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

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.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5297-2) contains supplementary material, which is available to authorized users.

Analysis of Copy-Number Variations and Feline Mammary Carcinoma Survival

“…Besides somatic-CNVs affecting neoplastic cells, normal cells also have variations in the number of copies, representing a source of genomic diversification during evolution 120,121 . Those mutations usually affect smaller genomic regions than somatic-CNVs and some of them-usually referred to as germline-CNVs-are implicated in cancer inheritance 15,16,[122][123][124] .…”

“…As far as we know, there is only one publication characterising CNVs in cats according to different breeds (Genova et al 121 ), and none characterising germline-CNVs associated with FMCs predisposition. When comparing our data with those of Genova et al, we observed that none of the animals in that study carried CNGs affecting B4 1-29 Mb and F2 64-82.3 Mb-enriched with cancer-related genes and significantly associated with poor outcome.…”

“…As recommended by Genova et al 121 , two different programs were used to call large size aneuploidies by depth of coverage analysis and results were compared to reduce false-positive calls. First, we applied two different programs to generate log2-copy-number-ratios for each cancer sample: 1.…”

Detection of copy number variants in African goats using whole genome sequence data

“…Use of WGS for CNV detection is highly encouraged, because it overcomes many of the shortcomings of the other CNV detection methods such as the ones using array CGH and SNP data [18][19][20]. Genome-wide studies to discover CNV have already been done in other domesticated species, such as in Sus scrofa [49], Bos taurus [37,50] and Felis catus [38]. Here we provide a first glimpse of the goat genome CNV map at a dense genome coverage, using animals from 34 diverse breeds from the African continent.…”

“…Many studies have been carried out to detect CNV using WGS data in various domesticated species: cattle [37], cats [38], chickens [39], dogs [40], etc. So far, there is no report of goat CNV discoveries using WGS data.…”