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

F. Genova,M. Longeri,M. G. Strillacci,A. Bagnato,L. A. Lyons,The 99Lives Consortium

doi:10.1186/s12864-018-5297-2

Abstract

BackgroundCopy 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.ResultsReads 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.ConclusionThis 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.

Highlights

Copy Number Variations (CNVs) have becoming very significant variants, representing a major source of genomic variation
The gene annotation performed in this study showed that 19% of the Copy Number Variants Region (CNVR) harbor genes
The clustering among the cat breeds that was possible to obtain in this study using CNVRs, complement findings of other studies based on other type of markers, leading to a closer insight of common and proprietary functional aspects of each population

Summary

Introduction

Copy Number Variations (CNVs) have becoming very significant variants, representing a major source of genomic variation. Other structural and more complex variants - like Copy Number Variants (CNV) - were known [1], and the recent advances in genome technologies, especially the development of array platforms and generation sequencing, has allowed more global analyses of CNVs at a genome-wide level. These variants consist of changes in copy number of DNA sequences in comparison to a reference genome, including duplications (gain state) and deletions (loss state). A loss of the chimpanzee TBC1D3 gene, compared to the eight paralog copies of this gene in the human reference individual, may reflect a positive selection and adaptive

Methods

Results

Discussion

Conclusion