb, Hannes Lohi, Darío G. Lupiáñez, Mark A. Magnuson, Richard Malik, Michael J. Montague, John S. Munday, William J. Murphy, Elaine A. Ostrander, Niels C. Pedersen, Simon M. Petersen-Jones, Max F. Rothschild, Beth Shapiro, Joshua A. Stern, William F. Swanson, Karen A. Terio, Rory J. Todhunter, Yu Ueda, Wesley C. Warren, Elizabeth A. Wilcox, Julia H. Wildschutte, Edward I. Ginns, M. G. Strillacci

Research output: Contribution to journalArticle

2 Scopus citations

Abstract

Background: Copy Number Variations (CNVs) have becoming very significant variants, representing a major source of genomic variation. CNVs involvement in phenotypic expression and different diseases has been widely demonstrated in humans as well as in many domestic animals. However, genome wide investigation on these structural variations is still missing in Felis catus. The present work is the first CNV mapping from a large data set of Next Generation Sequencing (NGS) data in the domestic cat, performed within the 99 Lives Consortium. Results: Reads have been mapped on the reference assembly-6.2 by Maverix Biomics. CNV detection with cn.MOPS and CNVnator detected 592 CNVs. These CNVs were used to obtain 154 CNV Regions (CNVRs) with BedTools, including 62 singletons. CNVRs covered 0.26% of the total cat genome with 129 losses, 19 gains and 6 complexes. Cluster Analysis and Principal Component Analysis of the detected CNVRs showed that breeds tend to cluster together as well as cats sharing the same geographical origins. The 46 genes identified within the CNVRs were annotated. Conclusion: This study has improved the genomic characterization of 14 cat breeds and has provided CNVs information that can be used for studies of traits in cats. It can be considered a sound starting point for genomic CNVs identification in this species.

Original languageEnglish (US)
Article number895
JournalBMC Genomics
Volume19
Issue number1
DOIs
StatePublished - Dec 10 2018

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Keywords

  • Cat breeds
  • Cn.MOPS
  • CNV
  • CNVnator
  • CNVR
  • Felis catus
  • NGS

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Genova, F., Longeri, M., Lyons, L. A., Bagnato, A., Gandolfi, B., Aberdein, D., Alves, P. C., Barsh, G. S., Beale, H. C., Bergström, T. F., Boyko, A. R., Brockman, J. A., Castelhano, M. G., Chan, P. P., Davis, B. W., Distl, O., Dodman, N. H., Matthew Ellinwood, N., Fogle, J. E., ... Strillacci, M. G. (2018). First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data. BMC Genomics, 19(1), [895]. https://doi.org/10.1186/s12864-018-5297-2