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Ahern DT, Bansal P, Faustino IV, Glatt-Deeley HR, Massey R, Kondaveeti Y, Banda EC, Pinter SF. Isogenic hiPSC models of Turner syndrome development reveal shared roles of inactive X and Y in the human cranial neural crest network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.08.531747. [PMID: 36945647 PMCID: PMC10028916 DOI: 10.1101/2023.03.08.531747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Modeling the developmental etiology of viable human aneuploidy can be challenging in rodents due to syntenic boundaries, or primate-specific biology. In humans, monosomy-X (45,X) causes Turner syndrome (TS), altering craniofacial, skeletal, endocrine, and cardiovascular development, which in contrast remain unaffected in 39,X-mice. To learn how human monosomy-X may impact early embryonic development, we turned to human 45,X and isogenic euploid induced pluripotent stem cells (hiPSCs) from male and female mosaic donors. Because neural crest (NC) derived cell types are hypothesized to underpin craniofacial and cardiovascular changes in TS, we performed a highly-powered differential expression study on hiPSC-derived anterior neural crest cells (NCCs). Across three independent isogenic panels, 45,X NCCs show impaired acquisition of PAX7+SOX10+ markers, and disrupted expression of other NCC-specific genes, relative to their isogenic euploid controls. In particular, 45,X NCCs increase cholesterol biosynthesis genes while reducing transcripts that feature 5' terminal oligopyrimidine (TOP) motifs, including those of ribosomal protein and nuclear-encoded mitochondrial genes. Such metabolic pathways are also over-represented in weighted co-expression gene modules that are preserved in monogenic neurocristopathy. Importantly, these gene modules are also significantly enriched in 28% of all TS-associated terms of the human phenotype ontology. Our analysis identifies specific sex-linked genes that are expressed from two copies in euploid males and females alike and qualify as candidate haploinsufficient drivers of TS phenotypes in NC-derived lineages. This study demonstrates that isogenic hiPSC-derived NCC panels representing monosomy-X can serve as a powerful model of early NC development in TS and inform new hypotheses towards its etiology.
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Affiliation(s)
- Darcy T. Ahern
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Prakhar Bansal
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Isaac V. Faustino
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Heather R. Glatt-Deeley
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Rachael Massey
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
| | - Yuvabharath Kondaveeti
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Erin C. Banda
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
| | - Stefan F. Pinter
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
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2
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Xu L, Ren Y, Wu J, Cui T, Dong R, Huang C, Feng Z, Zhang T, Yang P, Yuan J, Xu X, Liu J, Wang J, Chen W, Mi D, Irwin DM, Yan Y, Xu L, Yu X, Li G. Evolution and expression patterns of the neo-sex chromosomes of the crested ibis. Nat Commun 2024; 15:1670. [PMID: 38395916 PMCID: PMC10891136 DOI: 10.1038/s41467-024-46052-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Bird sex chromosomes play a unique role in sex-determination, and affect the sexual morphology and behavior of bird species. Core waterbirds, a major clade of birds, share the common characteristics of being sexually monomorphic and having lower levels of inter-sexual conflict, yet their sex chromosome evolution remains poorly understood. Here, by we analyse of a chromosome-level assembly of a female crested ibis (Nipponia nippon), a typical core waterbird. We identify neo-sex chromosomes resulting from fusion of microchromosomes with ancient sex chromosomes. These fusion events likely occurred following the divergence of Threskiornithidae and Ardeidae. The neo-W chromosome of the crested ibis exhibits the characteristics of slow degradation, which is reflected in its retention of abundant gametologous genes. Neo-W chromosome genes display an apparent ovary-biased gene expression, which is largely driven by genes that are retained on the crested ibis W chromosome but lost in other bird species. These results provide new insights into the evolutionary history and expression patterns for the sex chromosomes of bird species.
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Affiliation(s)
- Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yandong Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiahong Wu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China
| | - Tingting Cui
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Rong Dong
- Research Center for Qinling Giant Panda, Shaanxi Academy of Forestry, Xi'an, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Zhe Feng
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Tianmin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiao Liu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Wu Chen
- Guangzhou Wildlife Research Center, Guangzhou Zoo, Guangzhou, China
| | - Da Mi
- Xi'an Haorui Genomics Technology Co., LTD, Xi'an, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Yaping Yan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Luohao Xu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China.
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
- Guangzhou Wildlife Research Center, Guangzhou Zoo, Guangzhou, China.
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3
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Chiu ES, McDonald CA, Gagne RB, Dunkleberger H, Moxcey M, VandeWoude S. Endogenous feline leukemia virus long terminal repeat integration site diversity is highly variable in related and unrelated domestic cats. Retrovirology 2024; 21:3. [PMID: 38347535 PMCID: PMC10863107 DOI: 10.1186/s12977-024-00635-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 01/30/2024] [Indexed: 02/15/2024] Open
Abstract
Endogenous retroviruses (ERV) are indicators of vertebrate evolutionary history and play important roles as homeostatic regulators. ERV long terminal repeat (LTR) elements may act as cis-activating promoters or trans-activating enhancer elements modifying gene transcription distant from LTR insertion sites. We previously documented that endogenous feline leukemia virus (FeLV)-LTR copy number variation in individual cats tracks inversely with susceptibility to virulent FeLV disease. To evaluate FeLV-LTR insertion characteristics, we assessed enFeLV-LTR integration site diversity in 20 cats from three genetically distinct populations using a baited linker-mediated PCR approach. We documented 765 individual integration sites unequally represented among individuals. Only three LTR integration sites were shared among all individuals, while 412 sites were unique to a single individual. When primary fibroblast cultures were challenged with exogenous FeLV, we found significantly increased expression of both exogenous and endogenous FeLV orthologs, supporting previous findings of potential exFeLV-enFeLV interactions; however, viral challenge did not elicit transcriptional changes in genes associated with the vast majority of integration sites. This study assesses FeLV-LTR integration sites in individual animals, providing unique transposome genotypes. Further, we document substantial individual variation in LTR integration site locations, even in a highly inbred population, and provide a framework for understanding potential endogenous retroviral element position influence on host gene transcription.
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Affiliation(s)
- Elliott S Chiu
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Coby A McDonald
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Roderick B Gagne
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Henry Dunkleberger
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | | | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, 80523, USA.
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vonHoldt BM, Stahler DR, Brzeski KE, Musiani M, Peterson R, Phillips M, Stephenson J, Laudon K, Meredith E, Vucetich JA, Leonard JA, Wayne RK. Demographic history shapes North American gray wolf genomic diversity and informs species' conservation. Mol Ecol 2024; 33:e17231. [PMID: 38054561 DOI: 10.1111/mec.17231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023]
Abstract
Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, grey wolves in the northern Rocky Mountains have lower genomic diversity than wolves of the western Great Lakes and have declined over time. Effective population size estimates revealed the historical signatures of continental efforts of predator extermination, despite a quarter century of recovery efforts. We are the first to provide molecular estimates of effective population size across distinct grey wolf populations in North America, which ranged between Ne ~ 275 and 3050 since early 1980s. We provide data that inform managers regarding the status and importance of effective population size estimates for grey wolf conservation, which are on average 5.2-9.3% of census estimates for this species. We show that while grey wolves fall above minimum effective population sizes needed to avoid extinction due to inbreeding depression in the short term, they are below sizes predicted to be necessary to avoid long-term risk of extinction.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, Wyoming, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Marco Musiani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Bologna, Italy
| | - Rolf Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Kent Laudon
- California Department of Fish and Wildlife, Northern Region, Redding, California, USA
| | - Erin Meredith
- California Department of Fish and Wildlife, Wildlife Forensic Laboratory, Sacramento, California, USA
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
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5
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Jevit MJ, Castaneda C, Paria N, Das PJ, Miller D, Antczak DF, Kalbfleisch TS, Davis BW, Raudsepp T. Trio-binning of a hinny refines the comparative organization of the horse and donkey X chromosomes and reveals novel species-specific features. Sci Rep 2023; 13:20180. [PMID: 37978222 PMCID: PMC10656420 DOI: 10.1038/s41598-023-47583-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
We generated single haplotype assemblies from a hinny hybrid which significantly improved the gapless contiguity for horse and donkey autosomal genomes and the X chromosomes. We added over 15 Mb of missing sequence to both X chromosomes, 60 Mb to donkey autosomes and corrected numerous errors in donkey and some in horse reference genomes. We resolved functionally important X-linked repeats: the DXZ4 macrosatellite and ampliconic Equine Testis Specific Transcript Y7 (ETSTY7). We pinpointed the location of the pseudoautosomal boundaries (PAB) and determined the size of the horse (1.8 Mb) and donkey (1.88 Mb) pseudoautosomal regions (PARs). We discovered distinct differences in horse and donkey PABs: a testis-expressed gene, XKR3Y, spans horse PAB with exons1-2 located in Y and exon3 in the X-Y PAR, whereas the donkey XKR3Y is Y-specific. DXZ4 had a similar ~ 8 kb monomer in both species with 10 copies in horse and 20 in donkey. We assigned hundreds of copies of ETSTY7, a sequence horizontally transferred from Parascaris and massively amplified in equids, to horse and donkey X chromosomes and three autosomes. The findings and products contribute to molecular studies of equid biology and advance research on X-linked conditions, sex chromosome regulation and evolution in equids.
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Affiliation(s)
- Matthew J Jevit
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Caitlin Castaneda
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Nandina Paria
- Texas Scottish Rite Hospital for Children, Dallas, TX, 75219, USA
| | - Pranab J Das
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Donald Miller
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, 14853, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, 14853, USA
| | - Theodore S Kalbfleisch
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Brian W Davis
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
| | - Terje Raudsepp
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
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6
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The Trinh S, Nguyen NN, Thi Thu Le H, Thi My Pham H, Tien Trieu S, Tran NTM, Sy Ho H, Van Tran D, Van Trinh T, Trong Hoang Nguyen H, Pham Minh N, Duc Dang T, Huu Dinh V, Thi Doan H. Screening Y Chromosome Microdeletion in 1121 Men with Low Sperm Concentration and the Outcomes of Microdissection Testicular Sperm Extraction (mTESE) for Sperm Retrieval from Azoospermic Patients. Appl Clin Genet 2023; 16:155-164. [PMID: 37663123 PMCID: PMC10473397 DOI: 10.2147/tacg.s420030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
Background The Y chromosome has a specific region, namely the Azoospermia Factor (AZF) because azoospermia is typically reported in the microdeletion of the AZF region. This study aims to assess the characteristics of AZF microdeletion after screening a massive number of low sperm concentration men; and the Microdissection testicular sperm extraction (mTESE) outcomes for retrieving sperm from azoospermic patients. Materials and Methods This retrospective multiple-center study enrolled a total of 1121 men with azoospermia, cryptozoospermia, and severe oligozoospermia from December 2016 to June 2022. An extension analysis used a total of 17 STSs to detect the position-occurring microdeletion in the AZF region (AZFa, b, c, and/or d loci). Microdissection testicular sperm extraction (mTESE) was performed to retrieve sperm in azoospermic men diagnosed AZFc microdeletion. Results One hundred and fifty-three men carried AZF microdeletion were detected in the 1121 participants (13.64%). The incidences of AZF microdeletion were confined to AZF a, c, and d regions, both individual and concurrence, with the most common in the AZFc region accounting for 49.67%; There was no significant difference in clinical and paraclinical characteristics between the deleted regions, except FSH level (highest in AZFa microdeletion, p = 0.043). The AZFc region was the most common type of AZF microdeletion (49.67%), including complete microdeletion (4 patients) and gr/gr partial microdeletion (39 patients) with 50.00% and 63.63% in the success rate of mTESE, separately. Conclusion The absence of AZFa and/or AZFb regions often express the most severe phenotype - azoospermia and the increasing FSH level. The AZFc region played the most common microdeletion. Microdissection testicular sperm extraction (mTESE) was the possible therapy for sperm retrieval from the testis of azoospermia men having AZFc microdeletion.
