Annotated Draft Genome Assemblies for the Northern Bobwhite (<i>Colinus virginianus</i>) and the Scaled Quail (<i>Callipepla squamata</i>) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size

Oldeschulte, David L.; Halley, Yvette A.; Wilson, Miranda L.; Bhattarai, Eric K.; Brashear, Wesley; Hill, Joshua A.; Metz, Richard P.; Johnson, Charles D.; Rollins, Dale; Peterson, Markus J.; Bickhart, Derek M.; Decker, Jared E.; Sewell, John F.; Seabury, Christopher M.

doi:10.1534/g3.117.043083

Cited by 24 publications

(24 citation statements)

References 110 publications

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“…All trimmed reads were mapped to the WTD genome assembly (GCF_002102435.1 Ovir.te_1.0; https://www.ncbi.nlm.nih.gov/assembly/GCF_002102435.1/) using the CLC Genomics Workbench 10.1.1 reference mapping algorithm (Seabury et al 2011;Halley et al 2014;Halley et al 2015;Sollars et al 2017). Variant prediction was performed using a probabilistic approach implemented within CLC Genomics Workbench 10.1.1 (Halley et al 2014;Halley et al 2015;Oldeschulte et al 2017;Sollars et al 2017). This algorithm estimates error probabilities from quality scores, and uses these probabilities to determine the most likely allele combination per nucleotide position, thus facilitating a user-specified minimum probability threshold (P $ 0.95) for variant prediction, and variant quality scores (Halley et al 2014;Halley et al 2015;Oldeschulte et al 2017;Sollars et al 2017).…”

Section: Reduced Representation Libraries and Sequencingmentioning

confidence: 99%

“…Variant prediction was performed using a probabilistic approach implemented within CLC Genomics Workbench 10.1.1 (Halley et al 2014;Halley et al 2015;Oldeschulte et al 2017;Sollars et al 2017). This algorithm estimates error probabilities from quality scores, and uses these probabilities to determine the most likely allele combination per nucleotide position, thus facilitating a user-specified minimum probability threshold (P $ 0.95) for variant prediction, and variant quality scores (Halley et al 2014;Halley et al 2015;Oldeschulte et al 2017;Sollars et al 2017). Additional variant prediction parameters and filters were similar to those recently described (Seabury et al 2011;Oldeschulte et al 2017), and the probabilistic approach produced evidence for 6,268,706 variants, which included 5,561,550 putative SNPs (P $ 0.95; Minor Allele Frequency $ 0.01).…”

Section: Reduced Representation Libraries and Sequencingmentioning

confidence: 99%

“…This algorithm estimates error probabilities from quality scores, and uses these probabilities to determine the most likely allele combination per nucleotide position, thus facilitating a user-specified minimum probability threshold (P $ 0.95) for variant prediction, and variant quality scores (Halley et al 2014;Halley et al 2015;Oldeschulte et al 2017;Sollars et al 2017). Additional variant prediction parameters and filters were similar to those recently described (Seabury et al 2011;Oldeschulte et al 2017), and the probabilistic approach produced evidence for 6,268,706 variants, which included 5,561,550 putative SNPs (P $ 0.95; Minor Allele Frequency $ 0.01). Variant prediction results were exported from CLC as a single variant call formatted file (VCF), which was used for SNP array design.…”

Section: Reduced Representation Libraries and Sequencingmentioning

confidence: 99%

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Accurate Genomic Predictions for Chronic Wasting Disease in U.S. White-Tailed Deer

Seabury

Oldeschulte

Bhattarai

et al. 2020

G3 Genes|Genomes|Genetics

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The geographic expansion of chronic wasting disease (CWD) in U.S. white-tailed deer (Odocoileus virginianus) has been largely unabated by best management practices, diagnostic surveillance, and depopulation of positive herds. Using a custom Affymetrix Axiom single nucleotide polymorphism (SNP) array, we demonstrate that both differential susceptibility to CWD, and natural variation in disease progression, are moderately to highly heritable (h 2 ¼ 0:337 6 0:079 ─ 0:637 6 0:070Þ among farmed U.S. white-tailed deer, and that loci other than PRNP are involved. Genome-wide association analyses using 123,987 quality filtered SNPs for a geographically diverse cohort of 807 farmed U.S. white-tailed deer (n = 284 CWD positive; n = 523 CWD non-detect) confirmed the prion gene (PRNP; G96S) as a largeeffect risk locus (P-value , 6.3E-11), as evidenced by the estimated proportion of phenotypic variance explained (PVE $ 0.05), but also demonstrated that more phenotypic variance was collectively explained by loci other than PRNP. Genomic best linear unbiased prediction (GBLUP; n = 123,987 SNPs) with k-fold cross validation (k = 3; k = 5) and random sampling (n = 50 iterations) for the same cohort of 807 farmed U.S. whitetailed deer produced mean genomic prediction accuracies $ 0.81; thereby providing the necessary foundation for exploring a genomically-estimated CWD eradication program.

