scholarly journals Genomic Copy Number Variation Study of Nine Macaca Species Provides New Insights into Their Genetic Divergence, Adaptation, and Biomedical Application

2020 ◽  
Vol 12 (12) ◽  
pp. 2211-2230
Author(s):  
Jing Li ◽  
Zhenxin Fan ◽  
Feichen Shen ◽  
Amanda L Pendleton ◽  
Yang Song ◽  
...  
Keyword(s):  
Drug Metabolism ◽  
Copy Number Variation ◽  
Copy Number ◽  
Energy Homeostasis ◽  
Biomedical Application ◽  
Quantitative Polymerase Chain Reaction ◽  
Drug Study ◽  
Barbary Macaque ◽  
Number Variation

Abstract Copy number variation (CNV) can promote phenotypic diversification and adaptive evolution. However, the genomic architecture of CNVs among Macaca species remains scarcely reported, and the roles of CNVs in adaptation and evolution of macaques have not been well addressed. Here, we identified and characterized 1,479 genome-wide hetero-specific CNVs across nine Macaca species with bioinformatic methods, along with 26 CNV-dense regions and dozens of lineage-specific CNVs. The genes intersecting CNVs were overrepresented in nutritional metabolism, xenobiotics/drug metabolism, and immune-related pathways. Population-level transcriptome data showed that nearly 46% of CNV genes were differentially expressed across populations and also mainly consisted of metabolic and immune-related genes, which implied the role of CNVs in environmental adaptation of Macaca. Several CNVs overlapping drug metabolism genes were verified with genomic quantitative polymerase chain reaction, suggesting that these macaques may have different drug metabolism features. The CNV-dense regions, including 15 first reported here, represent unstable genomic segments in macaques where biological innovation may evolve. Twelve gains and 40 losses specific to the Barbary macaque contain genes with essential roles in energy homeostasis and immunity defense, inferring the genetic basis of its unique distribution in North Africa. Our study not only elucidated the genetic diversity across Macaca species from the perspective of structural variation but also provided suggestive evidence for the role of CNVs in adaptation and genome evolution. Additionally, our findings provide new insights into the application of diverse macaques to drug study.

scholarly journals The Human Genome Puzzle — the Role of Copy Number Variation in Somatic Mosaicism

2010 ◽  
Vol 11 (6) ◽  
pp. 426-431 ◽  
Author(s):  
Hasmik Mkrtchyan ◽  
Madeleine Gross ◽  
Sophie Hinreiner ◽  
Anna Polytiko ◽  
Marina Manvelyan ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Human Genome ◽  
Copy Number ◽  
Somatic Mosaicism ◽  
Number Variation

scholarly journals The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

2020 ◽  
Vol 375 (1806) ◽  
pp. 20190540 ◽  
Author(s):  
Henry L. North ◽  
Pierre Caminade ◽  
Dany Severac ◽  
Khalid Belkhir ◽  
Carole M. Smadja
Keyword(s):  
Mate Choice ◽  
Copy Number Variation ◽  
Reproductive Isolation ◽  
House Mouse ◽  
Copy Number ◽  
Structural Changes ◽  
Sexual Isolation ◽  
Number Variation ◽  
Tandem Duplications

Reinforcement has the potential to generate strong reproductive isolation through the evolution of barrier traits as a response to selection against maladaptive hybridization, but the genetic changes associated with this process remain largely unexplored. Building upon the increasing evidence for a role of structural variants in adaptation and speciation, we addressed the role of copy-number variation in the reinforcement of sexual isolation evidenced between the two European subspecies of the house mouse. We characterized copy-number divergence between populations of Mus musculus musculus that display assortative mate choice, and those that do not, using whole-genome resequencing data. Updating methods to detect deletions and tandem duplications (collectively: copy-number variants, CNVs) in Pool-Seq data, we developed an analytical pipeline dedicated to identifying genomic regions showing the expected pattern of copy-number displacement under a reinforcement scenario. This strategy allowed us to detect 1824 deletions and seven tandem duplications that showed extreme differences in frequency between behavioural classes across replicate comparisons. A subset of 480 deletions and four tandem duplications were specifically associated with the derived trait of assortative mate choice. These ‘Choosiness-associated’ CNVs occur in hundreds of genes. Consistent with our hypothesis, such genes included olfactory receptors potentially involved in the olfactory-based assortative mate choice in this system as well as one gene, Sp110 , that is known to show patterns of differential expression between behavioural classes in an organ used in mate choice—the vomeronasal organ. These results demonstrate that fine-scale structural changes are common and highly variable within species, despite being under-studied, and may be important targets of reinforcing selection in this system and others. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

scholarly journals Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1008 ◽  
Author(s):  
Fei Ge ◽  
Congjun Jia ◽  
Min Chu ◽  
Chunnian Liang ◽  
Ping Yan
Keyword(s):  
Body Weight ◽  
Copy Number Variation ◽  
Copy Number ◽  
Growth Traits ◽  
Quantitative Polymerase Chain Reaction ◽  
The Body ◽  
Gene Copy ◽  
Common Source ◽  
Economic Traits ◽  
Number Variation