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Affiliation(s)
- Son The Trinh
- Military Institute of Clinical Embryology and Histology, Vietnam Military Medical University, Hanoi, Vietnam
| | - Nhat Ngoc Nguyen
- Military Institute of Clinical Embryology and Histology, Vietnam Military Medical University, Hanoi, Vietnam
| | - Hien Thi Thu Le
- Department of Andrology, Andrology and Fertility Hospital of Hanoi, Hanoi, Vietnam
| | - Hanh Thi My Pham
- Department of Andrology, Andrology and Fertility Hospital of Hanoi, Hanoi, Vietnam
| | - Sang Tien Trieu
- Department of Biology and Genetics, Vietnam Military Medical University, Hanoi, Vietnam
| | - Ngoc Thao My Tran
- Department of Life Sciences, Biosciences Division, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Hung Sy Ho
- Department of Obstetrics and Gynecology, Hanoi Medical University, Hanoi, Vietnam
| | - Danh Van Tran
- Respiratory Center, Military Hospital 103, Vietnam Military Medical University, Hanoi, Vietnam
| | - Tam Van Trinh
- Department of Andrology, Andrology and Fertility Hospital of Hanoi, Hanoi, Vietnam
| | | | - Ngoc Pham Minh
- Department of Andrology, Andrology and Fertility Hospital of Hanoi, Hanoi, Vietnam
| | - Trinh Duc Dang
- Faculty of Mathematics and Computer Science, Vietnam Military Medical University, Hanoi, Vietnam
| | - Viet Huu Dinh
- Department of Andrology, Andrology and Fertility Hospital of Hanoi, Hanoi, Vietnam
| | - Hang Thi Doan
- Military Institute of Clinical Embryology and Histology, Vietnam Military Medical University, Hanoi, Vietnam
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7
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Meadows JRS, Kidd JM, Wang GD, Parker HG, Schall PZ, Bianchi M, Christmas MJ, Bougiouri K, Buckley RM, Hitte C, Nguyen AK, Wang C, Jagannathan V, Niskanen JE, Frantz LAF, Arumilli M, Hundi S, Lindblad-Toh K, Ginja C, Agustina KK, André C, Boyko AR, Davis BW, Drögemüller M, Feng XY, Gkagkavouzis K, Iliopoulos G, Harris AC, Hytönen MK, Kalthoff DC, Liu YH, Lymberakis P, Poulakakis N, Pires AE, Racimo F, Ramos-Almodovar F, Savolainen P, Venetsani S, Tammen I, Triantafyllidis A, vonHoldt B, Wayne RK, Larson G, Nicholas FW, Lohi H, Leeb T, Zhang YP, Ostrander EA. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biol 2023; 24:187. [PMID: 37582787 PMCID: PMC10426128 DOI: 10.1186/s13059-023-03023-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/25/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. RESULTS We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. CONCLUSIONS We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
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Affiliation(s)
- Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA.
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Katia Bougiouri
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Christophe Hitte
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Julia E Niskanen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Laurent A F Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E14NS, UK and Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, D-80539, Munich, Germany
| | - Meharji Arumilli
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Sruthi Hundi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catarina Ginja
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | | | - Catherine André
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Xin-Yao Feng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Konstantinos Gkagkavouzis
- Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Giorgos Iliopoulos
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Alexander C Harris
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Daniela C Kalthoff
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Petros Lymberakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Nikolaos Poulakakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | - Fernando Racimo
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | | | - Peter Savolainen
- Department of Gene Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, 17121, Solna, Sweden
| | - Semina Venetsani
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Imke Tammen
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Alexandros Triantafyllidis
- Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-7246, USA
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3TG, UK
| | - Frank W Nicholas
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA.
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8
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Tancredi D, Cardinali I. Being a Dog: A Review of the Domestication Process. Genes (Basel) 2023; 14:genes14050992. [PMID: 37239352 DOI: 10.3390/genes14050992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The process of canine domestication represents certainly one of the most interesting questions that evolutionary biology aims to address. A "multiphase" view of this process is now accepted, with a first phase during which different groups of wolves were attracted by the anthropogenic niche and a second phase characterized by the gradual establishment of mutual relationships between wolves and humans. Here, we provide a review of dog (Canis familiaris) domestication, highlighting the ecological differences between dogs and wolves, analyzing the molecular mechanisms which seem to have influenced the affiliative behaviors first observed in Belyaev's foxes, and describing the genetics of ancient European dogs. Then, we focus on three Mediterranean peninsulas (Balkan, Iberian and Italian), which together represent the main geographic area for studying canine domestication dynamics, as it has shaped the current genetic variability of dog populations, and where a well-defined European genetic structure was pinpointed through the analysis of uniparental genetic markers and their phylogeny.
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Affiliation(s)
- Domenico Tancredi
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
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9
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Recovery of a marine keystone predator transforms terrestrial predator-prey dynamics. Proc Natl Acad Sci U S A 2023; 120:e2209037120. [PMID: 36689656 PMCID: PMC9945949 DOI: 10.1073/pnas.2209037120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Sea otters (Enhydra lutris) and wolves (Canis lupus) are two apex predators with strong and cascading effects on ecosystem structure and function. After decades of recovery from near extirpation, their ranges now overlap, allowing sea otters and wolves to interact for the first time in the scientific record. We intensively studied wolves during 2015 to 2021 in an island system colonized by sea otters in the 2000s and by wolves in 2013. After wolf colonization, we quantified shifts in foraging behavior with DNA metabarcoding of 689 wolf scats and stable isotope analyses, both revealing a dietary switch from Sitka black-tailed deer (Odocoileus hemionus), the terrestrial in situ primary prey, to sea otters. Here we show an unexpected result of the reintroduction and restoration of sea otters, which became an abundant marine subsidy for wolves following population recovery. The availability of sea otters allowed wolves to persist and continue to reproduce, subsequently nearly eliminating deer. Genotypes from 390 wolf scats and telemetry data from 13 wolves confirmed island fidelity constituting one of the highest known wolf population densities and upending standardly accepted wolf density predictions based on ungulate abundance. Whereas marine subsidies in other systems are generally derived from lower trophic levels, here an apex nearshore predator became a key prey species and linked nearshore and terrestrial food webs in a recently deglaciated and rapidly changing ecosystem. These results underscore that species restoration may serve as an unanticipated nutrient pathway for recipient ecosystems even resulting in cross-boundary subsidy cascades.
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10
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Loss of Mitochondrial Genetic Diversity despite Population Growth: The Legacy of Past Wolf Population Declines. Genes (Basel) 2022; 14:genes14010075. [PMID: 36672816 PMCID: PMC9858670 DOI: 10.3390/genes14010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/28/2022] Open
Abstract
Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers have significantly increased and then stabilized in recent decades. We analyzed mitochondrial genomes from 54 historical specimens of Iberian wolves from across their historical range using ancient DNA methods. We compared historical and current mitochondrial diversity in Iberian wolves at the 5' end of the control region (n = 17 and 27) and the whole mitochondrial genome excluding the control region (n = 19 and 29). Despite an increase in population size since the 1970s, genetic diversity declined. We identified 10 whole mitochondrial DNA haplotypes in 19 historical specimens, whereas only six of them were observed in 29 modern Iberian wolves. Moreover, a haplotype that was restricted to the southern part of the distribution has gone extinct. Our results illustrate a lag between demographic and genetic diversity changes, and show that after severe population declines, genetic diversity can continue to be lost in stable or even expanding populations. This suggests that such populations may be of conservation concern even after their demographic trajectory has been reversed.
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11
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Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity. Genes (Basel) 2022; 13:genes13122272. [PMID: 36553539 PMCID: PMC9777570 DOI: 10.3390/genes13122272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Anna Tommasi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | | | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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12
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Castaneda C, Radović L, Felkel S, Juras R, Davis BW, Cothran EG, Wallner B, Raudsepp T. Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups. G3 (BETHESDA, MD.) 2022; 12:jkac278. [PMID: 36227030 PMCID: PMC9713435 DOI: 10.1093/g3journal/jkac278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/08/2022] [Indexed: 11/03/2023]
Abstract
Structural rearrangements like copy number variations in the male-specific Y chromosome have been associated with male fertility phenotypes in human and mouse but have been sparsely studied in other mammalian species. Here, we designed digital droplet PCR assays for 7 horse male-specific Y chromosome multicopy genes and SRY and evaluated their absolute copy numbers in 209 normal male horses of 22 breeds, 73 XY horses with disorders of sex development and/or infertility, 5 Przewalski's horses and 2 kulans. This established baseline copy number for these genes in horses. The TSPY gene showed the highest copy number and was the most copy number variable between individuals and breeds. SRY was a single-copy gene in most horses but had 2-3 copies in some indigenous breeds. Since SRY is flanked by 2 copies of RBMY, their copy number variations were interrelated and may lead to SRY-negative XY disorders of sex development. The Przewalski's horse and kulan had 1 copy of SRY and RBMY. TSPY and ETSTY2 showed significant copy number variations between cryptorchid and normal males (P < 0.05). No significant copy number variations were observed in subfertile/infertile males. Notably, copy number of TSPY and ETSTY5 differed between successive male generations and between cloned horses, indicating germline and somatic mechanisms for copy number variations. We observed no correlation between male-specific Y chromosome gene copy number variations and male-specific Y chromosome haplotypes. We conclude that the ampliconic male-specific Y chromosome reference assembly has deficiencies and further studies with an improved male-specific Y chromosome assembly are needed to determine selective constraints over horse male-specific Y chromosome gene copy number and their relation to stallion reproduction and male biology.
