Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds

Body size is an important trait in companion animals. Recently, a primitive Japanese dog breed, the Shiba Inu, has experienced artificial selection for smaller body size, resulting in the “Mame Shiba Inu” breed. To identify loci and genes that might explain the difference in the body size of these Shiba Inu dogs, we applied whole genome sequencing of pooled samples (pool-seq) on both Shiba Inu and Mame Shiba Inu. We identified a total of 13,618,261 unique SNPs in the genomes of these two breeds of dog. Using selective sweep approaches, including FST, Hp and XP-CLR with sliding windows, we identified a total of 12 genomic windows that show signatures of selection that overlap with nine genes (PRDM16, ZNF382, ZNF461, ERGIC2, ENSCAFG00000033351, CCDC61, ALDH3A2, ENSCAFG00000011141, and ENSCAFG00000018533). These results provide candidate genes and specific sites that might be associated with body size in dogs. Some of these genes are associated with body size in other mammals, but 8 of the 9 genes are novel candidate genes that need further study.

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Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting

BMC Genomics ◽

10.1186/s12864-020-6593-1 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Chun-Ji Li ◽

Die Zhao ◽

Bing-Xue Li ◽

Ning Zhang ◽

Jian-Yu Yan ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Candidate Genes ◽

Genome Sequencing ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Whole Genome ◽

Biotechnological Potential ◽

Red Yeast

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Enterobacter cloacae Complex Sequence Type 171 Isolates Expressing KPC-4 Carbapenemase Recovered from Canine Patients in Ohio

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01161-18 ◽

2018 ◽

Vol 62 (12) ◽

Cited By ~ 2

Author(s):

Joshua B. Daniels ◽

Liang Chen ◽

Susan V. Grooters ◽

Dixie F. Mollenkopf ◽

Dimitria A. Mathys ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Companion Animals ◽

Enterobacter Cloacae ◽

Sequence Type ◽

Resistant Bacteria ◽

Whole Genome ◽

Content Type ◽

Complex Sequence ◽

Enterobacter Cloacae Complex

ABSTRACT Companion animals are likely relevant in the transmission of antimicrobial-resistant bacteria. Enterobacter xiangfangensis sequence type 171 (ST171), a clone that has been implicated in clusters of infections in humans, was isolated from two dogs with clinical disease in Ohio. The canine isolates contained IncHI2 plasmids encoding blaKPC-4. Whole-genome sequencing was used to put the canine isolates in phylogenetic context with available human ST171 sequences, as well as to characterize their blaKPC-4 plasmids.

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Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

Genetics Selection Evolution ◽

10.1186/s12711-020-00553-7 ◽

2020 ◽

Vol 52 (1) ◽

Cited By ~ 1

Author(s):

Samuele Bovo ◽

Anisa Ribani ◽

Maria Muñoz ◽

Estefania Alves ◽

Jose P. Araujo ◽

...

Keyword(s):

Genetic Resources ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Production Systems ◽

Whole Genome ◽

Pig Breeds ◽

Signatures Of Selection ◽

Selection For

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iStopCancer: A database of 6,016 low pass whole genome sequencing of minimal invasive samples from 21 cancer types of Chinese population.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.7062 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. 7062-7062

Author(s):

Min Yuan ◽

Qian Ziliang ◽

Juemin Fang ◽

Zhongzheng Zhu ◽

Jianguo Wu ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Cancer Patients ◽

Genome Sequencing ◽

Minimal Invasive ◽

The Body ◽

Whole Genome Sequencing Data ◽

Low Grade ◽

Whole Genome ◽

Low Pass ◽

Low Coverage

7062 Background: Cancer is a group of genetic diseases that result from changes in the genome of cells in the body, leading them to grow uncontrollably. Recent researches suggest Chromosome instability (CIN), which is defined as an increased rate of chromosome gains and losses, manifests as cell-to-cell karyotypic heterogeneity and drives cancer initiation and evolution. Methods: In the past two years, we initiated iStopCancer project, and characterized 4515 ‘best available’ minimal-invasive samples from cancer patients and 1501 plasma samples from non-tumor diseases by using low-pass whole genome sequencing. DNA from ‘best available’ minimal-invasive samples, including peripheral plasma, urines, pancreatic juice, bile and effusions were analyzed by low coverage whole genome sequencing followed by the UCAD Bioinformatics workflow to characterize the CINs. In total, 32T bp nucleotide (coverage =1.7X for each sample) were collected. All the data can be visualized on website: http://www.istopcancer.net/pgweb/cn/istopcancer.jsp . Results: 3748(83%) of tumors present detectable CIN (CIN score>1000) in minimal-invasive samples. The missed cancer patients were majorly from patients with either tumor size less than 2cm or less-aggressive cancers, including thyroid cancer, low-grade urothelial carcinoma, lung cancer in-situ, et al. Of the 1501 non-tumor individuals, 30(2.0%) present detectable CIN (|Z|>=3) at the time of sample collection, 24(80.0%) was diagnosed as tumor patient in 3-6 months follow-up. There were 9 (0.59%) of non-cancer individuals without detectable CIN were also reported as tumor patients during 6-month following up. In summary, the positive and negative prediction value is 80.0% and 99.4% respectively. The false alarms were majorly from patients with EBV activations, which indicates virus may interference chromosome stability and drove virus-associated carcinogenesis. For the patient with repeated detections, plasma cfDNA CIN dynamics predicted clinical responses and disease recurrences. Quick clearance of plasma cfDNA CIN in 2-3 weeks was found in 153 (83.6%) patients. Meanwhile, no quick clearance was found in majority of SDs/PDs (73/88=83.0%). Furthermore, cfDNA CIN predicts clinical response 2-8 weeks ahead of traditional biomarkers (CEA, CA15-3, CA199, AFP et al). Conclusions: Large-scale low coverage whole genome sequencing data provides useful information for cancer detection and managements.

