ArticleBMC genomics2009
Analysis of recent segmental duplications in the bovine genome.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 101 citations in OpenAlex.
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- Structural variations in livestock genomes and their associations with phenotypic traits: a review.Frontiers in veterinary science · 2024Review
- Descriptive Statistics and Genome-Wide Copy Number Analysis of Milk Production Traits of Jiangsu Chinese Holstein Cows.Animals : an open access journal from MDPI · 2023Article
- Genomic structural variation: A complex but important driver of human evolution.American journal of biological anthropology · 2023Review
- Evolutionary trend of bovine β-defensin proteins toward functionality prediction: A domain-based bioinformatics study.Heliyon · 2023Article
- In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants.Genetics, selection, evolution : GSE · 2023Review
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- Towards the detection of copy number variation from single sperm sequencing in cattle.BMC genomics · 2022Article
- Comparative Genomic Characterization of Insulin-Like Growth Factor Binding Proteins in Cattle and Buffalo.BioMed research international · 2022Article
- Comparative Genomic Characterization of Relaxin Peptide Family in Cattle and Buffalo.BioMed research international · 2022Article
- Genomic Identification, Evolution, and Expression Analysis of Bromodomain Genes Family in Buffalo.Genes · 2022Article
- An atlas of CNV maps in cattle, goat and sheep.Science China. Life sciences · 2021Article
- Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids.BMC genomics · 2021Article
- Investigating the impact of reference assembly choice on genomic analyses in a cattle breed.BMC genomics · 2021Article
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- Genome-Wide Detection of CNVs and Association With Body Weight in Sheep Based on 600K SNP Arrays.Frontiers in genetics · 2020Article
- Accurate sequence variant genotyping in cattle using variation-aware genome graphs.Genetics, selection, evolution : GSE · 2019Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 5 institutions in 2 countries.
Funding
Abstract
backgroundDuplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. We performed the first systematic and genome-wide analysis of segmental duplications in the modern domesticated cattle (Bos taurus). Using two distinct computational analyses, we estimated that 3.1% (94.4 Mb) of the bovine genome consists of recently duplicated sequences (>or= 1 kb in length, >or= 90% sequence identity). Similar to other mammalian draft assemblies, almost half (47% of 94.4 Mb) of these sequences have not been assigned to cattle chromosomes.
resultsIn this study, we provide the first experimental validation large duplications and briefly compared their distribution on two independent bovine genome assemblies using fluorescent in situ hybridization (FISH). Our analyses suggest that the (75-90%) of segmental duplications are organized into local tandem duplication clusters. Along with rodents and carnivores, these results now confidently establish tandem duplications as the most likely mammalian archetypical organization, in contrast to humans and great ape species which show a preponderance of interspersed duplications. A cross-species survey of duplicated genes and gene families indicated that duplication, positive selection and gene conversion have shaped primates, rodents, carnivores and ruminants to different degrees for their speciation and adaptation. We identified that bovine segmental duplications corresponding to genes are significantly enriched for specific biological functions such as immunity, digestion, lactation and reproduction.
conclusionOur results suggest that in most mammalian lineages segmental duplications are organized in a tandem configuration. Segmental duplications remain problematic for genome and assembly and we highlight genic regions that require higher quality sequence characterization. This study provides insights into mammalian genome evolution and generates a valuable resource for cattle genomics research.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.