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Affiliation(s)
- Caitlin Castaneda
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Lara Radović
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Sabine Felkel
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Department of Biotechnology, Institute of Computational Biology, BOKU University of Life Sciences and Natural Resources, Vienna 1190, Austria
| | - Rytis Juras
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Ernest Gus Cothran
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Barbara Wallner
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
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13
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Kopania EEK, Watson EM, Rathje CC, Skinner BM, Ellis PJI, Larson EL, Good JM. The contribution of sex chromosome conflict to disrupted spermatogenesis in hybrid house mice. Genetics 2022; 222:iyac151. [PMID: 36194004 PMCID: PMC9713461 DOI: 10.1093/genetics/iyac151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/27/2022] [Indexed: 12/13/2022] Open
Abstract
Incompatibilities on the sex chromosomes are important in the evolution of hybrid male sterility, but the evolutionary forces underlying this phenomenon are unclear. House mice (Mus musculus) lineages have provided powerful models for understanding the genetic basis of hybrid male sterility. X chromosome-autosome interactions cause strong incompatibilities in M. musculus F1 hybrids, but variation in sterility phenotypes suggests a more complex genetic basis. In addition, XY chromosome conflict has resulted in rapid expansions of ampliconic genes with dosage-dependent expression that is essential to spermatogenesis. Here, we evaluated the contribution of XY lineage mismatch to male fertility and stage-specific gene expression in hybrid mice. We performed backcrosses between two house mouse subspecies to generate reciprocal Y-introgression strains and used these strains to test the effects of XY mismatch in hybrids. Our transcriptome analyses of sorted spermatid cells revealed widespread overexpression of the X chromosome in sterile F1 hybrids independent of Y chromosome subspecies origin. Thus, postmeiotic overexpression of the X chromosome in sterile F1 mouse hybrids is likely a downstream consequence of disrupted meiotic X-inactivation rather than XY gene copy number imbalance. Y chromosome introgression did result in subfertility phenotypes and disrupted expression of several autosomal genes in mice with an otherwise nonhybrid genomic background, suggesting that Y-linked incompatibilities contribute to reproductive barriers, but likely not as a direct consequence of XY conflict. Collectively, these findings suggest that rapid sex chromosome gene family evolution driven by genomic conflict has not resulted in strong male reproductive barriers between these subspecies of house mice.
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Affiliation(s)
- Emily E K Kopania
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Eleanor M Watson
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Claudia C Rathje
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | | | - Peter J I Ellis
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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14
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vonHoldt BM, Brzeski KE, Aardema ML, Schell CJ, Rutledge LY, Fain SR, Shutt AC, Linderholm A, Murphy WJ. Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast. Mol Ecol 2022; 31:5440-5454. [PMID: 34585803 DOI: 10.1111/mec.16200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022]
Abstract
Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographical and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 120,621 single nucleotiode polymorphism (SNP) loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along a west-to-east gradient across the southern United States associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographical zone where the last red wolves were known prior to extinction in the wild, contained the highest and oldest levels of red wolf ancestry. Further, given the paucity of inferences based on chromosome types, we compared patterns of ancestry on the X chromosome and autosomes. We additionally aimed to explore the relationship between admixture timing and recombination rate variation to investigate gene flow events. We found that X-linked regions of low recombination rates were depleted of introgression, relative to the autosomes, consistent with the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographical and genomic extent of cryptic red wolf ancestry can provide novel genomic resources for recovery plans targeting the conservation of the endangered red wolf.
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Affiliation(s)
- Bridgett M vonHoldt
- Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, Michigan, USA
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, New Jersey, USA.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
| | - Linda Y Rutledge
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Steven R Fain
- USFWS, Clark R. Bavin National Forensics Laboratory, Ashland, Oregon, USA
| | | | - Anna Linderholm
- Department of Anthropology, Texas A&M University, College Station, Texas, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
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15
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Stachowiak M, Szczerbal I, Nowacka-Woszuk J, Nowak T, Sowinska N, Lukomska A, Gogulski M, Badura M, Sklorz-Mencel K, Jagodka D, Nizanski W, Dzimira S, Switonski M. Cytogenetic and molecular insight into the genetic background of disorders of sex development in seventeen cats. Sci Rep 2022; 12:17807. [PMID: 36280698 PMCID: PMC9592617 DOI: 10.1038/s41598-022-21718-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/30/2022] [Indexed: 01/19/2023] Open
Abstract
The genetic background of feline disorders of sex development (DSDs) is poorly understood. We performed comprehensive cytogenetic, molecular, and histological studies of 17 cats with abnormal external genitalia, unusual behavior, or tricolor coats (atypical in males). The DSD phenotype of three cats was associated with sex chromosome abnormalities: X/Y translocation (38,XXSRY+), 37,X/38,XY mosaicism, and XX/XY leukocyte chimerism. The remaining 14 affected cats were classified as XY DSD (SRY-positive). In this group and 38 normal males, we analyzed a priori selected candidate genes (SRY, TAC3, CYP11B1 and LHCGR). Only a previously reported nonpathogenic variant was found in SRY. Moreover, SRY gene copy number was determined, and three variants were observed: 6, 5 (modal), and 4 copies in a single DSD case. The known variants in TAC3 and CYP11B1, responsible for testicular hypoplasia, persistent primary dentition or congenital adrenal hyperplasia, were not found in the study group. Nine novel polymorphisms were identified in the LHCGR gene, one of which, a potentially regulatory indel variant in 5'UTR, was significantly associated (p = 0.0467) with XY DSD. Our report confirmed that abnormalities of sex chromosomes are important causes of feline DSDs. We also showed that the indel variant of LHCGR can be considered a promising marker associated with XY DSD phenotype.
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Affiliation(s)
- Monika Stachowiak
- grid.410688.30000 0001 2157 4669Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Izabela Szczerbal
- grid.410688.30000 0001 2157 4669Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Joanna Nowacka-Woszuk
- grid.410688.30000 0001 2157 4669Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Tomasz Nowak
- grid.410688.30000 0001 2157 4669Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Natalia Sowinska
- grid.410688.30000 0001 2157 4669Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Anna Lukomska
- grid.410688.30000 0001 2157 4669Department of Preclinical Sciences and Infectious Diseases, Poznan University of Life Sciences, Poznan, Poland
| | - Maciej Gogulski
- grid.410688.30000 0001 2157 4669Department of Preclinical Sciences and Infectious Diseases, Poznan University of Life Sciences, Poznan, Poland ,grid.424906.d0000 0000 9858 6214Centre of Biosciences, Institute of Animal Physiology, Kosice, Slovakia ,grid.410688.30000 0001 2157 4669University Centre for Veterinary Medicine, Poznan University of Life Sciences, Poznan, Poland
| | - Malgorzata Badura
- grid.410688.30000 0001 2157 4669Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | | | | | - Wojciech Nizanski
- grid.411200.60000 0001 0694 6014Department of Reproduction and Clinic of Farm Animals, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Stanislaw Dzimira
- grid.411200.60000 0001 0694 6014Department of Pathology, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Marek Switonski
- grid.410688.30000 0001 2157 4669Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
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16
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Coyotes in New York City Carry Variable Genomic Dog Ancestry and Influence Their Interactions with Humans. Genes (Basel) 2022; 13:genes13091661. [PMID: 36140828 PMCID: PMC9498729 DOI: 10.3390/genes13091661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Coyotes are ubiquitous on the North American landscape as a result of their recent expansion across the continent. They have been documented in the heart of some of the most urbanized cities, such as Chicago, Los Angeles, and New York City. Here, we explored the genomic composition of 16 coyotes in the New York metropolitan area to investigate genomic demography and admixture for urban-dwelling canids in Queens County, New York. We identified moderate-to-high estimates of relatedness among coyotes living in Queens (r = 0.0–0.5) and adjacent neighborhoods, suggestive of a relatively small population. Although we found low background levels of domestic-dog ancestry across most coyotes in our sample (5%), we identified a male suspected to be a first-generation coyote–dog hybrid with 46% dog ancestry, as well as his two putative backcrossed offspring that carried approximately 25% dog ancestry. The male coyote–dog hybrid and one backcrossed offspring each carried two transposable element insertions that are associated with human-directed hypersociability in dogs and gray wolves. An additional, unrelated coyote with little dog ancestry also carried two of these insertions. These genetic patterns suggest that gene flow from domestic dogs may become an increasingly important consideration as coyotes continue to inhabit metropolitan regions.
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17
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Armstrong EE, Perry BW, Huang Y, Garimella KV, Jansen HT, Robbins CT, Tucker NR, Kelley JL. A beary good genome: Haplotype-resolved, chromosome-level assembly of the brown bear (Ursus arctos). Genome Biol Evol 2022; 14:6656105. [PMID: 35929770 PMCID: PMC9447482 DOI: 10.1093/gbe/evac125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2022] [Indexed: 11/30/2022] Open
Abstract
The brown bear (Ursus arctos) is the second largest and most widespread extant terrestrial carnivore on Earth and has recently emerged as a medical model for human metabolic diseases. Here, we report a fully phased chromosome-level assembly of a male North American brown bear built by combining Pacific Biosciences (PacBio) HiFi data and publicly available Hi-C data. The final genome size is 2.47 Gigabases (Gb) with a scaffold and contig N50 length of 70.08 and 43.94 Megabases (Mb), respectively. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis revealed that 94.5% of single copy orthologs from Mammalia were present in the genome (the highest of any ursid genome to date). Repetitive elements accounted for 44.48% of the genome and a total of 20,480 protein coding genes were identified. Based on whole genome alignment to the polar bear, the brown bear is highly syntenic with the polar bear, and our phylogenetic analysis of 7,246 single-copy orthologs supports the currently proposed species tree for Ursidae. This highly contiguous genome assembly will support future research on both the evolutionary history of the bear family and the physiological mechanisms behind hibernation, the latter of which has broad medical implications.
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Affiliation(s)
- Ellie E Armstrong
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Yongqing Huang
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kiran V Garimella
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heiko T Jansen
- Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, 99164, USA
| | - Charles T Robbins
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.,School of the Environment, Washington State University, Pullman, WA, 99164, USA
| | - Nathan R Tucker
- Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA.,Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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18
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Schwartz R, Sugai NJ, Eden K, Castaneda C, Jevit M, Raudsepp T, Cecere JT. Case Report: Disorder of Sexual Development in a Chinese Crested Dog With XX/XY Leukocyte Chimerism and Mixed Cell Testicular Tumors. Front Vet Sci 2022; 9:937991. [PMID: 35898552 PMCID: PMC9309221 DOI: 10.3389/fvets.2022.937991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
A 10-year-old intact female Chinese Crested dog was presented for evaluation and further diagnostics due to persistent symptoms of vulvar swelling, vaginal discharge, and an 8-year history of acyclicity. At presentation, generalized hyperpigmentation and truncal alopecia were identified, with no aberrations of the female phenotype. Vaginal cytology confirmed the influence of estrogen at multiple veterinary visits, and hormonal screening of progesterone and anti-Mullerian hormone indicated gonadal presence. Based on findings from abdominal laparotomy and gonadectomy, the tissue was submitted for histopathology. Histopathologic evaluation identified the gonads to be abnormal testes containing multiple Sertoli and interstitial (Leydig) cell tumors. The histopathologic diagnosis of testes and concurrent normal external female phenotype in the patient lead to a diagnosis of a disorder of sexual development (DSD). Karyotype evaluation by conventional and molecular analysis revealed a two cell line chimeric pattern of 78,XX (80%) and 78,XY (20%) among blood leukocytes, as well as a positive PCR test for the Y-linked SRY gene. Cytogenetic analysis of skin fibroblasts revealed the presence of 78,XX cells exclusively, and PCR tests for the Y-linked SRY gene were negative in the hair and skin samples. These results are consistent with an XX/XY blood chimerism. This is one of the few case reports of a canine with the diagnosis of leukocyte chimerism with normal female phenotypic external genitalia. This case illustrates a distinct presentation for hormonally active Sertoli cell tumorigenesis and demonstrates surgery as a curative treatment option for clinically affected patients.
