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Alexandrou A, Salameh N, Papaevripidou I, Nicolaou N, Myrianthopoulos P, Ketoni A, Kousoulidou L, Anastasiou AM, Evangelidou P, Tanteles GA, Sismani C. Hereditary multiple exostoses caused by a chromosomal inversion removing part of EXT1 gene. Mol Cytogenet 2023; 16:8. [PMID: 37217936 DOI: 10.1186/s13039-023-00638-0] [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: 01/10/2023] [Accepted: 05/07/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Hereditary multiple exostoses (HME) is an autosomal dominant skeletal disorder characterized by the development of multiple, circumscript and usually symmetric bony protuberances called osteochondromas. Most HME are caused by EXT1 and EXT2 loss of function mutations. Most pathogenic mutations are nonsense followed by missense mutations and deletions. CASE PRESENTATION Here we report on a patient with a rare and complex genotype resulting in a typical HME phenotype. Initial point mutation screening in EXT1 and EXT2 genes by Sanger sequencing did not reveal any pathogenic variants. The patient along with the healthy parents was subsequently referred for karyotype and array-Comparative Genomic Hybridization (CGH) analyses. Chromosomal analysis revealed two independent de novo apparently balanced rearrangements: a balanced translocation between the long arms of chromosomes 2 and 3 at breakpoints 2q22 and 3q13.2 and a pericentric inversion with breakpoints at 8p23.1q24.1. Both breakpoints were confirmed by Fluorescence In Situ Hybridization (FISH). Subsequently, array-CGH revealed a novel heterozygous deletion within the EXT1 gene at one of the inversion breakpoints, rendering the inversion unbalanced. The mode of inheritance, as well as the size of the deletion were further investigated by Quantitative Real-time PCR (qPCR), defining the deletion as de novo and of 3.1 kb in size, removing exon 10 of EXT1. The inversion in combination with the 8p23.1 deletion most likely abolishes the transcription of EXT1 downstream of exon 10 hence resulting in a truncated protein. CONCLUSIONS The identification of a rare and novel genetic cause of HME, highlights the importance of additional comprehensive investigation of patients with typical clinical manifestations, even when EXT1 and EXT2 mutation analysis is negative.
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Affiliation(s)
- Angelos Alexandrou
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, 6 Iroon Avenue, 2371, Ayios Dometios, PO Box 23462, 1683, Nicosia, Cyprus
| | - Nicole Salameh
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, 6 Iroon Avenue, 2371, Ayios Dometios, PO Box 23462, 1683, Nicosia, Cyprus
| | - Ioannis Papaevripidou
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, 6 Iroon Avenue, 2371, Ayios Dometios, PO Box 23462, 1683, Nicosia, Cyprus
| | - Nayia Nicolaou
- Clinical Genetics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Panayiotis Myrianthopoulos
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, 6 Iroon Avenue, 2371, Ayios Dometios, PO Box 23462, 1683, Nicosia, Cyprus
| | - Andria Ketoni
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, 6 Iroon Avenue, 2371, Ayios Dometios, PO Box 23462, 1683, Nicosia, Cyprus
| | - Ludmila Kousoulidou
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, 6 Iroon Avenue, 2371, Ayios Dometios, PO Box 23462, 1683, Nicosia, Cyprus
| | - Anna-Maria Anastasiou
- Clinical Genetics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Paola Evangelidou
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, 6 Iroon Avenue, 2371, Ayios Dometios, PO Box 23462, 1683, Nicosia, Cyprus
| | - George A Tanteles
- Clinical Genetics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Carolina Sismani
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, 6 Iroon Avenue, 2371, Ayios Dometios, PO Box 23462, 1683, Nicosia, Cyprus.
