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

Genova, F; Longeri, M; Lyons, L A; Bagnato, A; the 99Lives, Consortium; Strillacci, M G (2018). First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data. BMC Genomics, 19(1), p. 895. BioMed Central 10.1186/s12864-018-5297-2

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH)

Subjects:

500 Science > 570 Life sciences; biology
500 Science > 590 Animals (Zoology)
600 Technology > 610 Medicine & health

ISSN:

1471-2164

Publisher:

BioMed Central

Language:

English

Submitter:

Tosso Leeb

Date Deposited:

20 Sep 2019 14:15

Last Modified:

28 Nov 2020 02:29

Publisher DOI:

10.1186/s12864-018-5297-2

PubMed ID:

30526495

Additional Information:

Tosso Leeb: member of the 99Lives Consortium

Uncontrolled Keywords:

CNV CNVR CNVnator Cat breeds Cn.MOPS Felis catus NGS

BORIS DOI:

10.7892/boris.133172

URI:

https://boris.unibe.ch/id/eprint/133172

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