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Affiliation(s)
- Rebecca Schwartz
- Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
| | - Nicole J. Sugai
- Department of Veterinary Clinical Sciences, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
| | - Kristin Eden
- Virginia Tech Animal Laboratory Services, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
- Department of Basic Science Education, Virginia Tech Carilion School of Medicine, Roanoke, VA, United States
| | - Caitlin Castaneda
- Department of Veterinary Integrative Biosciences, Molecular Cytogenetics Laboratory, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Matthew Jevit
- Department of Veterinary Integrative Biosciences, Molecular Cytogenetics Laboratory, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Molecular Cytogenetics Laboratory, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Julie T. Cecere
- Department of Veterinary Clinical Sciences, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
- *Correspondence: Julie T. Cecere
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19
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Steinberg ER, Bressa MJ, Mudry MD. Sex chromosome systems in Neotropical Primates: What have we learnt so far from cytogenetics and genomics? J Evol Biol 2022; 35:1589-1600. [PMID: 35731796 DOI: 10.1111/jeb.14039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/10/2022] [Accepted: 05/26/2022] [Indexed: 11/29/2022]
Abstract
Neotropical Primates (Platyrrhini) show great diversity in their life histories, ecology, behaviour and genetics. This diversity extends to their chromosome complements, both to autosomes and to sex chromosomes. In this contribution, we will review what is currently known about sex chromosomes in this group, both from cytogenetic and from genomic evidence. The X and Y chromosomes in Neotropical Primates, also known as New World Monkeys, have striking structural differences compared with Old World Monkeys when Catarrhini sex chromosomes are considered. The XY bivalent displays a different meiotic behaviour in prophase I, and their Y chromosome shows extensive genomic differences. Even though the most widespread sex chromosome system is the XX/XY and thus considered the ancestral one for Platyrrhini, modifications of this sexual system are observed within this group. Multiple sex chromosome systems originated from Y-autosome translocations were described in several genera (Aotus, Callimico and Alouatta). In the howler monkeys, genus Alouatta, an independent origin of the sexual systems in South American and Mesoamerican species was postulated. All the above-mentioned evidence suggests that the Y chromosome of Platyrrhini has a different evolutionary history compared with the Catarrhini Y. There is still much to understand regarding their sex chromosome systems.
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Affiliation(s)
- Eliana Ruth Steinberg
- Grupo de Investigación en Biología Evolutiva (GIBE). Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), CONICET, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - María José Bressa
- Grupo de Citogenética de Insectos. Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), CONICET, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Marta Dolores Mudry
- Grupo de Investigación en Biología Evolutiva (GIBE). Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), CONICET, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
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20
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Hughes JF, Skaletsky H, Nicholls PK, Drake A, Pyntikova T, Cho TJ, Bellott DW, Page DC. A gene deriving from the ancestral sex chromosomes was lost from the X and retained on the Y chromosome in eutherian mammals. BMC Biol 2022; 20:133. [PMID: 35676717 PMCID: PMC9178871 DOI: 10.1186/s12915-022-01338-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/25/2022] [Indexed: 11/14/2022] Open
Abstract
Background The mammalian X and Y chromosomes originated from a pair of ordinary autosomes. Over the past ~180 million years, the X and Y have become highly differentiated and now only recombine with each other within a short pseudoautosomal region. While the X chromosome broadly preserved its gene content, the Y chromosome lost ~92% of the genes it once shared with the X chromosome. PRSSLY is a Y-linked gene identified in only a few mammalian species that was thought to be acquired, not ancestral. However, PRSSLY’s presence in widely divergent species—bull and mouse—led us to further investigate its evolutionary history. Results We discovered that PRSSLY is broadly conserved across eutherians and has ancient origins. PRSSLY homologs are found in syntenic regions on the X chromosome in marsupials and on autosomes in more distant animals, including lizards, indicating that PRSSLY was present on the ancestral autosomes but was lost from the X and retained on the Y in eutherian mammals. We found that across eutheria, PRSSLY’s expression is testis-specific, and, in mouse, it is most robustly expressed in post-meiotic germ cells. The closest paralog to PRSSLY is the autosomal gene PRSS55, which is expressed exclusively in testes, involved in sperm differentiation and migration, and essential for male fertility in mice. Outside of eutheria, in species where PRSSLY orthologs are not Y-linked, we find expression in a broader range of somatic tissues, suggesting that PRSSLY has adopted a germ-cell-specific function in eutherians. Finally, we generated Prssly mutant mice and found that they are fully fertile but produce offspring with a modest female-biased sex ratio compared to controls. Conclusions PRSSLY appears to be the first example of a gene that derives from the mammalian ancestral sex chromosomes that was lost from the X and retained on the Y. Although the function of PRSSLY remains to be determined, it may influence the sex ratio by promoting the survival or propagation of Y-bearing sperm. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01338-8.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, MA, 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, 02142, USA
| | - Peter K Nicholls
- Whitehead Institute, Cambridge, MA, 02142, USA.,Present Address: Faculty of Life Sciences, University of Bradford, BD71DP, Bradford, UK
| | | | | | | | | | - David C Page
- Whitehead Institute, Cambridge, MA, 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
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21
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Carey SB, Lovell JT, Jenkins J, Leebens-Mack J, Schmutz J, Wilson MA, Harkess A. Representing sex chromosomes in genome assemblies. CELL GENOMICS 2022; 2. [PMID: 35720975 PMCID: PMC9205529 DOI: 10.1016/j.xgen.2022.100132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sex chromosomes have evolved hundreds of independent times across eukaryotes. As genome sequencing, assembly, and scaffolding techniques rapidly improve, it is now feasible to build fully phased sex chromosome assemblies. Despite technological advances enabling phased assembly of whole chromosomes, there are currently no standards for representing sex chromosomes when publicly releasing a genome. Furthermore, most computational analysis tools are unable to efficiently investigate their unique biology relative to autosomes. We discuss a diversity of sex chromosome systems and consider the challenges of representing sex chromosome pairs in genome assemblies. By addressing these issues now as technologies for full phasing of chromosomal assemblies are maturing, we can collectively ensure that future genome analysis toolkits can be broadly applied to all eukaryotes with diverse types of sex chromosome systems. Here we provide best practice guidelines for presenting a genome assembly that contains sex chromosomes. These guidelines can also be applied to other non-recombining genomic regions, such as S-loci in plants and mating-type loci in fungi and algae.
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Affiliation(s)
- Sarah B Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.,US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Melissa A Wilson
- School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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22
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Vogt PH, Zimmer J, Bender U, Strowitzki T. AZFa candidate gene UTY and its X homologue UTX are expressed in human germ cells. REPRODUCTION AND FERTILITY 2022; 2:151-160. [PMID: 35128450 PMCID: PMC8812439 DOI: 10.1530/raf-20-0049] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/11/2021] [Indexed: 12/15/2022] Open
Abstract
The Ubiquitous Transcribed Y (UTY a.k.a. KDM6C) AZFa candidate gene on the human Y chromosome and its paralog on the X chromosome, UTX (a.k.a. KDM6A), encode a histone lysine demethylase removing chromatin H3K27 methylation marks at genes transcriptional start sites for activation. Both proteins harbour the conserved Jumonji C (JmjC) domain, functional in chromatin metabolism, and an extended N-terminal tetratricopeptide repeat (TPR) block involved in specific protein interactions. Specific antisera for human UTY and UTX proteins were developed to distinguish the expression of both proteins in human germ cells by immunohistochemical experiments on appropriate tissue sections. In the male germ line, UTY was expressed in the fraction of A spermatogonia located at the basal membrane, probably including spermatogonia stem cells. UTX expression was more spread in all spermatogonia and in early spermatids. In female germ line, UTX expression was found in the primordial germ cells of the ovary. UTY was also expressed during fetal male germ cell development, whereas UTX expression was visible only at distinct gestation weeks. Based on these results and the conserved neighboured location of UTY and DDX3Y in Yq11 found in mammals of distinct lineages, we conclude that UTY, such as DDX3Y, is part of the Azoospermia factor a (AZFa) locus functioning in human spermatogonia to support the balance of their proliferation-differentiation rate before meiosis. Comparable UTY and DDX3Y expression was also found in gonadoblastoma and dysgerminoma cells found in germ cell nests of the dysgenetic gonads of individuals with disorders of sexual development and a Y chromosome in karyotype (DSD-XY). This confirms that AZFa overlaps with GBY, the Gonadoblastoma susceptibility Y locus, and includes the UTY gene.
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Affiliation(s)
- Peter H Vogt
- Division of Reproduction Genetics, Department of, Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Germany
| | - Jutta Zimmer
- Division of Reproduction Genetics, Department of, Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Germany
| | - Ulrike Bender
- Division of Reproduction Genetics, Department of, Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Germany
| | - Thomas Strowitzki
- Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Germany
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23
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Bredemeyer KR, Seabury CM, Stickney MJ, McCarrey JR, vonHoldt BM, Murphy WJ. Rapid Macrosatellite Evolution Promotes X-Linked Hybrid Male Sterility in a Feline Interspecies Cross. Mol Biol Evol 2021; 38:5588-5609. [PMID: 34519828 PMCID: PMC8662614 DOI: 10.1093/molbev/msab274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The sterility or inviability of hybrid offspring produced from an interspecific mating result from incompatibilities between parental genotypes that are thought to result from divergence of loci involved in epistatic interactions. However, attributes contributing to the rapid evolution of these regions also complicates their assembly, thus discovery of candidate hybrid sterility loci is difficult and has been restricted to a small number of model systems. Here we reported rapid interspecific divergence at the DXZ4 macrosatellite locus in an interspecific cross between two closely related mammalian species: the domestic cat (Felis silvestris catus) and the Jungle cat (Felis chaus). DXZ4 is an interesting candidate due to its structural complexity, copy number variability, and described role in the critical yet complex biological process of X-chromosome inactivation. However, the full structure of DXZ4 was absent or incomplete in nearly every available mammalian genome assembly given its repetitive complexity. We compared highly continuous genomes for three cat species, each containing a complete DXZ4 locus, and discovered that the felid DXZ4 locus differs substantially from the human ortholog, and that it varies in copy number between cat species. Additionally, we reported expression, methylation, and structural conformation profiles of DXZ4 and the X chromosome during stages of spermatogenesis that have been previously associated with hybrid male sterility. Collectively, these findings suggest a new role for DXZ4 in male meiosis and a mechanism for feline interspecific incompatibility through rapid satellite divergence.
