Bovine Genome Database: new annotation tools for a new reference genome

Shamimuzzaman, Md.; Tourneau, J. J. Le; Unni, Deepak; Diesh, Colin; Triant, Deborah A.; Walsh, Amy T.; Tayal, Aditi; Conant, Gavin C.; Hagen, Darren E.; Elsik, Christine G.

doi:10.1093/nar/gkz944

Cited by 23 publications

(28 citation statements)

References 50 publications

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“…The information on the genomic architecture of the bovine immunoglobulin loci has been derived from work on European Bos taurus breeds, with the most complete genome assembly and associated resources deriving from a Hereford cow (31)(32)(33)(34). Immune gene loci tend to be highly repetitive by nature, and therefore difficult to accurately assemble without the use of resource-intensive sequencing technologies that enable accurate construction across large stretches of multiple and similar gene members-for example, long-read or chromatin-linking sequencing approaches.…”

Section: Genomic Organization Of Immunoglobulin Genes In the Cow And mentioning

confidence: 99%

Molecular Dissection of the Antibody Response: Opportunities and Needs for Application in Cattle

Barroso

Morrison

2020

Front. Immunol.

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Improving understanding of the bovine adaptive immune response would equip researchers to more efficiently design interventions against pathogens that impact upon food security and animal welfare. There are features of the bovine antibody response that differ substantially from other mammalian species, including the best understood models in the human and mouse. These include the ability to generate a functionally diverse immunoglobulin response despite having a fraction of the germline gene diversity that underpins this process in humans and mice, and the unique structure of a subset of immunoglobulins with "ultralong" HCDR3 domains, which are of significant interest with respect to potential therapeutics, including against human pathogens. However, a more detailed understanding of the B cell response and the production of an effective antibody response in the bovine is currently hampered by the lack of reagents for the B cell lineage. In this article we outline the current state of knowledge and capabilities with regard to B cell and antibody responses in cattle, highlight resource gaps, and summarize recent advances that have the potential to fundamentally advance our understanding of this process in the bovine host.

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Section: Genomic Organization Of Immunoglobulin Genes In the Cow And mentioning

confidence: 99%

Molecular Dissection of the Antibody Response: Opportunities and Needs for Application in Cattle

Barroso

Morrison

2020

Front. Immunol.

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“…Low quality (average phred quality <15) and single reads were removed resulting in ∼9.4 × 10 8 reads per sample. Final fastq files were aligned against bovine reference genome ARS-UCD1.2 with BWA-MEM, processed with Samtools v1.10 and resulting VCF files imported into SVS8.8.3 (Li and Durbin, 2009;Li, 2011;Shamimuzzaman et al, 2019;Rosen et al, 2020). Low-quality variant calls were filtered by genotype quality >0.8, read depth >10, and Alt read ratios (Ref_Ref <0.2, Ref_Alt inside 0.35 to 0.65 and Alt_Alt >0.8).…”

Section: Identification Of Candidate Variants By Whole Genome Resequementioning

confidence: 99%

Frameshift Variant in Novel Adenosine-A1-Receptor Homolog Associated With Bovine Spastic Syndrome/Late-Onset Bovine Spastic Paresis in Holstein Sires

et al. 2020

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Since their first description almost 100 years ago, bovine spastic paresis (BSP) and bovine spastic syndrome (BSS) are assumed to be inherited neuronal-progressive diseases in cattle. Affected animals are characterized by (frequent) spasms primarily located in the hind limbs, accompanied by severe pain symptoms and reduced vigor, thus initiating premature slaughter or euthanasia. Due to the late onset of BSP and BSS and the massively decreased lifespan of modern cattle, the importance of these diseases is underestimated. In the present study, BSP/BSS-affected German Holstein breeding sires from artificial insemination centers were collected and pedigree analysis, genome-wide association studies, whole genome resequencing, protein–protein interaction network analysis, and protein-homology modeling were performed to elucidate the genetic background. The analysis of 46 affected and 213 control cattle revealed four significantly associated positions on chromosome 15 (BTA15), i.e., AC_000172.1:g.83465449A>G (–log10P = 19.17), AC_000172.1:g.81871849C>T (–log10P = 8.31), AC_000172.1:g.81872621A>T (–log10P = 6.81), and AC_000172.1:g.81872661G>C (–log10P = 6.42). Two additional loci were significantly associated located on BTA8 and BTA19, i.e., AC_000165.1:g.71177788T>C and AC_000176.1:g.30140977T>G, respectively. Whole genome resequencing of five affected individuals and six unaffected relatives (two fathers, two mothers, a half sibling, and a full sibling) belonging to three different not directly related families was performed. After filtering, a homozygous loss of function variant was identified in the affected cattle, causing a frameshift in the so far unknown gene locus LOC100848076 encoding an adenosine-A1-receptor homolog. An allele frequency of the variant of 0.74 was determined in 3,093 samples of the 1000 Bull Genomes Project.

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“…RNA-seq data were obtained for adipose tissue samples of cattle-yak (N = 3), Qaidamford cattle (N = 3), and Angus cattle (N = 5). The reads were mapped against the cattle reference genome (UMD_3.1.1) [14] (https://bovinegenome.elsiklab.missouri.edu/). The number of total raw reads and the percentage of clean reads of each sample were determined and are listed in (Table S2).…”

Section: Characterization Of Bovine Adipose Tissue Transcriptome Sequmentioning

confidence: 99%

RNA-Seq Analysis Identifies Differentially Expressed Genes in Subcutaneous Adipose Tissue in Qaidaford Cattle, Cattle-Yak, and Angus Cattle

Huang

Song

et al. 2019

Animals

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In the beef industry, fat tissue is closely related to meat quality. In this study, high-throughput RNA sequencing was utilized for adipose tissue transcriptome analysis between cattle-yak, Qaidamford cattle, and Angus cattle. The screening and identification of differentially expressed genes (DEGs) between different breeds of cattle would facilitate cattle breeding. Compared to Angus cattle adipose tissue, a total of 4167 DEGs were identified in cattle-yak adipose tissue and 3269 DEGs were identified in Qaidamford cattle adipose tissue. Considering cattle-yak as a control group, 154 DEGs were identified in Qaidamford cattle adipose tissue. GO analysis indicated the significant enrichment of some DEGs related to lipid metabolism. The KEGG pathway database was also used to map DEGs and revealed that most annotated genes were involved in ECM-receptor interaction and the PI3K-Akt signal pathway, which are closely related to cell metabolism. Eight selected DEGs related to adipose tissue development or metabolism were verified by RT-qPCR, indicating the reliability of the RNA-seq data. The results of this comparative transcriptome analysis of adipose tissue and screening DEGs suggest several candidates for further investigations of meat quality in different cattle breeds.

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Bovine Genome Database: new annotation tools for a new reference genome

Cited by 23 publications

References 50 publications

Molecular Dissection of the Antibody Response: Opportunities and Needs for Application in Cattle

Molecular Dissection of the Antibody Response: Opportunities and Needs for Application in Cattle

Frameshift Variant in Novel Adenosine-A1-Receptor Homolog Associated With Bovine Spastic Syndrome/Late-Onset Bovine Spastic Paresis in Holstein Sires

RNA-Seq Analysis Identifies Differentially Expressed Genes in Subcutaneous Adipose Tissue in Qaidaford Cattle, Cattle-Yak, and Angus Cattle

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