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2
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Součková K, Jasík M, Sovadinová I, Sember A, Sychrová E, Konieczna A, Bystrý V, Dyková I, Blažek R, Lukšíková K, Pavlica T, Jankásek M, Altmanová M, Žák J, Zbončáková A, Reichard M, Slabý O. From fish to cells: Establishment of continuous cell lines from embryos of annual killifish Nothobranchius furzeri and N. kadleci. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 259:106517. [PMID: 37087860 DOI: 10.1016/j.aquatox.2023.106517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
There is a growing need of alternative experimental models that avoid or minimize the use of animals due to ethical, economical, and scientific reasons. Surprisingly, the stable embryonic cell lines representing Nothobranchius spp., emerging vertebrate models in aging research, regenerative medicine, ecotoxicology, or genomics, have been not derived so far. This paper reports establishment and deep characterization of ten continuous cell lines from annual killifish embryos of N. furzeri and N. kadleci. The established cell lines exhibited mostly fibroblast- and epithelial-like morphology and steady growth rates with cell doubling time ranging from 27 to 40 h. All cell lines retained very similar characteristics even after continuous subcultivation (more than 100 passages) and extended storage in liquid nitrogen (∼3 years). The cytogenetic analysis of the cell lines revealed a diploid chromosome number mostly equal to 38 elements (i.e., the native chromosome count for both killifish species), with minor but diverse line/passage-specific karyotype changes compared to the patterns observed in non-cultured N. furzeri and N. kadleci somatic cells. Based on transcriptional analysis of marker genes, the cell lines displayed features of an undifferentiated state without signs of senescence even in advanced passages. We confirmed that the cell lines are transfectable and can form viable 3-D spheroids. The applicability of the cell lines for (eco)toxicological surveys was confirmed by assessing the effect of cytotoxic and growth inhibitory agents. Properties of established Nothobranchius embryonic cell lines open new possibilities for the application of this model in various fields of life sciences including molecular mechanisms of aging, karyotype (in)stability or differences in lifespan.
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Affiliation(s)
- Kamila Součková
- Ondřej Slabý Group, Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.
| | - Matej Jasík
- Ondřej Slabý Group, Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Iva Sovadinová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno 602 00, Czech Republic
| | - Alexandr Sember
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov 277 21, Czech Republic
| | - Eliška Sychrová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno 602 00, Czech Republic
| | - Anna Konieczna
- Ondřej Slabý Group, Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Vojtěch Bystrý
- Ondřej Slabý Group, Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Iva Dyková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 611 37, Czech Republic
| | - Radim Blažek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 611 37, Czech Republic; Institute of Vertebrate Biology, Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Karolína Lukšíková
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov 277 21, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague 128 44, Czech Republic
| | - Tomáš Pavlica
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov 277 21, Czech Republic; Department of Zoology, Faculty of Science, Charles University, Prague 128 44, Czech Republic
| | - Marek Jankásek
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov 277 21, Czech Republic; Department of Zoology, Faculty of Science, Charles University, Prague 128 44, Czech Republic
| | - Marie Altmanová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov 277 21, Czech Republic; Department of Ecology, Faculty of Science, Charles University, Prague 128 44, Czech Republic
| | - Jakub Žák
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 611 37, Czech Republic; Institute of Vertebrate Biology, Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Adriana Zbončáková
- Ondřej Slabý Group, Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Martin Reichard
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 611 37, Czech Republic; Institute of Vertebrate Biology, Czech Academy of Sciences, Brno 603 00, Czech Republic; Department of Ecology and Vertebrate Zoology, University of Łódź, Łódź 90-237, Poland
| | - Ondřej Slabý
- Ondřej Slabý Group, Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic; Department of Biology, Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic
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3
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Carreras-Gallo N, Cáceres A, Balagué-Dobón L, Ruiz-Arenas C, Andrusaityte S, Carracedo Á, Casas M, Chatzi L, Grazuleviciene R, Gutzkow KB, Lepeule J, Maitre L, Nieuwenhuijsen M, Slama R, Stratakis N, Thomsen C, Urquiza J, Wright J, Yang T, Escaramís G, Bustamante M, Vrijheid M, Pérez-Jurado LA, González JR. The early-life exposome modulates the effect of polymorphic inversions on DNA methylation. Commun Biol 2022; 5:455. [PMID: 35550596 PMCID: PMC9098634 DOI: 10.1038/s42003-022-03380-2] [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: 10/18/2021] [Accepted: 04/19/2022] [Indexed: 11/14/2022] Open
Abstract
Polymorphic genomic inversions are chromosomal variants with intrinsic variability that play important roles in evolution, environmental adaptation, and complex traits. We investigated the DNA methylation patterns of three common human inversions, at 8p23.1, 16p11.2, and 17q21.31 in 1,009 blood samples from children from the Human Early Life Exposome (HELIX) project and in 39 prenatal heart tissue samples. We found inversion-state specific methylation patterns within and nearby flanking each inversion region in both datasets. Additionally, numerous inversion-exposure interactions on methylation levels were identified from early-life exposome data comprising 64 exposures. For instance, children homozygous at inv-8p23.1 and higher meat intake were more susceptible to TDH hypermethylation (P = 3.8 × 10−22); being the inversion, exposure, and gene known risk factors for adult obesity. Inv-8p23.1 associated hypermethylation of GATA4 was also detected across numerous exposures. Our data suggests that the pleiotropic influence of inversions during development and lifetime could be substantially mediated by allele-specific methylation patterns which can be modulated by the exposome. Analysis of the relationship between presence of common DNA sequence inversions and DNA methylation patterns suggests a role for environmental exposures (such as food intake) in mediating inversion state-specific methylation patterns.