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Affiliation(s)
- Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | | | - Mark J Stickney
- Veterinary Medical Teaching Hospital, Texas A&M University, College Station, TX, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | | | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
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24
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Douglas C, Maciulyte V, Zohren J, Snell DM, Mahadevaiah SK, Ojarikre OA, Ellis PJI, Turner JMA. CRISPR-Cas9 effectors facilitate generation of single-sex litters and sex-specific phenotypes. Nat Commun 2021; 12:6926. [PMID: 34862376 PMCID: PMC8642469 DOI: 10.1038/s41467-021-27227-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/05/2021] [Indexed: 11/09/2022] Open
Abstract
Animals are essential genetic tools in scientific research and global resources in agriculture. In both arenas, a single sex is often required in surplus. The ethical and financial burden of producing and culling animals of the undesired sex is considerable. Using the mouse as a model, we develop a synthetic lethal, bicomponent CRISPR-Cas9 strategy that produces male- or female-only litters with one hundred percent efficiency. Strikingly, we observe a degree of litter size compensation relative to control matings, indicating that our system has the potential to increase the yield of the desired sex in comparison to standard breeding designs. The bicomponent system can also be repurposed to generate postnatal sex-specific phenotypes. Our approach, harnessing the technological applications of CRISPR-Cas9, may be applicable to other vertebrate species, and provides strides towards ethical improvements for laboratory research and agriculture.
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Affiliation(s)
- Charlotte Douglas
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Valdone Maciulyte
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Jasmin Zohren
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Daniel M Snell
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - Obah A Ojarikre
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK.
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25
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Krzeminska P, Nowacka-Woszuk J, Switonski M. Copy number variation of the SRY gene showed an association with disorders of sex development in Yorkshire Terrier dogs. Anim Genet 2021; 53:152-155. [PMID: 34664728 DOI: 10.1111/age.13147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 11/29/2022]
Abstract
The molecular background of disorders of sex development (DSD) in dogs is poorly understood. Several copies of the SRY genes have been reported in the dog genome. We used droplet digital PCR with the aim of determining variability in SRY copy number and its association with DSD in dogs. Altogether 19 DSD male dogs (XY DSD) of 10 breeds and 87 control dogs of eight breeds were analyzed. Moreover, we performed a comparative analysis of SRY copy number in other canids: wolves (3), red foxes (16), and Chinese raccoon dogs (10). We found that the modal number of SRY copies in dogs, wolves, red foxes, and Chinese raccoon dogs was 3, 3, 1, and 3 respectively. Variability of copy number was only observed in Yorkshire Terriers (two or three copies) and red foxes (one or two copies). An analysis of six DSD Yorkshire Terriers and 38 control males of this breed showed that 50% of the DSD dogs had two copies, while the incidence of this variant was significantly lower in the control dogs (10.5%). Searching for the copy number of the coding and 5'-flanking fragments revealed full concordance with the copy number. These fragments were also sequenced in DSD (19) and control (24) dogs, and no DNA variants were found. We conclude that, in the dog, two or three functional copies of the SRY gene are present, and a smaller number of copies showed an association with the risk of DSD phenotype in Yorkshire Terriers.
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Affiliation(s)
- P Krzeminska
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, Poznan, 60-637, Poland
| | - J Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, Poznan, 60-637, Poland
| | - M Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, Poznan, 60-637, Poland
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26
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Subrini J, Turner J. Y chromosome functions in mammalian spermatogenesis. eLife 2021; 10:67345. [PMID: 34606444 PMCID: PMC8489898 DOI: 10.7554/elife.67345] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/09/2021] [Indexed: 12/12/2022] Open
Abstract
The mammalian Y chromosome is critical for male sex determination and spermatogenesis. However, linking each Y gene to specific aspects of male reproduction has been challenging. As the Y chromosome is notoriously hard to sequence and target, functional studies have mostly relied on transgene-rescue approaches using mouse models with large multi-gene deletions. These experimental limitations have oriented the field toward the search for a minimum set of Y genes necessary for male reproduction. Here, considering Y-chromosome evolutionary history and decades of discoveries, we review the current state of research on its function in spermatogenesis and reassess the view that many Y genes are disposable for male reproduction.
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Affiliation(s)
- Jeremie Subrini
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - James Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, United Kingdom
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27
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Janssenswillen S, Roelants K, Carpentier S, de Rooster H, Metzemaekers M, Vanschoenwinkel B, Proost P, Bossuyt F. Odorant-binding proteins in canine anal sac glands indicate an evolutionarily conserved role in mammalian chemical communication. BMC Ecol Evol 2021; 21:182. [PMID: 34565329 PMCID: PMC8474896 DOI: 10.1186/s12862-021-01910-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 09/10/2021] [Indexed: 11/29/2022] Open
Abstract
Background Chemical communication is an important aspect of the behavioural ecology of a wide range of mammals. In dogs and other carnivores, anal sac glands are thought to convey information to conspecifics by secreting a pallet of small volatile molecules produced by symbiotic bacteria. Because these glands are unique to carnivores, it is unclear how their secretions relate to those of other placental mammals that make use of different tissues and secretions for chemical communication. Here we analyse the anal sac glands of domestic dogs to verify the secretion of proteins and infer their evolutionary relationship to those involved in the chemical communication of non-carnivoran mammals. Results Proteomic analysis of anal sac gland secretions of 17 dogs revealed the consistently abundant presence of three related proteins. Homology searches against online databases indicate that these proteins are evolutionary related to ‘odorant binding proteins’ (OBPs) found in a wide range of mammalian secretions and known to contribute to chemical communication. Screening of the dog’s genome sequence show that the newly discovered OBPs are encoded by a single cluster of three genes in the pseudoautosomal region of the X-chromosome. Comparative genomic screening indicates that the same locus is shared by a wide range of placental mammals and that it originated at least before the radiation of extant placental orders. Phylogenetic analyses suggest a dynamic evolution of gene duplication and loss, resulting in large gene clusters in some placental taxa and recurrent loss of this locus in others. The homology of OBPs in canid anal sac glands and those found in other mammalian secretions implies that these proteins maintained a function in chemical communication throughout mammalian evolutionary history by multiple shifts in expression between secretory tissues involved in signal release and nasal mucosa involved in signal reception. Conclusions Our study elucidates a poorly understood part of the biology of a species that lives in close association with humans. In addition, it shows that the protein repertoire underlying chemical communication in mammals is more evolutionarily stable than the variation of involved glands and tissues would suggest. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01910-w.
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Affiliation(s)
- Sunita Janssenswillen
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Kim Roelants
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
| | - Sebastien Carpentier
- Proteomics Core - SyBioMa, Katholieke Universiteit Leuven, Herestraat 49 - 03.313, 3000, Leuven, Belgium
| | - Hilde de Rooster
- Small Animal Department, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Mieke Metzemaekers
- Rega Institute, Molecular Immunology, Katholieke Universiteit Leuven, Herestraat 49 - Bus1042, 3000, Leuven, Belgium
| | - Bram Vanschoenwinkel
- Community Ecology Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,Center for Environmental Management, University of the Free State, Bloemfontein, 9030, South Africa
| | - Paul Proost
- Rega Institute, Molecular Immunology, Katholieke Universiteit Leuven, Herestraat 49 - Bus1042, 3000, Leuven, Belgium
| | - Franky Bossuyt
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
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28
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Yu H, Xing YT, Meng H, He B, Li WJ, Qi XZ, Zhao JY, Zhuang Y, Xu X, Yamaguchi N, Driscoll CA, O'Brien SJ, Luo SJ. Genomic evidence for the Chinese mountain cat as a wildcat conspecific ( Felis silvestris bieti) and its introgression to domestic cats. SCIENCE ADVANCES 2021; 7:7/26/eabg0221. [PMID: 34162544 PMCID: PMC8221621 DOI: 10.1126/sciadv.abg0221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 05/13/2021] [Indexed: 06/13/2023]
Abstract
The Qinghai-Tibet Plateau endemic Chinese mountain cat has a controversial taxonomic status, whether it is a true species or a wildcat (Felis silvestris) subspecies and whether it has contributed to cat (F. s. catus) domestication in East Asia. Here, we sampled F. silvestris lineages across China and sequenced 51 nuclear genomes, 55 mitogenomes, and multilocus regions from 270 modern or museum specimens. Genome-wide analyses classified the Chinese mountain cat as a wildcat conspecific F. s. bieti, which was not involved in cat domestication of China, thus supporting a single domestication origin arising from the African wildcat (F. s. lybica). A complex hybridization scenario including ancient introgression from the Asiatic wildcat (F. s. ornata) to F. s. bieti, and contemporary gene flow between F. s. bieti and sympatric domestic cats that are likely recent Plateau arrivals, raises the prospect of disrupted wildcat genetic integrity, an issue with profound conservation implications.
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Affiliation(s)
- He Yu
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences (CLS), Peking-Tsinghua-NIBS (PTN) Program, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yue-Ting Xing
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences (CLS), Peking-Tsinghua-NIBS (PTN) Program, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hao Meng
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences (CLS), Peking-Tsinghua-NIBS (PTN) Program, School of Life Sciences, Peking University, Beijing 100871, China
| | - Bing He
- World Wide Fund for Nature, Beijing 100037, China
| | - Wen-Jing Li
- CAS Key Laboratory of Adaptation and Evolution of Plateau Biota and Qinghai-Tibetan Plateau Museum of Biology, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
| | - Xin-Zhang Qi
- Tibetan Plateau Wildlife Zoo, Xining, Qinghai 810001, China
| | - Jian-You Zhao
- Gansu Endangered Animals Protection Center, Wuwei, Gansu 733000, China
| | - Yan Zhuang
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences (CLS), Peking-Tsinghua-NIBS (PTN) Program, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiao Xu
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences (CLS), Peking-Tsinghua-NIBS (PTN) Program, School of Life Sciences, Peking University, Beijing 100871, China
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | | | - Stephen J O'Brien
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, St. Petersburg 197101, Russia
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL 33004, USA
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences (CLS), Peking-Tsinghua-NIBS (PTN) Program, School of Life Sciences, Peking University, Beijing 100871, China.
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL 33004, USA
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29
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Xiao C, Li J, Xie T, Chen J, Zhang S, Elaksher SH, Jiang F, Jiang Y, Zhang L, Zhang W, Xiang Y, Wu Z, Zhao S, Du X. The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat. Ecol Evol 2021; 11:7779-7795. [PMID: 34188851 PMCID: PMC8216945 DOI: 10.1002/ece3.7611] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 02/05/2023] Open
Abstract
The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y-linked scaffolds using existing data. A total of 11.5 Mb Y-linked sequences were clustered into 33 scaffolds, and 187 protein-coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat radiation hybrid map (RH map). The existing whole-genome resequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post-Neolithic period.
