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1. GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes

Author

Tuggle, Christopher, Giuffra, Elisabetta, White, Stephen, Clarke, Laura, Zhou, Huaijun, Ross, Pablo, Finno, Carrie, Acloque, H., Reecy, James, Archibald, Alan, Bellone ¶ ¶, Rebecca, Boichard, Michèle, Chamberlain, Amanda, Cheng, Hans, Crooijmans, Richard, Delany, Mary, Finno, Carrie J., Groenen, Martien, Hayes, Ben, Lunney, Joan, Petersen, Jessica, Plastow, Graham, Schmidt, Carl, Song, Jiuzhou, Watson, Mick, Iowa State University (ISU), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, USDA-ARS : Agricultural Research Service, Center for Reproductive Biology, Washington State University (WSU), Department of Veterinary Microbiology and Pathology, European Molecular Biology Laboratory, European Bioinformatics Institute, Department of Animal Science, University of California, Department of Population Health and Reproduction, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Department of Population Health and Reproduction, School of Veterinary Medicine, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Avian Disease and Oncology Laboratory, 4279 E Mount Hope Road, Animal Breeding and Genomics Centre, Wageningen University and Research [Wageningen] (WUR), Centre for Nutrition and Food Sciences - Queensland Alliance for Agriculture and Food Innovation, University of Southern Queensland (USQ), Animal Parasitic Diseases Laboratory [Beltsville, USA], United States Department of Agriculture (USDA)-USDA Agricultural Research Service [Beltsville, Maryland], USDA-ARS : Agricultural Research Service-USDA-ARS : Agricultural Research Service, Department of Agricultural, Food & Nutritional Science, University of Alberta, Department of Animal & Food Sciences, University of Delaware [Newark], Department of Animal and Avian Sciences, University of Maryland [College Park], University of Maryland System-University of Maryland System, National Science Foundation (NSF) NSF-IOS-1548275, United States Department of Agriculture (USDA) USDA-NIFA-AFRI, 2015-68004-24104, Illumina, Inc, Iowa State University, USDA-NRSP-8 Bioinformatics, United States Department of Agriculture (USDA) 2016-67015-24579, Genome Canada, Affymetrix, Inc, Geneseek, Inc, Biotechnology and Biological Sciences Research Council including Institute Strategic Programme and National Capability Grants (BBSRC) BBS/E/D/20310000 BB/J004243/1, INRA through the SelGen metaprogramme (Fr-AgENCODE project), Biotechnology and Biological Sciences Research Council (BBSRC) : BBS/E/D/20211551, BBS/E/D/20211550, BBS/E/D/20310000, BB/M01844X/1., United States Department of Agriculture (USDA), European Molecular Biology Laboratory European Bioinformatics Institute, University of California [Davis] (UC Davis), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT], Roslin Institute, Wageningen University and Research Centre (WUR), University of Queensland [Brisbane], Dept Anim & Food Sci, and University of Maryland System

Subjects
data coordination centre (DCC), Dairy & Animal Science, [SDV]Life Sciences [q-bio], International Cooperation, data sharing, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, dna, Animal Breeding and Genomics, metanalysis, genomic, Genetics, Animals, [INFO]Computer Science [cs], Fokkerij en Genomica, Veterinary Sciences, Domestic, [SDV.GEN]Life Sciences [q-bio]/Genetics, regulatory variation, Genome, Genomics, Articles, Congresses as Topic, Reference Standards, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, reveal principle, data coordination centre, Animals, Domestic, District of Columbia, WIAS, chromatin, Original Article, Zoology
Abstract

International audience; The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO-FAANG) Workshop in Washington, DC on October 7-8, 2015. This consortium is a grass-roots organization formed to advance the annotation of newly assembled genomes of domesticated and non-model organisms (www.faang.org). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org. In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO-FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta-data analysis standards were established.

Published
2016
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2. Algorithms predicting gestational stage from the maternal steroid metabolome of mares

Author

Alan J Conley, Paul R. Shorten, Pascale Chavatte-Palmer, Erin L. Legacki, AGRESEARCH RUAKURA RESEARCH CENTRE HAMILTON NZL, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Department of Population Health and Reproduction Davis, California, University of California [Davis] (UC Davis), University of California-University of California, Biologie de la Reproduction, Environnement, Epigénétique & Développement (BREED), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École nationale vétérinaire d'Alfort (ENVA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), and IFCE Foetalim Project

Subjects
endocrine system, Pregnancy Tests, Endocrinology, Diabetes and Metabolism, Population, Dehydroepiandrosterone, Datasets as Topic, 030209 endocrinology & metabolism, Gestational Age, Biology, progesterone, 03 medical and health sciences, 0302 clinical medicine, Endocrinology, Pregnancy, Tandem Mass Spectrometry, Prenatal Diagnosis, medicine, Animals, Horses, education, reproductive and urinary physiology, progestagens, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Fetus, education.field_of_study, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV.BA]Life Sciences [q-bio]/Animal biology, Gestational age, Models, Theoretical, medicine.disease, Breed, Gonadotropin secretion, horse, Metabolome, Gestation, Feasibility Studies, Pregnancy, Animal, Female, Steroids, Algorithm, Algorithms, Chromatography, Liquid
Abstract