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Whole Genome Sequencing and Rare Variant Analysis in Essential Tremor Families

10.1101/248443 ◽

2018 ◽

Cited By ~ 1

Author(s):

Zagaa Odgerel ◽

Nora Hernandez ◽

Jemin Park ◽

Ruth Ottman ◽

Elan D. Louis ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Essential Tremor ◽

Candidate Genes ◽

Genome Sequencing ◽

Rare Variant ◽

Complex Disease ◽

Mixed Model ◽

Whole Genome ◽

Inheritance Patterns ◽

Disease Inheritance

ABSTRACTEssential tremor (ET) is one of the most common movement disorders. The etiology of ET remains largely unexplained. Whole genome sequencing (WGS) is likely to be of value in understanding a large proportion of ET with Mendelian and complex disease inheritance patterns. In ET families with Mendelian inheritance patterns, WGS may lead to gene identification where WES analysis failed to identify the causative variant due to incomplete coverage of the entire coding region of the genome. Alternatively, in ET families with complex disease inheritance patterns with gene x gene and gene x environment interactions enrichment of functional rare coding and non-coding variants may explain the heritability of ET. We performed WGS in eight ET families (n=40 individuals) enrolled in the Family Study of Essential Tremor. The analysis included filtering WGS data based on allele frequency in population databases, rare variant classification and association testing using the Mixed-Model Kernel Based Adaptive Cluster (MM-KBAC) test and prioritization of candidate genes identified within families using phenolyzer. WGS analysis identified candidate genes for ET in 5/8 (62.5%) of the families analyzed. WES analysis in a subset of these families in our previously published study failed to identify candidate genes. In one family, we identified a deleterious and damaging variant (c.1367G>A, p.(Arg456Gln)) in the candidate gene, CACNA1G, which encodes the pore forming subunit of T-type Ca(2+) channels, CaV3.1, and is expressed in various motor pathways and has been previously implicated in neuronal autorhythmicity and ET. Other candidate genes identified include SLIT3 (family D), which encodes an axon guidance molecule and in three families, phenolyzer prioritized genes that are associated with hereditary neuropathies (family A, KARS, family B, KIF5A and family F, NTRK1). This work has identified candidate genes and pathways for ET that can now be prioritized for functional studies.

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740. Elucidation of the Mode of Clostridioides difficile Transmission Based on One Health Approach

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab466.937 ◽

2021 ◽

Vol 8 (Supplement_1) ◽

pp. S468-S468

Author(s):

Sadako Yoshizawa ◽

Tomoka Sawa ◽

Kohji Komori ◽

Masakazu Sasaki ◽

Nobuaki Mori ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

One Health ◽

Companion Animals ◽

Living Environment ◽

Animal Origin ◽

Toxin Gene ◽

Whole Genome ◽

Mlst Analysis ◽

Clostridioides Difficile

Abstract Background Community-onset Clostridioides difficile (C. difficile) infection (CACDI) has been increasing in recent years. To explore the transmission route of CACDI, we performed the whole-genome sequencing of C. difficile isolated from CACDI patients and compared it to the isolates from livestock, companion animals, and soil. Methods From October 2020 until April 2021, fecal specimens of cattle, poultry, swine, felines, canines, CACDI patients, their families, and soil from the CACDI patients' living environment were applied for isolation of C.difficile. Whole-genome sequencing of C. difficile was performed on the MiSeq system (Illumina). Using the draft genome obtained from these analyses, the house-keeping gene (tpi), MLST, toxin genes (tcdA, tcdB, cdtA, cdtB), and resistance genes (gyrA, gyrB, rpoA, rpoB, rpoC) were comprehensively analyzed. Results As of March 31, 2021, 275 specimens were collected. Forty-five fecal specimens of companion animal origin (23 feline and 22 canines) were collected and the positive rate of C.difficile was 28.9% (2 felines, 11 canines). In MLST analysis, ST 15 (4 strains), ST 26 (2 strains), ST 42, ST 3, ST 28, ST 100, and ST 185 were detected in canines, and ST 203 and ST 297 strains were detected in felines. Samples of livestock origin were collected from 135 cattle, 41 poultries, and 20 swine. The detection rate in cattle was 11%, toxin-gene positivity was 60%. MLST analysis of 9 strains revealed ST 11 (5 strains), ST 2, ST 15, ST 58, and ST 101. No isolates were found from poultry or swine. Patient-derived strains of CACDI were collected from 14 patients at 2 sites. MLST analysis revealed ST42, ST37, ST100, and ST203(two isolates, respectively), ST 224, ST 81, ST 28, and ST 47. 2 isolates were unclassifiable. One case was a healthy 1-year-old girl, whose family revealed no isolation of C.difficile. Impressively, the soil in the parks (A and B) related to the child detected C.difficile from 4/4 samples (toxin-gene positivity; 75%) in Park A and 1/4 samples (toxin-gene positive) in Park B. MLST analysis demonstrated ST 42, the same as that in the affected child and core-genome single-nucleotide polymorphisms(SNPs) analysis suggested closely related strain. Conclusion Our results suggest one health approach is fundamental to prevent the transmission of C.difficile. Disclosures All Authors: No reported disclosures