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Affiliation(s)
- Changyi Xiao
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Jingjin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Tanghui Xie
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Jianhai Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- Institutes for Systems GeneticsFrontiers Science Center for Disease‐related Molecular NetworkWest China HospitalSichuan UniversityChengduChina
| | - Sijia Zhang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Salma Hassan Elaksher
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- Genetics and Genetic Engineering DepartmentFaculty of AgricultureBenha UniversityMoshtohorEgypt
| | - Fan Jiang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Yaoxin Jiang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Lu Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Wei Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Yue Xiang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Zhenyang Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- College of Agroforestry Engineering and PlanningTongren UniversityTongrenChina
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Xiaoyong Du
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
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30
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A domestic cat whole exome sequencing resource for trait discovery. Sci Rep 2021; 11:7159. [PMID: 33785770 PMCID: PMC8009874 DOI: 10.1038/s41598-021-86200-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
Over 94 million domestic cats are susceptible to cancers and other common and rare diseases. Whole exome sequencing (WES) is a proven strategy to study these disease-causing variants. Presented is a 35.7 Mb exome capture design based on the annotated Felis_catus_9.0 genome assembly, covering 201,683 regions of the cat genome. Whole exome sequencing was conducted on 41 cats with known and unknown genetic diseases and traits, of which ten cats had matching whole genome sequence (WGS) data available, used to validate WES performance. At 80 × mean exome depth of coverage, 96.4% of on-target base coverage had a sequencing depth > 20-fold, while over 98% of single nucleotide variants (SNVs) identified by WGS were also identified by WES. Platform-specific SNVs were restricted to sex chromosomes and a small number of olfactory receptor genes. Within the 41 cats, we identified 31 previously known causal variants and discovered new gene candidate variants, including novel missense variance for polycystic kidney disease and atrichia in the Peterbald cat. These results show the utility of WES to identify novel gene candidate alleles for diseases and traits for the first time in a feline model.
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31
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Rabinowitz MJ, Huffman PJ, Haney NM, Kohn TP. Y-Chromosome Microdeletions: A Review of Prevalence, Screening, and Clinical Considerations. Appl Clin Genet 2021; 14:51-59. [PMID: 33603438 PMCID: PMC7886244 DOI: 10.2147/tacg.s267421] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/18/2021] [Indexed: 11/24/2022] Open
Abstract
Deletions within the male-specific region of the Y-chromosome, known as Y-Chromosome Microdeletions (YCMs), are present in as many as 5% and 10% of severe oligospermic and azoospermic men, respectively. These microdeletions are distinguished by which segment of the Y chromosome is absent, identified as AZFa (the most proximal segment), AZFb (middle), and AZFc (distal). The reported prevalence of YCMs within the world’s populations of infertile men displays vast heterogeneity, ranging from less than 2% to over 24% based on region and ethnicity. AZFc is the most commonly identified YCM, and its phenotypic presentation provides for the highest chance for fertility through artificial reproductive techniques. Conversely, deletions identified in the subregions of AZFa, AZFb, or any combination of regions containing these segments, are associated with low probabilities of achieving pregnancy. A putative mechanism explaining this discrepancy lies within the expression of autosomal, DAZ-like genes which could serve to “rescue” wild type AZFc gene expression and hence spermatogenesis. Nevertheless, recent reports challenge this dogma and stress the importance of further analysis when an AZFb deletion is detected. The screening thresholds to determine which oligospermic and azoospermic men are tested for potential YCMs has been recently contested. More recent literature supports lowering the threshold from 5 million sperm/mL of ejaculate to 1 million/mL as the frequency of YCMs in men with sperm concentrations between 1 and 5 million sperm/mL is very low (~0.8%). As such, subsequent guidelines should recommend a lower screening threshold. While YCMs are extremely common globally, the understanding of their clinical significance in the field remains scattered and without consensus. Furthermore, very little is currently known about partial deletions within the AZFc region, such as b1/b3, b2/b3, and gr/gr. Hence, this review aimed to summarize and discuss modern trends in the epidemiology, screening guidelines, and clinical considerations pertaining to YCMs.
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Affiliation(s)
- Matthew J Rabinowitz
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Phillip J Huffman
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nora M Haney
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Taylor P Kohn
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Bellott DW, Page DC. Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals. Genome Res 2021; 31:198-210. [PMID: 33479023 PMCID: PMC7849413 DOI: 10.1101/gr.268516.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022]
Abstract
Different ancestral autosomes independently evolved into sex chromosomes in snakes, birds, and mammals. In snakes and birds, females are ZW and males are ZZ; in mammals, females are XX and males are XY. Although X and Z Chromosomes retain nearly all ancestral genes, sex-specific W and Y Chromosomes suffered extensive genetic decay. In both birds and mammals, the genes that survived on sex-specific chromosomes are enriched for broadly expressed, dosage-sensitive regulators of gene expression, subject to strong purifying selection. To gain deeper insight into the processes that govern survival on sex-specific chromosomes, we carried out a meta-analysis of survival across 41 species-three snakes, 24 birds, and 14 mammals-doubling the number of ancestral genes under investigation and increasing our power to detect enrichments among survivors relative to nonsurvivors. Of 2564 ancestral genes, representing an eighth of the ancestral amniote genome, only 324 survive on present-day sex-specific chromosomes. Survivors are enriched for dosage-sensitive developmental processes, particularly development of neural crest-derived structures, such as the face. However, there was no enrichment for expression in sex-specific tissues, involvement in sex determination or gonadogenesis pathways, or conserved sex-biased expression. Broad expression and dosage sensitivity contributed independently to gene survival, suggesting that pleiotropy imposes additional constraints on the evolution of dosage compensation. We propose that maintaining the viability of the heterogametic sex drove gene survival on amniote sex-specific chromosomes, and that subtle modulation of the expression of survivor genes and their autosomal orthologs has disproportionately large effects on development and disease.
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Affiliation(s)
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Player RA, Forsyth ER, Verratti KJ, Mohr DW, Scott AF, Bradburne CE. A novel canis lupus familiaris reference genome improves variant resolution for use in breed-specific GWAS. Life Sci Alliance 2021; 4:4/4/e202000902. [PMID: 33514656 PMCID: PMC7898556 DOI: 10.26508/lsa.202000902] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 11/24/2022] Open
Abstract
Reference genome fidelity is critically important for genome wide association studies, yet most vary widely from the study population. A typical whole genome sequencing approach implies short-read technologies resulting in fragmented assemblies with regions of ambiguity. Further information is lost by economic necessity when genotyping populations, as lower resolution technologies such as genotyping arrays are commonly used. Here, we present a phased reference genome for Canis lupus familiaris using high molecular weight DNA-sequencing technologies. We tested wet laboratory and bioinformatic approaches to demonstrate a minimum workflow to generate the 2.4 gigabase genome for a Labrador Retriever. The de novo assembly required eight Oxford Nanopore R9.4 flowcells (∼23X depth) and running a 10X Genomics library on the equivalent of one lane of an Illumina NovaSeq S1 flowcell (∼88X depth), bringing the cost of generating a nearly complete reference genome to less than $10K (USD). Mapping of short-read data from 10 Labrador Retrievers against this reference resulted in 1% more aligned reads versus the current reference (CanFam3.1, P < 0.001), and a 15% reduction of variant calls, increasing the chance of identifying true, low-effect size variants in a genome-wide association studies. We believe that by incorporating the cost to produce a full genome assembly into any large-scale genotyping project, an investigator can improve study power, decrease costs, and optimize the overall scientific value of their study.
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Affiliation(s)
- Robert A Player
- Asymmetric Operations Sector, The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA
| | - Ellen R Forsyth
- Asymmetric Operations Sector, The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA
| | - Kathleen J Verratti
- Asymmetric Operations Sector, The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA
| | - David W Mohr
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alan F Scott
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Christopher E Bradburne
- Asymmetric Operations Sector, The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA .,McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
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An 8.22 Mb Assembly and Annotation of the Alpaca ( Vicugna pacos) Y Chromosome. Genes (Basel) 2021; 12:genes12010105. [PMID: 33467186 PMCID: PMC7830431 DOI: 10.3390/genes12010105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/07/2021] [Accepted: 01/14/2021] [Indexed: 12/26/2022] Open
Abstract
The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology.
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35
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Sacks BN, Lounsberry ZT, Rando HM, Kluepfel K, Fain SR, Brown SK, Kukekova AV. Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography. Genes (Basel) 2021; 12:genes12010097. [PMID: 33466657 PMCID: PMC7828831 DOI: 10.3390/genes12010097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/01/2021] [Accepted: 01/11/2021] [Indexed: 11/28/2022] Open
Abstract
The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (~100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography.
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Affiliation(s)
- Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA; (Z.T.L.); (K.K.); (S.K.B.)
- Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA
- Correspondence:
| | - Zachary T. Lounsberry
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA; (Z.T.L.); (K.K.); (S.K.B.)
| | - Halie M. Rando
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (H.M.R.); (A.V.K.)
| | - Kristopher Kluepfel
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA; (Z.T.L.); (K.K.); (S.K.B.)
| | - Steven R. Fain
- U. S. Fish & Wildlife Service, National Forensics Laboratory, Ashland, OR 97520, USA;
| | - Sarah K. Brown
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA; (Z.T.L.); (K.K.); (S.K.B.)
| | - Anna V. Kukekova
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (H.M.R.); (A.V.K.)
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36
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Martínez-Pacheco M, Tenorio M, Almonte L, Fajardo V, Godínez A, Fernández D, Cornejo-Páramo P, Díaz-Barba K, Halbert J, Liechti A, Székely T, Urrutia AO, Cortez D. Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals. Genome Biol Evol 2020; 12:2015-2028. [PMID: 32790864 PMCID: PMC7674692 DOI: 10.1093/gbe/evaa173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
Placental mammals present 180 million-year-old Y chromosomes that have retained a handful of dosage-sensitive genes. However, the expression evolution of Y-linked genes across placental groups has remained largely unexplored. Here, we expanded the number of Y gametolog sequences by analyzing ten additional species from previously unexplored groups. We detected seven remarkably conserved genes across 25 placental species with known Y repertoires. We then used RNA-seq data from 17 placental mammals to unveil the expression evolution of XY gametologs. We found that Y gametologs followed, on average, a 3-fold expression loss and that X gametologs also experienced some expression reduction, particularly in primates. Y gametologs gained testis specificity through an accelerated expression decay in somatic tissues. Moreover, despite the substantial expression decay of Y genes, the combined expression of XY gametologs in males is higher than that of both X gametologs in females. Finally, our work describes several features of the Y chromosome in the last common mammalian ancestor.