Hormone secretion by the maternal ovaries, trophoblast/placenta and fetus occurs sequentially, creating distinct steroid metabolomic ‘signatures’ in systemic blood of pregnant mares that vary with gestational stage. Algorithms were developed to predict the gestational day (GD) from the maternal steroid metabolome (nine steroids; pregnenolone (P5), progesterone (P4), 5α-dihydroprogesterone (DHP), 17α-hydroxyprogesterone, allopregnanolone, 20α-hydroxy-DHP, 3β,20α-dihydroxy-DHP, DHEA and androstenedione) determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS) of eight thoroughbred mares sampled longitudinally throughout pregnancy. A physiologically based model was developed to infer rates of steroid secretion during chorionic gonadotropin secretion, the luteo-placental shift and by the equine feto-placenta unit, demonstrating more variability in P5 and DHP than P4. The average of four empirical models, using nine steroids to predict GD, was calibrated (five mares, R2 = 0.94, RMSE = 20 days) and validated (three mares, R2 = 0.84, RMSE = 32 days). Validation performance was improved using paired samples taken 14 or 30 days apart (RMSE = 29 and 19 days, respectively). A second validation used an independent dataset (single serum samples from 56 mixed breed mares, RMSE = 79 days) and an additional longitudinal subset from the same population sampled monthly throughout gestation (seven mares, RMSE = 42 days). Again, using paired samples improved model performance (RMSE = 32.5 days). Despite less predictive performance of the mixed breed than the thoroughbred datasets, these models demonstrate the feasibility and potential for using maternal steroid metabolomic algorithms to estimate the stage of gestation in pregnant mares and perhaps monitor fetal development.

Published
2021
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3. Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition

Author

Ian T. Fiddes, Carrie J. Finno, Michael S. DePriest, Alisa O. Vershinina, Jessica L. Petersen, Edward S. Rice, Richard E. Green, Rebecca R. Bellone, Douglas F. Antczak, Samantha A. Brooks, Nedda F. Saremi, Matthew S. Hestand, Ludovic Orlando, Brian P. Walenz, Theodore S. Kalbfleisch, Brendan O'Connell, James N. MacLeod, Molly E. McCue, Donald Miller, Joris Vermeesch, Ernest Bailey, Department of Population Health and Reproduction and the Veterinary Genetics Laboratory, University of California [Davis] (UC Davis), University of California-University of California, College of Veterinary Medicine, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Mathematics, University of Colorado, and University of Colorado [Boulder]

Subjects
[SDV]Life Sciences [q-bio], Contiguity, Medicine (miscellaneous), Genome informatics, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Bellone, Author Correction, lcsh:QH301-705.5, Composition (language), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, biology, Agriculture, Genomics, 16. Peace & justice, biology.organism_classification, lcsh:Biology (General), 030220 oncology & carcinogenesis, Next-generation sequencing, General Agricultural and Biological Sciences, Humanities, Reference genome
Abstract

Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of non-N bases in the incorporated chromosomes is improved from 2.33 Gb in EquCab2 to 2.41 Gb in EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5 Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold.

Published
2019
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4. Bartonella Endocarditis

Author

Renaud Maillard, Jennifer B. Henn, Cathy V. Williams, Ricardo G. Maggi, Henri-Jean Boulouis, Edward B. Breitschwerdt, Rickie W. Kasten, Bruno B Chomel, Jonna A. K. Mazet, Sebastian E. Carrasco, Aaron C. Wey, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Animal Surgical and Emergency Center, Partenaires INRAE, Upstate Veterinary Specialties, Napa County, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), University of California [Davis] (UC Davis), Unité mixte de recherche biologie moléculaire et immunologie parasitaires et fongiques, Agence Française de Sécurité Sanitaire des Aliments (AFSSA)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), École nationale vétérinaire d'Alfort (ENVA), University of California (UC), Agence Française de Sécurité Sanitaire des Aliments (AFSSA)-École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), and École nationale vétérinaire - Alfort (ENVA)

Subjects
Male, Bartonella, Bartonella koehlerae, Disease reservoir, Pathology, medicine.medical_specialty, 040301 veterinary sciences, [SDV]Life Sciences [q-bio], CATTLE, Cattle Diseases, Animals, Wild, Cat Diseases, General Biochemistry, Genetics and Molecular Biology, 0403 veterinary science, 03 medical and health sciences, History and Philosophy of Science, Bartonella Infections, Zoonoses, ENDOCARDITIS, CATS, medicine, Animals, Humans, Endocarditis, Natural reservoir, Dog Diseases, Disease Reservoirs, 0303 health sciences, Bartonella vinsonii, biology, 030306 microbiology, Myocardium, General Neuroscience, Heart, Cat-scratch disease, 04 agricultural and veterinary sciences, bacterial infections and mycoses, medicine.disease, biology.organism_classification, 3. Good health, DOGS, BARTONELLA, Bartonella quintana, Female, RESERVOIR
Abstract