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An oligogenic risk model for Gilles de la Tourette syndrome based on whole-genome sequencing data

10.1101/2021.12.09.21266782 ◽

2021 ◽

Author(s):

Malgorzata Borczyk ◽

Jakup P Fichna ◽

Marcin Piechota ◽

Sławomir Gołda ◽

Michał Korostyński ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Candidate Genes ◽

Tourette Syndrome ◽

Genome Sequencing ◽

Risk Model ◽

Neurodevelopmental Disorder ◽

Tic Disorders ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Pathogenic Variants

Gilles de la Tourette syndrome (GTS) is a neurodevelopmental disorder from the spectrum of tic disorders (TDs). GTS and other TDs have a substantial genetic component with the heritability estimated at between 60 and 80%. Here we propose an oligogenic risk model of GTS and other TDs using whole-genome sequencing (WGS) data from a group of Polish GTS patients and their families (n=185). The model is based on the overrepresentation of putatively pathogenic coding and non-coding genetic variants in genes selected from a set of 86 genes previously suggested to be associated with GTS. Based on the variant overrepresentation (SKAT test results) between unrelated GTS patients and controls based on gnomAD database allele frequencies five genes (HDC, CHADL, MAOA, NAA11, and PCDH10) were selected for the risk model. Putatively pathogenic variants (n = 98) with the median allele frequency of ~0.04 in and near these genes were used to build an additive classifier which was then validated on the GTS patients and their families. This risk model successfully assigned individuals from 22 families to either healthy or GTS groups (AUC-ROC = 0.6, p < 0.00001). These results were additionally validated using the GTS GWAS data from the Psychiatric Genomic Consortium. To investigate the GTS genetics further we identified 32 genes from the list of 86 genes as candidate genes in 14 multiplex families, including NEGR1 and NRXN with variants overrepresented in multiple families. WGS data allowed the construction of an oligogenic risk model of GTS based on possibly pathogenic variants likely contributing to the risk of GTS and TDs. The model includes putatively deleterious rare and non-coding variants in and near GTS candidate genes that may cooperatively contribute to GTS etiology and provides a novel approach to the analysis of clinical WGS data.

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Method comparison of targeted influenza A virus typing and whole-genome sequencing from respiratory specimens of companion animals

Journal of Veterinary Diagnostic Investigation ◽

10.1177/1040638720933875 ◽

2020 ◽

pp. 104063872093387

Author(s):

Patrick K. Mitchell ◽

Brittany D. Cronk ◽

Ian E. H. Voorhees ◽

Derek Rothenheber ◽

Renee R. Anderson ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Influenza A ◽

Sequence Data ◽

Companion Animals ◽

The United States ◽

Quality Data ◽

Whole Genome ◽

Influenza A Viruses ◽

Respiratory Specimens

Epidemics of H3N8 and H3N2 influenza A viruses (IAVs) in dogs, along with recognition of spillover infections from IAV strains typically found in humans or other animals, have emphasized the importance of efficient laboratory testing. Given the lack of active IAV surveillance or immunization requirements for dogs, cats, or horses imported into the United States, serotype prediction and whole-genome sequencing of positive specimens detected at veterinary diagnostic laboratories are also needed. The conserved sequences at the ends of the viral genome segments facilitate universal amplification of all segments of viral genomes directly from respiratory specimens. Although several methods for genomic analysis have been reported, no optimization focusing on companion animal strains has been described, to our knowledge. We compared 2 sets of published universal amplification primers using 26 IAV-positive specimens from dogs, horses, and a cat. Libraries prepared from the resulting amplicons were sequenced using Illumina chemistry, and reference-based assemblies were generated from the data produced by both methods. Although both methods produced high-quality data, coverage profiles and base calling differed between the 2 methods. The sequence data were also used to identify the subtype of the IAV strains sequenced and then compared to standard PCR assays for neuraminidase types N2 and N8.

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