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Affiliation(s)
| | - Alejandro Cáceres
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Department of Mathematics, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya, Barcelona, 08019, Spain
| | | | - Carlos Ruiz-Arenas
- Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sandra Andrusaityte
- Department of Environmental Science, Vytautas Magnus University, 44248, Kaunas, Lithuania
| | - Ángel Carracedo
- Medicine Genomics Group, Centro de Investigación Biomédica en Red Enfermedades Raras (CIBERER), University of Santiago de Compostela, CEGEN-PRB3, Santiago de Compostela, Spain.,Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Servicio Gallego de Salud (SERGAS), Santiago de Compostela, Galicia, Spain
| | - Maribel Casas
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Leda Chatzi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Regina Grazuleviciene
- Department of Environmental Science, Vytautas Magnus University, 44248, Kaunas, Lithuania
| | - Kristine Bjerve Gutzkow
- Department of Environmental Health, Norwegian Institute of Public Health, 0456, Oslo, Norway
| | - Johanna Lepeule
- Institut national de la santé et de la recherche médicale (Inserm) and Université Grenoble-Alpes, Institute for Advanced Biosciences (IAB), Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, Grenoble, France
| | - Léa Maitre
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mark Nieuwenhuijsen
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Remy Slama
- Institut national de la santé et de la recherche médicale (Inserm) and Université Grenoble-Alpes, Institute for Advanced Biosciences (IAB), Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, Grenoble, France
| | - Nikos Stratakis
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Cathrine Thomsen
- Department of Environmental Health, Norwegian Institute of Public Health, 0456, Oslo, Norway
| | - Jose Urquiza
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Tiffany Yang
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Geòrgia Escaramís
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Department of Biomedical Science, Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain.,Research Group on Statistics, Econometrics and Health (GRECS), UdG, Girona, Spain
| | - Mariona Bustamante
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Martine Vrijheid
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luis A Pérez-Jurado
- Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Genetics Service, Hospital del Mar, Barcelona, Spain
| | - Juan R González
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain. .,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. .,Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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4
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Frequency and clinical significance of chromosomal inversions prenatally diagnosed by second trimester amniocentesis. Sci Rep 2022; 12:2215. [PMID: 35140290 PMCID: PMC8828714 DOI: 10.1038/s41598-022-06024-x] [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: 06/19/2021] [Accepted: 01/07/2022] [Indexed: 11/09/2022] Open
Abstract
To compare the frequency and clinical significance of familial and de novo chromosomal inversions during prenatal diagnosis. This was a retrospective study of inversions diagnosed prenatally in an Asian population by applying conventional GTG-banding to amniocyte cultures. Data from 2005 to 2019 were extracted from a single-center laboratory database. The types, frequencies, and inheritance patterns of multiple inversions were analyzed. Pericentric variant inversions of chromosome 9 or Y were excluded. In total, 56 (0.27%) fetuses with inversions were identified in the 15-year database of 21,120 confirmative diagnostic procedures. Pericentric and paracentric inversions accounted for 62.5% (35/56) and 37.5% of the inversions, respectively. Familial inversions accounted for nearly 90% of cases, and de novo mutation was identified in two pericentric and two paracentric cases. Inversions were most frequently identified on chromosomes 1 and 2 (16.1% of all inversions), followed by chromosomes 6, 7, and 10 (8.9% of all cases). The indications for invasive testing were as follows: advanced maternal age (67.3%), abnormal ultrasound findings (2.1%), abnormal serum aneuploidy screening (20.4%), and other indications (10.2%). The mode of inheritance was available for 67.9% of cases (38/56), with 89.5% of inversions being inherited (34/38). A slight preponderance of inheritance in female fetuses was observed. Three patients with inherited inversions opted for termination (two had severe central nervous system lesions and one had thalassemia major). Gestation continued for 53 fetuses, who exhibited no structural defects at birth or significant developmental problems a year after birth. Our study indicates that approximately 90% of prenatally diagnosed inversions involve familial inheritance, are spreading, and behave like founder effect mutations in this isolated population on an island. This finding can help to alleviate anxiety during prenatal counseling, which further underscores the importance of parental chromosomal analysis, further genetic studies, and appropriate counseling in cases where a nonfamilial inversion is diagnosed.
