Using sheep genomes from diverse U.S. breeds to identify missense variants in genes affecting fecundity

Heaton, Michael P.; Smith, Timothy P. L.; Freking, B. A.; Workman, Aspen M.; Bennett, G. L.; Carnahan, Jacky K.; Kalbfleisch, Theodore S.

doi:10.12688/f1000research.12216.1

Cited by 20 publications

(18 citation statements)

References 59 publications

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“…Since the role of host genetic variability in morbillivirus entry has not been fully characterized ( 11 ), especially with respect to nonsynonymous single nucleotide polymorphisms (nsSNPs) within SLAMF1, we generated variant SLAMF1 sequences for oSLAM and hSLAM, based on those known in sheep and human populations ( 31 , 32 ), and examined their capacity to support PPRV- and MeV-induced fusion ( Fig. 7 and 8 ).…”

Section: Resultsmentioning

confidence: 99%

Structure-Guided Identification of a Nonhuman Morbillivirus with Zoonotic Potential

Abdullah

Kelly

Graham

et al. 2018

J Virol

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A significant proportion of viral pandemics occur following zoonotic transmission events, where animal-associated viruses jump species into human populations. In order to provide forewarnings of the emergence of these viruses, it is necessary to develop a better understanding of what determines virus host range, often at the genetic and structural levels. In this study, we demonstrated that the small-ruminant morbillivirus, a close relative of measles, is unable to use human receptors to enter cells; however, a change of a single amino acid in the virus is sufficient to overcome this restriction. This information will be important for monitoring this virus’s evolution in the field. Of note, this study was undertaken in vitro, without generation of a fully infectious virus with this phenotype.

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Section: Resultsmentioning

confidence: 99%

Structure-Guided Identification of a Nonhuman Morbillivirus with Zoonotic Potential

Abdullah

Kelly

Graham

et al. 2018

J Virol

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“… Key: a Based on the observed linear relationship between aligned read depth (y) and total gigabases (Gb) of genomic sequence collected (x) with a quality score ≥ to 20, where y = 0.3x in cattle and sheep genomes 38 , 39 . b NCBI BioProject number 325061 c NCBI BioProject number 324822 d Not determined e NCBI BioProject number 324837 …”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

A SNP resource for studying North American moose

et al. 2018

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Background: Moose ( Alces alces) colonized the North American continent from Asia less than 15,000 years ago, and spread across the boreal forest regions of Canada and the northern United States (US). Contemporary populations have low genetic diversity, due either to low number of individuals in the original migration (founder effect), and/or subsequent population bottlenecks in North America. Genetic tests based on informative single nucleotide polymorphism (SNP) markers are helpful in forensic and wildlife conservation activities, but have been difficult to develop for moose, due to the lack of a reference genome assembly and whole genome sequence (WGS) data. Methods: WGS data were generated for four individual moose from the US states of Alaska, Idaho, Wyoming, and Vermont with minimum and average genome coverage depths of 14- and 19-fold, respectively. Cattle and sheep reference genomes were used for aligning sequence reads and identifying moose SNPs. Results: Approximately 11% and 9% of moose WGS reads aligned to cattle and sheep genomes, respectively. The reads clustered at genomic segments, where sequence identity between these species was greater than 95%. In these segments, average mapped read depth was approximately 19-fold. Sets of 46,005 and 36,934 high-confidence SNPs were identified from cattle and sheep comparisons, respectively, with 773 and 552 of those having minor allele frequency of 0.5 and conserved flanking sequences in all three species. Among the four moose, heterozygosity and allele sharing of SNP genotypes were consistent with decreasing levels of moose genetic diversity from west to east. A minimum set of 317 SNPs, informative across all four moose, was selected as a resource for future SNP assay design. Conclusions: All SNPs and associated information are available, without restriction, to support development of SNP-based tests for animal identification, parentage determination, and estimating relatedness in North American moose.

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“…For example if the sire was homozygous for allele A, the dam homozygous for allele B, and the progeny homozygous for B, in the absence of a genotyping error, this pattern suggests that the reported sire is not in fact the sire. We expect some genotyping errors [33,34] , but whatever exclusions are identified when analyzing the verifiable trio should be dwarfed in number when one of the actual parents is swapped in the analysis with an unrelated animal. For this comparison we did trio analysis of the yak × cattle offspring versus the reported Highland sire and yak dam as well as the reported dam versus four unrelated Highland bulls, and the reported sire versus an unrelated yak dam.…”

Section: Parentage Confirmationmentioning

confidence: 99%

Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid

Rice

Koren

Rhie

et al. 2019

Preprint

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words max)Background Assemblies of diploid genomes are generally unphased, pseudo-haploid representations that do not correctly reconstruct the two parental haplotypes present in the individual sequenced. Instead, the assembly alternates between parental haplotypes and may contain duplications in regions where the parental haplotypes are sufficiently different. Trio binning is an approach to genome assembly that uses short reads from both parents to classify long reads from the offspring according to maternal or paternal haplotype origin, and is thus helped rather than impeded by heterozygosity. Using this approach, it is possible to derive two assemblies from an individual, accurately representing both parental contributions in their entirety with higher continuity and accuracy than is possible with other methods. ResultsWe used trio binning to assemble reference genomes for two species from a single individual using an interspecies cross of yak ( Bos grunniens ) and cattle ( Bos taurus ). The high heterozygosity inherent to interspecies hybrids allowed us to confidently assign >99% of long reads from the F1 offspring to parental bins using unique k-mers from parental short reads. Both the maternal (yak) and paternal (cattle) assemblies contain over one third of the acrocentric chromosomes, including the two largest chromosomes, in single haplotigs.Conclusions These haplotigs are the first vertebrate chromosome arms to be assembled gap-free and fully phased, and the first time assemblies for two species have been created from a single individual. Both assemblies are the most continuous currently available for non-model vertebrates.

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Using sheep genomes from diverse U.S. breeds to identify missense variants in genes affecting fecundity

Cited by 20 publications

References 59 publications

Structure-Guided Identification of a Nonhuman Morbillivirus with Zoonotic Potential

Structure-Guided Identification of a Nonhuman Morbillivirus with Zoonotic Potential

A SNP resource for studying North American moose

Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid

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