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Affiliation(s)
| | | | - Laura Almonte
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| | | | - Alan Godínez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| | | | | | | | - Jean Halbert
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Tamas Székely
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Araxi O Urrutia
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom.,Ecology Institute, UNAM, Mexico
| | - Diego Cortez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
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37
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Xu L, Irestedt M, Zhou Q. Sequence Transpositions Restore Genes on the Highly Degenerated W Chromosomes of Songbirds. Genes (Basel) 2020; 11:E1267. [PMID: 33126459 PMCID: PMC7692361 DOI: 10.3390/genes11111267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 12/30/2022] Open
Abstract
The female-specific W chromosomes of most Neognathae birds are highly degenerated and gene-poor. Previous studies have demonstrated that the gene repertoires of the Neognathae bird W chromosomes, despite being in small numbers, are conserved across bird species, likely due to purifying selection maintaining the regulatory and dosage-sensitive genes. Here we report the discovery of DNA-based sequence duplications from the Z to the W chromosome in birds-of-paradise (Paradisaeidae, Passeriformes), through sequence transposition. The original transposition involved nine genes, but only two of them (ANXA1 and ALDH1A1) survived on the W chromosomes. Both ANXA1 and ALDH1A1 are predicted to be dosage-sensitive, and the expression of ANXA1 is restricted to ovaries in all the investigated birds. These analyses suggest the newly transposed gene onto the W chromosomes can be favored for their role in restoring dosage imbalance or through female-specific selection. After examining seven additional songbird genomes, we further identified five other transposed genes on the W chromosomes of Darwin's finches and one in the great tit, expanding the observation of the Z-to-W transpositions to a larger range of bird species, but not all transposed genes exhibit dosage-sensitivity or ovary-biased expression We demonstrate a new mechanism by which the highly degenerated W chromosomes of songbirds can acquire genes from the homologous Z chromosomes, but further functional investigations are needed to validate the evolutionary forces underlying the transpositions.
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Affiliation(s)
- Luohao Xu
- Department of Neurosciences and Developmental Biology, University of Vienna, 1090 Vienna, Austria;
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden;
| | - Qi Zhou
- Department of Neurosciences and Developmental Biology, University of Vienna, 1090 Vienna, Austria;
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou 310012, China
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310012, China
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38
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Affiliation(s)
- Wengang Zhang
- The Roslin Institute and Royal (Dick) School for Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Jeffrey J. Schoenebeck
- The Roslin Institute and Royal (Dick) School for Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
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39
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Li R, Yang P, Li M, Fang W, Yue X, Nanaei HA, Gan S, Du D, Cai Y, Dai X, Yang Q, Cao C, Deng W, He S, Li W, Ma R, Liu M, Jiang Y. A Hu sheep genome with the first ovine Y chromosome reveal introgression history after sheep domestication. SCIENCE CHINA-LIFE SCIENCES 2020; 64:1116-1130. [PMID: 32997330 DOI: 10.1007/s11427-020-1807-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/25/2020] [Indexed: 01/21/2023]
Abstract
The Y chromosome plays key roles in male fertility and reflects the evolutionary history of paternal lineages. Here, we present a de novo genome assembly of the Hu sheep with the first draft assembly of ovine Y chromosome (oMSY), using nanopore sequencing and Hi-C technologies. The oMSY that we generated spans 10.6 Mb from which 775 Y-SNPs were identified by applying a large panel of whole genome sequences from worldwide sheep and wild Iranian mouflons. Three major paternal lineages (HY1a, HY1b and HY2) were defined across domestic sheep, of which HY2 was newly detected. Surprisingly, HY2 forms a monophyletic clade with the Iranian mouflons and is highly divergent from both HY1a and HY1b. Demographic analysis of Y chromosomes, mitochondrial and nuclear genomes confirmed that HY2 and the maternal counterpart of lineage C represented a distinct wild mouflon population in Iran that diverge from the direct ancestor of domestic sheep, the wild mouflons in Southeastern Anatolia. Our results suggest that wild Iranian mouflons had introgressed into domestic sheep and thereby introduced this Iranian mouflon specific lineage carrying HY2 to both East Asian and Africa sheep populations.
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Affiliation(s)
- Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Peng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Wenwen Fang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiangpeng Yue
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shangquan Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Duo Du
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Qimeng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Chunna Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Weidong Deng
- Faculty of Animal Science and Technology, Yunan Agricultural University, Kunming, 650201, China
| | - Sangang He
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, 830026, China
| | - Wenrong Li
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, 830026, China
| | - Runlin Ma
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mingjun Liu
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, 830026, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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40
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Deschepper CF. Regulatory effects of the Uty/Ddx3y locus on neighboring chromosome Y genes and autosomal mRNA transcripts in adult mouse non-reproductive cells. Sci Rep 2020; 10:14900. [PMID: 32913328 PMCID: PMC7484786 DOI: 10.1038/s41598-020-71447-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/13/2020] [Indexed: 12/22/2022] Open
Abstract
In addition to sperm-related genes, the male-specific chromosome Y (chrY) contains a class of ubiquitously expressed and evolutionary conserved dosage-sensitive regulator genes that include the neighboring Uty, Ddx3y and (in mice) Eif2s3y genes. However, no study to date has investigated the functional impact of targeted mutations of any of these genes within adult non-reproductive somatic cells. We thus compared adult male mice carrying a gene trap within their Uty gene (UtyGT) to their wild-type (WT) isogenic controls, and performed deep sequencing of RNA and genome-wide profiling of chromatin features in extracts from either cardiac tissue, cardiomyocyte-specific nuclei or purified cardiomyocytes. The apparent impact of UtyGT on gene transcription concentrated mostly on chrY genes surrounding the locus of insertion, i.e. Uty, Ddx3y, long non-coding RNAs (lncRNAs) contained within their introns and Eif2s3y, in addition to possible effects on the autosomal Malat1 lncRNA. Notwithstanding, UtyGT also caused coordinate changes in the abundance of hundreds of mRNA transcripts related to coherent cell functions, including RNA processing and translation. The results altogether indicated that tightly co-regulated chrY genes had nonetheless more widespread effects on the autosomal transcriptome in adult somatic cells, most likely due to mechanisms other than just transcriptional regulation of corresponding protein-coding genes.
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Affiliation(s)
- Christian F Deschepper
- Cardiovascular Biology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM) and Université de Montréal, 100 Pine Ave West, Montréal, QC, H2W 1R7, Canada.
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Peichel CL, McCann SR, Ross JA, Naftaly AFS, Urton JR, Cech JN, Grimwood J, Schmutz J, Myers RM, Kingsley DM, White MA. Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution. Genome Biol 2020; 21:177. [PMID: 32684159 PMCID: PMC7368989 DOI: 10.1186/s13059-020-02097-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/08/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Heteromorphic sex chromosomes have evolved repeatedly across diverse species. Suppression of recombination between X and Y chromosomes leads to degeneration of the Y chromosome. The progression of degeneration is not well understood, as complete sequence assemblies of heteromorphic Y chromosomes have only been generated across a handful of taxa with highly degenerate sex chromosomes. Here, we describe the assembly of the threespine stickleback (Gasterosteus aculeatus) Y chromosome, which is less than 26 million years old and at an intermediate stage of degeneration. Our previous work identified that the non-recombining region between the X and the Y spans approximately 17.5 Mb on the X chromosome. RESULTS We combine long-read sequencing with a Hi-C-based proximity guided assembly to generate a 15.87 Mb assembly of the Y chromosome. Our assembly is concordant with cytogenetic maps and Sanger sequences of over 90 Y chromosome BAC clones. We find three evolutionary strata on the Y chromosome, consistent with the three inversions identified by our previous cytogenetic analyses. The threespine stickleback Y shows convergence with more degenerate sex chromosomes in the retention of haploinsufficient genes and the accumulation of genes with testis-biased expression, many of which are recent duplicates. However, we find no evidence for large amplicons identified in other sex chromosome systems. We also report an excellent candidate for the master sex-determination gene: a translocated copy of Amh (Amhy). CONCLUSIONS Together, our work shows that the evolutionary forces shaping sex chromosomes can cause relatively rapid changes in the overall genetic architecture of Y chromosomes.
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Affiliation(s)
- Catherine L. Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Shaugnessy R. McCann
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Joseph A. Ross
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | | | - James R. Urton
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | - Jennifer N. Cech
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - David M. Kingsley
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Michael A. White
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
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42
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Bugno-Poniewierska M, Kij B, Witarski W, Wojtaszek M, Radko A, Podbielska A, Szczerbal I, Murphy WJ. Fertile male tortoiseshell cat with true chimerism 38,XY/38,XY. Reprod Domest Anim 2020; 55:1139-1144. [PMID: 32574385 DOI: 10.1111/rda.13752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/16/2020] [Indexed: 11/29/2022]
Abstract
The tortoiseshell coat colour is characteristic to female cats, and its occurrence in tomcats is very rare and associated with chromosome abnormalities (additional copy of X chromosome). The aim of this study was identification of the genetic basis of a case of tortoiseshell colour in a fertile Maine coon tomcat. Cytogenetic and molecular genetic studies were carried out with painting molecular probes (WCPP) specific to the X and Y sex chromosomes as well as a DNA microsatellite panel for the parentage verification of cats. Cytogenetic analysis revealed only a single set of sex chromosomes typical for male - 38,XY. The results of the microsatellite polymorphism obtained from DNA showed three alleles in locus FCA201 and four alleles in loci FCA149 and FCA441 in different tissues (blood, hair roots and testicles). Based on these results, the case was diagnosed as a true chimerism 38,XY/38,XY. To the best of our knowledge, this is the first case of a 38,XY/38,XY chimera diagnosed in cats, confirmed by genetic analysis.
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Affiliation(s)
- Monika Bugno-Poniewierska
- Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Krakow, Krakow, Poland
| | - Barbara Kij
- Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Krakow, Krakow, Poland
| | - Wojciech Witarski
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Magdalena Wojtaszek
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Anna Radko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Angelika Podbielska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Izabela Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Science, Poznan, Poland
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
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Szczerbal I, Switonski M. Genetic disorders of sex development in cats: An update. Anim Reprod Sci 2020; 216:106353. [PMID: 32414464 DOI: 10.1016/j.anireprosci.2020.106353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 12/17/2022]
Abstract
Disorders of sex development (DSD) are rarely reported in cats, but this does not mean these occurrences are an insignificant reproductive and health problem in this species. The DSD condition affects reproduction and can be associated with an increased risk of gonadal tumorigenesis. In this review, an overview of findings since 2012 are presented that focus on cytogenetic and molecular genetic studies of cats with abnormal external genitalia. Results from advanced cytogenetic analysis of sex chromosomes indicate there is a range of abnormalities, including aneuploidies, structural rearrangements and freemartinism, which manifests as leukocyte XX/XY chimerism. The molecular abnormalities that result in feline monogenic and multifactorial DSD (such as hypospadias and cryptorchidism) are very few. There are only two mutations of genes (CYP11B1 and TAC3) which are known to be responsible for syndromes associated with abnormal sexual development. Several candidate genes (SRY, AR, SRD5A2, MAMLD1, DHH, HSD3B2, and HSD17B3) have also been examined, but no associations were identified between these polymorphisms and DSD phenotypes. The findings in developing the present review indicate sex chromosome abnormalities are quite common causes of feline DSD. The study of the molecular disorders that lead to the development of DSD in cats with normal XX or XY sex chromosome complements is still in its infancy, and further research is needed into this topic. It can be anticipated that the use of next generation sequencing technologies to study the genetic disorders that result in the DSD condition in cats will lead to an increase the detection of several causative mutations.
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Affiliation(s)
- I Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - M Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland.