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Section: Reduced Representation Libraries and Sequencingmentioning

confidence: 99%

Section: Reduced Representation Libraries and Sequencingmentioning

confidence: 99%

Section: Reduced Representation Libraries and Sequencingmentioning

confidence: 99%

See 1 more Smart Citation

Accurate Genomic Predictions for Chronic Wasting Disease in U.S. White-Tailed Deer

Seabury

Oldeschulte

Bhattarai

et al. 2020

G3 Genes|Genomes|Genetics

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“…Available C. virginianus and P. catodon assemblies were analysed with BlobToolKit to determine the presence of Apicomplexan-assigned scaffolds in these assemblies (Table 3). A total of 48 Mb of the 1.2Gb (4%) of the C. virginianus assembly AWGT02 (GCA_000599465.2 (Oldeschulte et al 2017) ) is inferred to be derived from an apicomplexan parasite. For P. catodon , the only published assembly, AWZP01 (GCA_000472045.1 (Warren et al 2017) ) is inferred to be free of contamination with sequences of apicomplexan origin.…”

Section: Identification Of Mis-annotated Records In Public Databasesmentioning

confidence: 99%

BlobToolKit – Interactive quality assessment of genome assemblies

Challis

Richards

Ragan

et al. 2019

Preprint

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Reconstruction of target genomes from sequence data produced by instruments that are agnostic as to the species-of-origin may be confounded by contaminant DNA. Whether introduced during sample processing or through co-extraction alongside the target DNA, if insufficient care is taken during the assembly process, the final assembled genome may be a mixture of data from several species. Such assemblies can confound sequence-based biological inference and, when deposited in public databases, may be included in downstream analyses by users unaware of underlying problems.We present BlobToolKit, a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. BlobToolKit can be used to process assembly, read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility.We have been running an automated BlobToolKit pipeline on eukaryotic assemblies publicly available in the International Nucleotide Sequence Data Collaboration and are making the results available through a public instance of the Viewer at https://blobtoolkit.genomehubs.org/view. We aim to complete analysis of all publicly available genomes and then maintain currency with the flow of new genomes. We have worked to embed these views into the presentation of genome assemblies at the European Nucleotide Archive, providing an indication of assembly quality alongside the public record with links out to allow full exploration in the Viewer.

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“…lumpy-sv VCF files were converted to BEDPE format using the vcfToBedpe script included in the lumpy-sv software package. Copy number estimates for genomic segments were calculated from normalized WGS read depth using JaRMS v0.0.13 as previously described 57 . As JaRMS estimates of genomic copy number are distributed around a value of "1" as the normal diploid copy number count, we multiplied the "levels" estimates from the JaRMS program by two to receive the adjusted copy number state of genomic regions.…”

Section: Structural Variant and Copy Number Variant Analysesmentioning

confidence: 99%

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

Tearle

et al. 2019

Preprint

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We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosomelevel genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. The very high quality of the assemblies from both sub-species enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought. MainAbout 10,000 years ago, cattle were domesticated from the aurochs which ranged across Eurasia and North Africa but are now extinct 1 . Modern day cattle belong to two subspecies, the humped zebu or indicine breeds (Bos taurus indicus) and the humpless taurine breeds (Bos taurus taurus), which arose from independent domestication events of genetically distinct aurochs populations 2 .During the last century, taurine breeds have been intensively selected for production traits, particularly milk and/or meat yield and quality, and generally have higher fertility than indicine breeds. European taurine breeds, such as Angus, have excellent carcass and meat quality, high fertility, and reach puberty early. These breeds have been imported by farmers around the world to improve or replace less-productive breeds. However, while European taurine animals are well adapted to temperate environments, they do not thrive and perform in hot, humid tropical environments with high disease and parasite burden.Indicine breeds originate from the Indus valley and later spread to Africa and across southeast Asia 3 . Between 1854 and 1926, the four indicine breeds, Ongole, Krishna, Gir and Gujarat, were imported into the United States and crossed with European taurine cattle to create the Brahman breed. Current US Brahman cattle retain ~10% of their genome of taurine origin 4 . Brahman have short, thick, glossy coat that reflects sunlight and loose skin that increases the body surface area exposed for cooling. While the Brahman are less productive and have lower fertility than taurine breeds, they have desirable traits, such as heat tolerance, and lower susceptibility to parasites such as ticks, and are disease and drought resistant 5 .We previously demonstrated a novel trio binning approach to assemble haplotypes of diploid individuals at the contig level. The quality of the contigs exceeded those of the best livestock reference genomes 6 . Here we present chromosome-level taurine (Angus) and indicine (Brahman) cattle ge...

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Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size

Cited by 24 publications

References 110 publications

Accurate Genomic Predictions for Chronic Wasting Disease in U.S. White-Tailed Deer

Accurate Genomic Predictions for Chronic Wasting Disease in U.S. White-Tailed Deer

BlobToolKit – Interactive quality assessment of genome assemblies

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

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