1
|
Axelsson E, Ljungvall I, Bhoumik P, Conn LB, Muren E, Ohlsson Å, Olsen LH, Engdahl K, Hagman R, Hanson J, Kryvokhyzha D, Pettersson M, Grenet O, Moggs J, Rio-Espinola AD, Epe C, Taillon B, Tawari N, Mane S, Hawkins T, Hedhammar Å, Gruet P, Häggström J, Lindblad-Toh K. Correction: The genetic consequences of dog breed formation—Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels. PLoS Genet 2022; 18:e1010039. [PMID: 35085237 PMCID: PMC8794096 DOI: 10.1371/journal.pgen.1010039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
2
|
Axelsson E, Ljungvall I, Bhoumik P, Conn LB, Muren E, Ohlsson Å, Olsen LH, Engdahl K, Hagman R, Hanson J, Kryvokhyzha D, Pettersson M, Grenet O, Moggs J, Del Rio-Espinola A, Epe C, Taillon B, Tawari N, Mane S, Hawkins T, Hedhammar Å, Gruet P, Häggström J, Lindblad-Toh K. The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels. PLoS Genet 2021; 17:e1009726. [PMID: 34473707 PMCID: PMC8412370 DOI: 10.1371/journal.pgen.1009726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a ~10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs–the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heart-derived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity. As a consequence of selective breeding, specific disease-causing mutations have become more frequent in certain dog breeds. Whether the breeding practice also resulted in a general increase in the overall number of disease-causing mutations per dog genome is however not clear. To address this question, we compare the amount of harmful, potentially disease-causing, mutations in dogs from eight common breeds that have experienced varying degrees of intense selective breeding. We find that individuals belonging to the breed affected by the most intense breeding—cavalier King Charles spaniel (cKCs)—carry more harmful variants than other breeds, indicating that past breeding practices may have increased the overall levels of harmful genetic variation in dogs. The most common disease in cKCs is myxomatous mitral valve disease (MMVD). To identify variants linked to this disease we next characterize mutations that are common in cKCs, but rare in other breeds, and then investigate if these mutations can predict MMVD in dachshunds. We find that variants that regulate the expression of the gene NEBL in papillary muscles may increase the risk of the disease, indicating that loss of papillary muscle integrity could contribute to the development of MMVD.
Collapse
Affiliation(s)
- Erik Axelsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Ingrid Ljungvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Priyasma Bhoumik
- Translational Medicine, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Laura Bas Conn
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Eva Muren
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Åsa Ohlsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lisbeth Høier Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karolina Engdahl
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ragnvi Hagman
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jeanette Hanson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Dmytro Kryvokhyzha
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mats Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Olivier Grenet
- Translational Medicine, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Jonathan Moggs
- Translational Medicine, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Christian Epe
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Bruce Taillon
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Nilesh Tawari
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Shrinivas Mane
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Troy Hawkins
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Åke Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| |
Collapse
|
3
|
Fletcher SP, Chin DJ, Ji Y, Iniguez AL, Taillon B, Swinney DC, Ravindran P, Cheng DT, Bitter H, Lopatin U, Ma H, Klumpp K, Menne S. Transcriptomic analysis of the woodchuck model of chronic hepatitis B. Hepatology 2012; 56:820-30. [PMID: 22431061 PMCID: PMC3401284 DOI: 10.1002/hep.25730] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 03/06/2012] [Indexed: 01/03/2023]
Abstract
UNLABELLED The Eastern woodchuck (Marmota monax) is naturally infected with woodchuck hepatitis virus (WHV), a hepadnavirus closely related to the human hepatitis B virus (HBV). The woodchuck is used as an animal model for studying chronic hepatitis B (CHB) and HBV-associated hepatocellular carcinoma (HCC) in humans, but the lack of sequence information has hitherto precluded functional genomics analysis. To address this major limitation of the model, we report here the sequencing, assembly, and annotation of the woodchuck transcriptome, together with the generation of custom woodchuck microarrays. Using this new platform, we characterized the transcriptional response to persistent WHV infection and WHV-induced HCC. This revealed that chronic WHV infection, like HBV, is associated with (1) a limited intrahepatic type I interferon response; (2) intrahepatic induction of markers associated with T cell exhaustion; (3) elevated levels of suppressor of cytokine signaling 3 (SOCS3) in the liver; and (4) intrahepatic accumulation of neutrophils. Underscoring the translational value of the woodchuck model, this study also determined that WHV-induced HCC shares molecular characteristics with a subtype of human HCC with poor prognosis. CONCLUSION Our data establish the translational value of the woodchuck model and provide new insight into immune pathways which may play a role either in the persistence of HBV infection or the sequelae of CHB.
Collapse
Affiliation(s)
- Simon P. Fletcher
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Daniel J. Chin
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Yongmei Ji
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | | | - Bruce Taillon
- 454 Life Sciences, A Roche Company, 1 Commercial Street, Branford, CT 06457, USA
| | - David C. Swinney
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | | | - Donavan T. Cheng
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Hans Bitter
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Uri Lopatin
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Han Ma
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Klaus Klumpp
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Stephan Menne
- Georgetown University Medical Center, Department of Microbiology & Immunology, Medical-Dental Building, Room C 301, 3900 Reservoir Road, Washington, DC 20057, USA
| |
Collapse
|
4
|
Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti D, Macalma T, Facci M, Mitchell JT, Perazzolli M, Eldredge G, Gatto P, Oyzerski R, Moretto M, Gutin N, Stefanini M, Chen Y, Segala C, Davenport C, Demattè L, Mraz A, Battilana J, Stormo K, Costa F, Tao Q, Si-Ammour A, Harkins T, Lackey A, Perbost C, Taillon B, Stella A, Solovyev V, Fawcett JA, Sterck L, Vandepoele K, Grando SM, Toppo S, Moser C, Lanchbury J, Bogden R, Skolnick M, Sgaramella V, Bhatnagar SK, Fontana P, Gutin A, Van de Peer Y, Salamini F, Viola R. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One 2007; 2:e1326. [PMID: 18094749 PMCID: PMC2147077 DOI: 10.1371/journal.pone.0001326] [Citation(s) in RCA: 579] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 11/21/2007] [Indexed: 01/11/2023] Open
Abstract
Background Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented. Principal Findings We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before). Conclusions Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape.
Collapse
|