Copy number variation (CNV) is currently accepted as a common source of genetic variation. It is reported that CNVs may influence the resistance to disease and complex economic traits, such as residual feed intake, muscle formation, and fat deposition in livestock. Cell adhesion molecule 2 (CADM2) is expressed widely in the brain and adipose tissue and can regulate body weight through the central nervous system. Growth traits are important economic traits for animal selection. In this study, we aimed to explore the effect of CADM2 gene copy number variants on yak growth traits. Here, two CNVs in the CADM2 gene were investigated using the quantitative polymerase chain reaction (qPCR), and the association of the CNVs with growth traits in yak was analyzed using statistical methods by SPSS software. Differences were considered significant if the p value was < 0.05. Statistical analysis indicated significant association of CADM2-CNV2 with the body weight of the Chinese Ashidan yak. A significant effect of CNV2 (p < 0.05) was found on body weight at 6 months. In CNV2, the gain-type copy number variation exhibited greater performance than the other variants, with greater body weight observed at 6 months (p < 0.05). To the best of our knowledge, this is the first attempt to investigate the function of CADM2-CNVs and their association with growth traits in animals. This may be a useful candidate marker in marker-assisted selection of yaks.

scholarly journals Copy Number Variation of TLR-7 Gene and its Association with the Development of Systemic Lupus Erythematosus in Female Patients from Yucatan Mexico

2014 ◽  
Vol 6 ◽  
pp. GEG.S16707 ◽  
Author(s):  
Guillermo Valencia Pacheco ◽  
Darig Cámara Cruz ◽  
Lizbeth J. González Herrera ◽  
Gerardo J. Pérez Mendoza ◽  
Guadalupe I. Adrián Amaro ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Copy Number Variation ◽  
Lupus Erythematosus ◽  
Copy Number ◽  
Target Genes ◽  
Quantitative Polymerase Chain Reaction ◽  
Systemic Autoimmune Disease ◽  
Systemic Lupus ◽  
Number Variation ◽  
Polymerase Chain

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by the production of autoantibodies against self-antigens, which occurs most often in women between 15 and 40 years of age. The innate immunity is involved in the pathogenesis of SLE through TLR-7. Genetic factors such as copy number variation (CNV) of target genes may contribute to disease development, but this possible risk has not yet been studied in SLE patients from Yucatan, Mexico. The CNV of TLR-7 gene was determined by quantitative polymerase chain reaction assay using TaqMan probes in 80 SLE women and 150 control subjects. The results showed that 10% of SLE patients exhibited more than two copies of TLR-7 gene, whereas no mRNA overexpression was detected. These data suggested that increased CNV of the TLR-7 gene in Yucatan SLE women can be a risk factor for this disease.

scholarly journals Direct evidence for the adaptive role of copy number variation on antifolate susceptibility inPlasmodium falciparum

2013 ◽  
Vol 88 (4) ◽  
pp. 702-712 ◽  
Author(s):  
Adina Heinberg ◽  
Edwin Siu ◽  
Chaya Stern ◽  
Elizabeth A. Lawrence ◽  
Michael T. Ferdig ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Direct Evidence ◽  
Number Variation ◽  
Adaptive Role

scholarly journals Genome-wide analysis of the role of copy-number variation in pancreatic cancer risk

2014 ◽  
Vol 5 ◽  
Author(s):  
Jason A. Willis ◽  
Semanti Mukherjee ◽  
Irene Orlow ◽  
Agnes Viale ◽  
Kenneth Offit ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Cancer Risk ◽  
Copy Number Variation ◽  
Copy Number ◽  
Genome Wide Analysis ◽  
Pancreatic Cancer Risk ◽  
Genome Wide ◽  
Number Variation

Role of rare germline copy number variation in melanoma-prone patients

2016 ◽  
Vol 12 (11) ◽  
pp. 1345-1357 ◽  
Author(s):  
Felipe Fidalgo ◽  
Tatiane Cristina Rodrigues ◽  
Amanda Gonçalves Silva ◽  
Luciana Facure ◽  
Bianca Costa Soares de Sá ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Number Variation
Sign in / Sign up

Export Citation Format

Share Document