National audience; Bartonellae were first recognized to cause endocarditis in humans in 1993 when cases caused by Bartonella quintana, B. elizabethae, and B. henselae were reported. Since the first isolation of Bartonella vinsonii subspecies berkhoffii from a dog with endocarditis, this organism has emerged as an important pathogen in dogs and an emerging pathogen in people. Subsequently, four types of B. vinsonii subsp. berkhoffii have been described, all of which have been associated with endocarditis in dogs. A limited number of dog endocarditis cases have also been associated with B. clarridgeiae, B. washoensis, B. quintana, and B. rochalimae. The second canine B. clarridgeiae endocarditis case is presented. The clinical and pathological characteristics of Bartonella endocarditis in dogs are similar to disease observed in humans, more often affecting the aortic valve, presenting with highly vegetative lesions with accompanying calcification, and in most instances high antibody titers. Pathological features in dogs include a combination of fibrosis, mineralization, endothelial proliferation, and neovascularization with variable inflammation. Endocarditis has also been described in animal species, which are the natural reservoir of specific Bartonella species, once thought to be solely healthy carriers of these pathogens. A few Bartonella endocarditis cases, including B. henselae, have been reported in cats in the USA and Australia. The second case of B. henselae type Houston I identified in the USA is presented. Furthermore, two cases of B. bovis endocarditis were recently described in adult cows from France. Finally, on-going investigation of valvular endocarditis in free-ranging Alaskan sea otters suggests the involvement of Bartonella species.

Published
2009
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5. Clinical Impact of PersistentBartonellaBacteremia in Humans and Animals

Author

Jane E. Sykes, Rickie W. Kasten, Edward B. Breitschwerdt, Henri Jean Boulouis, Bruno B Chomel, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California (UC), University of California [Davis] (UC Davis), Unité mixte de recherche biologie moléculaire et immunologie parasitaires et fongiques, Agence Française de Sécurité Sanitaire des Aliments (AFSSA)-École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Department of Clinical Sciences, College of Veterinary Medicine, Cornell University [New York], University of California, and Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Agence Française de Sécurité Sanitaire des Aliments (AFSSA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)

Subjects
Bartonella, BACTEREMIA, 040301 veterinary sciences, [SDV]Life Sciences [q-bio], Animals, Wild, Rodentia, Biology, Cat Diseases, Asymptomatic, General Biochemistry, Genetics and Molecular Biology, Rodent Diseases, 0403 veterinary science, 03 medical and health sciences, Dogs, History and Philosophy of Science, Bartonella Infections, medicine, Animals, Humans, Endocarditis, VECTOR-BORNE PATHOGENS, Natural reservoir, Dog Diseases, 0303 health sciences, 030306 microbiology, General Neuroscience, 04 agricultural and veterinary sciences, bacterial infections and mycoses, Bacillary angiomatosis, medicine.disease, biology.organism_classification, United States, Bacillary peliosis, 3. Good health, Chronic infection, BARTONELLA, Bacteremia, Immunology, Cats, medicine.symptom
Abstract

Part III. Clinical Aspects and Diagnostics; International audience; Bartonella spp. are emerging vector-borne pathogens that cause persistent, often asymptomatic bacteremia in their natural hosts. As our knowledge progresses, it appears that chronic infection may actually predispose the host to mild, insidious nonspecific manifestations or induce, in selected instances, severe diseases. Persistent asymptomatic bacteremia is most common in animals that serve as the main reservoir for the specific Bartonella. In humans, these organisms are B. bacilliformis and B. quintana. Other Bartonella species, for which humans are not the natural reservoir, tend to cause persistent bacteremia only in immunodeficient individuals. In some of these individuals, endothelial cell proliferation may create lesions such as bacillary angiomatosis or bacillary peliosis. In cats, bacteremia of variable level and continuity may last for years. Some strains of B. henselae may induce clinical manifestations, including fever, mild neurological signs, reproductive disorders, whereas others do not induce clinically obvious disease. Reproductive disorders have also been reported in mice experimentally infected with B. birtlesii. Finally, canids constitute the most interesting naturally occurring animal model for the human disease. Like immunocompetent people, healthy dogs only occasionally demonstrate long-term bacteremia when infected with Bartonella spp. However, some dogs develop severe clinical manifestations, such as endocarditis, and the pathologic spectrum associated with Bartonella spp., infection in domestic dogs is rapidly expanding and resembles the infrequently reported clinical entities observed in humans. In coyotes, persistent bacteremia is more common than in domestic dogs. It will,be of interest to determine if coyotes develop clinical or pathological indications of infection.

Published
2003
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