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Spracklen CN, Sim X. Progress in Defining the Genetic Contribution to Type 2 Diabetes in Individuals of East Asian Ancestry. Curr Diab Rep 2021; 21:17. [PMID: 33846905 DOI: 10.1007/s11892-021-01388-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/25/2021] [Indexed: 02/08/2023]
Abstract
PURPOSE OF REVIEW Prevalence of type 2 diabetes (T2D) and progression of complications differ between worldwide populations. While obesity is a major contributing risk factor, variations in physiological manifestations, e.g., developing T2D at lower body mass index in some populations, suggest other contributing factors. Early T2D genetic associations were mostly discovered in European ancestry populations. This review describes the progression of genetic discoveries associated with T2D in individuals of East Asian ancestry in the last 10 years and highlights the shared genetic susceptibility between the population groups and additional insights into genetic contributions to T2D. RECENT FINDINGS Through increased sample size and power, new genetic associations with T2D were discovered in East Asian ancestry populations, often with higher allele frequencies than European ancestry populations. As we continue to generate maps of T2D-associated variants across diverse populations, there will be a critical need to expand and diversify other omics resources to enable integration for clinical translation.
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Affiliation(s)
- Cassandra N Spracklen
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, 715 North Pleasant Street, 429 Arnold House, Amherst, MA, 01002, USA.
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, 12 Science Drive 2, #10-01, Tahir Foundation Building, Singapore, 117549, Singapore.
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6
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Guan J, Xu Y, Yu Y, Fu J, Ren F, Guo J, Zhao J, Jiang Q, Wei J, Xie H. Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape. Genome Biol 2021; 22:13. [PMID: 33402202 PMCID: PMC7784018 DOI: 10.1186/s13059-020-02239-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops. RESULTS Here, we generate a high-quality de novo genome assembly for a flat-fruit peach cultivar and produce a comprehensive SV map for peach, as a high proportion of genomic sequence is occupied by heterozygous SVs in the peach genome. We conduct population-level analyses that indicate SVs have undergone strong purifying selection during peach domestication, and find evidence of positive selection, with a significant preference for upstream and intronic regions during later peach improvement. We perform a SV-based GWAS that identifies a large 1.67-Mb heterozygous inversion that segregates perfectly with flat-fruit shape. Mechanistically, this derived allele alters the expression of the PpOFP2 gene positioned near the proximal breakpoint of the inversion, and we confirm in transgenic tomatoes that PpOFP2 is causal for flat-fruit shape. CONCLUSIONS Thus, beyond introducing new genomics resources for peach research, our study illustrates how focusing on SV data can drive basic functional discoveries in plant science.
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Affiliation(s)
- Jiantao Guan
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, People's Republic of China
| | - Yaoguang Xu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, People's Republic of China
| | - Yang Yu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, People's Republic of China
| | - Jun Fu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, People's Republic of China
| | - Fei Ren
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
| | - Jiying Guo
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
| | - Jianbo Zhao
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
| | - Quan Jiang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China.
| | - Jianhua Wei
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China.
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, People's Republic of China.
| | - Hua Xie
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China.
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, People's Republic of China.
