Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo ( Bubalus bubalis ).

Animals Buffaloes / genetics DNA Copy Number Variations Genome Segmental Duplications, Genomic
Array Comparative Genomic Hybridization Bubalus bubalis Copy number variation Fluorescent in situ hybridization Quantitative PCR Segmental duplication

Journal

Functional & integrative genomics
ISSN: 1438-7948
Titre abrégé: Funct Integr Genomics
Pays: Germany
ID NLM: 100939343

Informations de publication

Date de publication:
May 2019
Historique:
received: 16 08 2018
accepted: 09 01 2019
revised: 13 12 2018
pubmed: 9 2 2019
medline: 28 7 2019
entrez: 9 2 2019
Statut: ppublish

Résumé

Duplicated sequences are an important source of gene evolution and structural variation within mammalian genomes. Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variations (CNVs) in the water buffalo (Bubalus bubalis). By aligning short reads of Olimpia (the reference water buffalo) to the UMD3.1 cattle genome, we identified 1,038 segmental duplications comprising 44.6 Mb (equivalent to ~1.73% of the cattle genome) of the autosomal and X chromosomal sequence in the buffalo genome. We experimentally validated 70.3% (71/101) of these duplications using fluorescent in situ hybridization. We also detected a total of 1,344 CNV regions across 14 additional water buffaloes, amounting to 59.8 Mb of variable sequence or the equivalent of 2.2% of the cattle genome. The CNV regions overlap 1,245 genes that are significantly enriched for specific biological functions including immune response, oxygen transport, sensory system and signal transduction. Additionally, we performed array Comparative Genomic Hybridization (aCGH) experiments using the 14 water buffaloes as test samples and Olimpia as the reference. Using a linear regression model, a high Pearson correlation (r = 0.781) was observed between the log

Identifiants

DOI: 10.1007/s10142-019-00657-4 PMID: 30734132
pubmed: 30734132
doi: 10.1007/s10142-019-00657-4
pii: 10.1007/s10142-019-00657-4
doi:

Types de publication

Journal Article

Langues

eng

Pagination

409-419

Subventions

Organisme : National Institute of Food and Agriculture
ID : 2013-67015-20951
Organisme : United States - Israel Binational Agricultural Research and Development Fund
ID : US-4997-17

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Auteurs

Shuli Liu (S)

USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA.
College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.

Xiaolong Kang (X)

USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA.
College of Agriculture, Ningxia University, Yinchuan, 750021, China.

Claudia R Catacchio (CR)

Department of Biology, University of Bari, 70126, Bari, Italy.

Mei Liu (M)

USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA.
College of Animal Science and Technology, Shaanxi Key Laboratory of Agricultural Molecular Biology, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Lingzhao Fang (L)

USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA.
Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, 20742, USA.

Steven G Schroeder (SG)

USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA.

Wenli Li (W)

The Cell Wall Utilization and Biology Laboratory, US Dairy Forage Research Center, USDA, ARS, Madison, WI 53706, USA.

Benjamin D Rosen (BD)

USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA.

Daniela Iamartino (D)

AIA-LGS, Associazione Italiana Allevatori - Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 (CR), Cremona, Italy.
Parco Tecnologico Padano, Via Einstein, Polo Universitario, 26900, Lodi, Italy.

Leopoldo Iannuzzi (L)

Laboratory of Animal Cytogenetics and Gene Mapping, Nationa Research Council (CNR), ISPAAM, Via Argine 1085, 80147, Naples, Italy.

Tad S Sonstegard (TS)

Recombinetics, 1246 University Ave W, St Paul, MN, 55104, USA.

Curtis P Van Tassell (CP)

USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA.

Mario Ventura (M)

Department of Biology, University of Bari, 70126, Bari, Italy.

Wai Yee Low (WY)

Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.

John L Williams (JL)

Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.

Derek M Bickhart (DM)

The Cell Wall Utilization and Biology Laboratory, US Dairy Forage Research Center, USDA, ARS, Madison, WI 53706, USA. Derek.Bickhart@ARS.USDA.GOV.

George E Liu (GE)

USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA. George.Liu@ARS.USDA.GOV.
ORCID: 0000-0003-0192-6705

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