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44
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Hu JY, Hao ZQ, Frantz L, Wu SF, Chen W, Jiang YF, Wu H, Kuang WM, Li H, Zhang YP, Yu L. Genomic consequences of population decline in critically endangered pangolins and their demographic histories. Natl Sci Rev 2020; 7:798-814. [PMID: 34692098 PMCID: PMC8288997 DOI: 10.1093/nsr/nwaa031] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/29/2020] [Accepted: 02/19/2020] [Indexed: 12/14/2022] Open
Abstract
Pangolins are among the most critically endangered animals due to heavy poaching and worldwide trafficking. However, their demographic histories and the genomic consequences of their recent population declines remain unknown. We generated high-quality de novo reference genomes for critically endangered Malayan (Manis javanica, MJ) and Chinese (M. pentadactyla, MP) pangolins and re-sequencing population genomic data from 74 MJs and 23 MPs. We recovered the population identities of illegally traded pangolins and previously unrecognized genetic populations that should be protected as evolutionarily distinct conservation units. Demographic reconstruction suggested environmental changes have resulted in a population size fluctuation of pangolins. Additionally, recent population size declines due to human activities have resulted in an increase in inbreeding and genetic load. Deleterious mutations were enriched in genes related to cancer/diseases and cholesterol homeostasis, which may have increased their susceptibility to diseases and decreased their survival potential to adapt to environmental changes and high-cholesterol diets. This comprehensive study provides not only high-quality pangolin reference genomes, but also valuable information concerning the driving factors of long-term population size fluctuations and the genomic impact of recent population size declines due to human activities, which is essential for pangolin conservation management and global action planning.
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Affiliation(s)
- Jing-Yang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Zi-Qian Hao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
- The Palaeogenomics and Bio-Archaeology Research Network, Department of Archaeology, University of Oxford, Oxford OX1 3TG, UK
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou 510070, China
| | - Yun-Fang Jiang
- Lushui Management and Conservation Branch of Gaoligong Mountain National Nature Reserve, Nujiang 673100, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Wei-Min Kuang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Haipeng Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
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45
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Fan H, Hu Y, Shan L, Yu L, Wang B, Li M, Wu Q, Wei F. Synteny search identifies carnivore Y chromosome for evolution of male specific genes. Integr Zool 2019; 14:224-234. [PMID: 30019860 DOI: 10.1111/1749-4877.12352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The explosive accumulation of mammalian genomes has provided a valuable resource to characterize the evolution of the Y chromosome. Unexpectedly, the Y-chromosome sequence has been characterized in only a small handful of species, with the majority being model organisms. Thus, identification of Y-linked scaffolds from unordered genome sequences is becoming more important. Here, we used a syntenic-based approach to generate the scaffolds of the male-specific region of the Y chromosome (MSY) from the genome sequence of 6 male carnivore species. Our results identified 14, 15, 9, 28, 14 and 11 Y-linked scaffolds in polar bears, pacific walruses, red pandas, cheetahs, ferrets and tigers, covering 1.55 Mbp, 2.62 Mbp, 964 Kb, 1.75 Mb, 2.17 Mbp and 1.84 Mb MSY, respectively. All the candidate Y-linked scaffolds in 3 selected species (red pandas, polar bears and tigers) were successfully verified using polymerase chain reaction. We re-annotated 8 carnivore MSYs including these 6 Y-linked scaffolds and domestic dog and cat MSY; a total of 11 orthologous genes conserved in at least 7 of the 8 carnivores were identified. These 11 Y-linked genes have significantly higher evolutionary rates compared with their X-linked counterparts, indicating less purifying selection for MSY genes. Taken together, our study shows that the approach of synteny search is a reliable and easily affordable strategy to identify Y-linked scaffolds from unordered carnivore genomes and provides a preliminary evolutionary study for carnivore MSY genes.
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Affiliation(s)
- Huizhong Fan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yibo Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Lei Shan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lijun Yu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bing Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Min Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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46
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Pei SW, Qin F, Li WH, Li FD, Yue XP. Copy number variation of ZNF280AY across 21 cattle breeds and its association with the reproductive traits of Holstein and Simmental bulls. J Dairy Sci 2019; 102:7226-7236. [PMID: 31202648 DOI: 10.3168/jds.2018-16063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/23/2019] [Indexed: 11/19/2022]
Abstract
The mammalian Y chromosome gene families in the ampliconic region are expressed predominantly or exclusively in the testis, and their copy number variations (CNV) are significantly associated with male reproductive traits, suggesting they have important roles in spermatogenesis and testicular development. ZNF280AY (zinc finger protein 280A, Y-linked) is a member of the zinc finger protein family and has been identified as a bovid-specific Y-chromosome gene. The current study applied a reliable quantitative real-time PCR method to estimate the CNV of ZNF280AY in 715 bulls across 21 cattle breeds and to further investigate the association of the CNV of ZNF280AY with bull reproductive traits and ZNF280AY mRNA expression levels in adult testis. The results revealed that the median copy number of ZNF280AY was 47, and the copy number varied from 11 to 154, showing significant CNV between and within the investigated cattle breeds. In addition, all 715 bulls were classified into Y1, Y2, and Y3 lineage groups based on a rapid genotyping method described previously. Pairwise comparisons indicated that bulls belonging to the Y1 lineage had a significantly lower median copy number (40) than bulls belonging to the Y2 (52) and Y3 lineages (57). Association analysis revealed that the CNV of ZNF280AY was correlated negatively with the percentage of normal sperm and sperm concentration in Holstein bulls, whereas no significant correlation was observed with ejaculation volume, total sperm count, sperm motility, postthaw motility (PTM), and scrotal circumference in Holstein and Simmental bulls. Furthermore, no correlation was observed between ZNF280AY copy number and ZNF280AY mRNA expression levels in the testis. The current study suggests that the CNV of the ZNF280AY gene family is associated with male reproductive traits and may serve as a valuable marker for early bull fertility selection in Holstein breeding programs.
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Affiliation(s)
- S W Pei
- State Key Laboratory of Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China
| | - F Qin
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, P. R. China
| | - W H Li
- State Key Laboratory of Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China
| | - F D Li
- State Key Laboratory of Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China; Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin 733300, P. R. China
| | - X P Yue
- State Key Laboratory of Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China.
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47
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Rando HM, Wadlington WH, Johnson JL, Stutchman JT, Trut LN, Farré M, Kukekova AV. The Red Fox Y-Chromosome in Comparative Context. Genes (Basel) 2019; 10:E409. [PMID: 31142040 PMCID: PMC6627929 DOI: 10.3390/genes10060409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat (Feliscatus), dog (Canislupusfamiliaris), and grey wolf (Canislupuslupus), providing the opportunity to examine the red fox (Vulpesvulpes) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific k-mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of BCORY2 and UBE1Y than has been reported in related species and fewer copies of SRY than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution.
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Affiliation(s)
- Halie M Rando
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - William H Wadlington
- Tropical Research and Education Center, Agronomy Department, University of Florida, Homestead, FL 33031, USA.
| | - Jennifer L Johnson
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Jeremy T Stutchman
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Lyudmila N Trut
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Marta Farré
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Anna V Kukekova
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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48
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Gažová I, Lengeling A, Summers KM. Lysine demethylases KDM6A and UTY: The X and Y of histone demethylation. Mol Genet Metab 2019; 127:31-44. [PMID: 31097364 DOI: 10.1016/j.ymgme.2019.04.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/29/2019] [Accepted: 04/29/2019] [Indexed: 12/15/2022]
Abstract
Histone demethylases remove transcriptional repressive marks from histones in the nucleus. KDM6A (also known as UTX) is a lysine demethylase which acts on the trimethylated lysine at position 27 in histone 3. The KDM6A gene is located on the X chromosome but escapes X inactivation even though it is not located in the pseudoautosomal region. There is a homologue of KDM6A on the Y chromosome, known as UTY. UTY was thought to have lost its demethylase activity and to represent a non-functional remnant of the ancestral KDM6A gene. However, results with knockout mice suggest that the gene is expressed and the protein performs some function within the cell. Female mice with homozygous deletion of Kdm6a do not survive, but hemizygous males are viable, attributed to the presence of the Uty gene. KDM6A is mutated in the human condition Kabuki syndrome type 2 (OMIM 300867) and in many cases of cancer. The amino acid sequence of KDM6A has been conserved across animal phyla, although it is only found on the X chromosome in eutherian mammals. In this review, we reanalyse existing data from various sources (protein sequence comparison, evolutionary genetics, transcription factor binding and gene expression analysis) to determine the function, expression and evolution of KDM6A and UTY and show that UTY has a functional role similar to KDM6A in metabolism and development.
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Affiliation(s)
- Iveta Gažová
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Andreas Lengeling
- Max Planck Society, Administrative Headquarters, Hofgartenstrasse 8, 80539 Munich, Germany
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia.
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49
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Tsai KL, Evans JM, Noorai RE, Starr-Moss AN, Clark LA. Novel Y Chromosome Retrocopies in Canids Revealed through a Genome-Wide Association Study for Sex. Genes (Basel) 2019; 10:genes10040320. [PMID: 31027231 PMCID: PMC6523286 DOI: 10.3390/genes10040320] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 12/12/2022] Open
Abstract
The lack of an annotated reference sequence for the canine Y chromosome has limited evolutionary studies, as well as our understanding of the role of Y-linked sequences in phenotypes with a sex bias. In genome-wide association studies (GWASs), we observed spurious associations with autosomal SNPs when sex was unbalanced in case-control cohorts and hypothesized that a subset of SNPs mapped to autosomes are in fact sex-linked. Using the Illumina 230K CanineHD array in a GWAS for sex, we identified SNPs that amplify in both sexes but possess significant allele frequency differences between males and females. We found 48 SNPs mapping to 14 regions of eight autosomes and the X chromosome that are Y-linked, appearing heterozygous in males and monomorphic in females. Within these 14 regions are eight genes: three autosomal and five X-linked. We investigated the autosomal genes (MITF, PPP2CB, and WNK1) and determined that the SNPs are diverged nucleotides in retrocopies that have transposed to the Y chromosome. MITFY and WNK1Y are expressed and appeared recently in the Canidae lineage, whereas PPP2CBY represents a much older insertion with no evidence of expression in the dog. This work reveals novel canid Y chromosome sequences and provides evidence for gene transposition to the Y from autosomes and the X.
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Affiliation(s)
- Kate L Tsai
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
| | - Jacquelyn M Evans
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-2152, USA.
| | - Rooksana E Noorai
- Clemson University Genomics and Bioinformatics Facility, Clemson University, Clemson, SC 29634, USA.
| | - Alison N Starr-Moss
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
| | - Leigh Anne Clark
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
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Smeds L, Kojola I, Ellegren H. The evolutionary history of grey wolf Y chromosomes. Mol Ecol 2019; 28:2173-2191. [PMID: 30788868 PMCID: PMC6850511 DOI: 10.1111/mec.15054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/30/2022]
Abstract
Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male-specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified ≈1,500 Y-linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Ilpo Kojola
- Natural Resources Institute Finland (Luke), Rovaniemi, Finland
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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