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7
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Spracklen CN, Horikoshi M, Kim YJ, Lin K, Bragg F, Moon S, Suzuki K, Tam CHT, Tabara Y, Kwak SH, Takeuchi F, Long J, Lim VJY, Chai JF, Chen CH, Nakatochi M, Yao J, Choi HS, Iyengar AK, Perrin HJ, Brotman SM, van de Bunt M, Gloyn AL, Below JE, Boehnke M, Bowden DW, Chambers JC, Mahajan A, McCarthy MI, Ng MCY, Petty LE, Zhang W, Morris AP, Adair LS, Akiyama M, Bian Z, Chan JCN, Chang LC, Chee ML, Chen YDI, Chen YT, Chen Z, Chuang LM, Du S, Gordon-Larsen P, Gross M, Guo X, Guo Y, Han S, Howard AG, Huang W, Hung YJ, Hwang MY, Hwu CM, Ichihara S, Isono M, Jang HM, Jiang G, Jonas JB, Kamatani Y, Katsuya T, Kawaguchi T, Khor CC, Kohara K, Lee MS, Lee NR, Li L, Liu J, Luk AO, Lv J, Okada Y, Pereira MA, Sabanayagam C, Shi J, Shin DM, So WY, Takahashi A, Tomlinson B, Tsai FJ, van Dam RM, Xiang YB, Yamamoto K, Yamauchi T, Yoon K, Yu C, Yuan JM, Zhang L, Zheng W, Igase M, Cho YS, Rotter JI, Wang YX, Sheu WHH, Yokota M, Wu JY, Cheng CY, Wong TY, Shu XO, Kato N, Park KS, Tai ES, Matsuda F, Koh WP, Ma RCW, Maeda S, Millwood IY, Lee J, Kadowaki T, Walters RG, Kim BJ, Mohlke KL, Sim X. Identification of type 2 diabetes loci in 433,540 East Asian individuals. Nature 2020; 582:240-245. [PMID: 32499647 PMCID: PMC7292783 DOI: 10.1038/s41586-020-2263-3] [Citation(s) in RCA: 236] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 03/02/2020] [Indexed: 12/30/2022]
Abstract
Meta-analyses of genome-wide association studies (GWAS) have identified more than 240 loci that are associated with type 2 diabetes (T2D)1,2; however, most of these loci have been identified in analyses of individuals with European ancestry. Here, to examine T2D risk in East Asian individuals, we carried out a meta-analysis of GWAS data from 77,418 individuals with T2D and 356,122 healthy control individuals. In the main analysis, we identified 301 distinct association signals at 183 loci, and across T2D association models with and without consideration of body mass index and sex, we identified 61 loci that are newly implicated in predisposition to T2D. Common variants associated with T2D in both East Asian and European populations exhibited strongly correlated effect sizes. Previously undescribed associations include signals in or near GDAP1, PTF1A, SIX3, ALDH2, a microRNA cluster, and genes that affect the differentiation of muscle and adipose cells3. At another locus, expression quantitative trait loci at two overlapping T2D signals affect two genes-NKX6-3 and ANK1-in different tissues4-6. Association studies in diverse populations identify additional loci and elucidate disease-associated genes, biology, and pathways.
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Affiliation(s)
- Cassandra N Spracklen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, USA
| | - Momoko Horikoshi
- Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan
| | - Young Jin Kim
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Fiona Bragg
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Sanghoon Moon
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Ken Suzuki
- Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan
- Laboratory for Statistical and Translational Genetics, RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Claudia H T Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Soo-Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Victor J Y Lim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Masahiro Nakatochi
- Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, UCLA School of Medicine, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Hyeok Sun Choi
- Biomedical Science, Hallym University, Chuncheon, South Korea
| | - Apoorva K Iyengar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hannah J Perrin
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah M Brotman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Martijn van de Bunt
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
- Stanford University, Stanford, CA, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Donald W Bowden
- Center for Genomics and Personalized Medicine Research, Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - John C Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Anubha Mahajan
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Maggie C Y Ng
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Genomics and Personalized Medicine Research, Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Lauren E Petty
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, London, UK
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- School of Biological Sciences, University of Manchester, Manchester, UK
| | - Linda S Adair
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Masato Akiyama
- Laboratory for Statistical and Translational Genetics, RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan
- Laboratory for Statistical Analysis, RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Zheng Bian
- Chinese Academy of Medical Sciences, Beijing, China
| | - Juliana C N Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Li-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Miao-Li Chee
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, UCLA School of Medicine, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lee-Ming Chuang
- Division of Endocrinology & Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Institute of Preventive Medicine, School of Public Health, National Taiwan University, Taipei, Taiwan
| | - Shufa Du
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Myron Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, UCLA School of Medicine, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yu Guo
- Chinese Academy of Medical Sciences, Beijing, China
| | - Sohee Han
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Annie-Green Howard
- Department of Biostatistics, Carolina Population Center, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Yi-Jen Hung
- Division of Endocrine and Metabolism, Tri-Service General Hospital Songshan Branch, Taipei, Taiwan
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Mi Yeong Hwang
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Chii-Min Hwu
- Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Sahoko Ichihara
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke, Japan
| | - Masato Isono
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hye-Mi Jang
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Guozhi Jiang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Jost B Jonas
- Department of Ophthalmology, Medical Faculty Mannheim of the University of Heidelberg, Mannheim, Germany
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Geriatric and General Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Chiea-Chuen Khor
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Katsuhiko Kohara
- Department of Regional Resource Management, Ehime University Faculty of Collaborative Regional Innovation, Ehime, Japan
| | - Myung-Shik Lee
- Severance Biomedical Science Institute and Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Nanette R Lee
- Department of Anthropology, Sociology and History, University of San Carlos, Cebu City, Philippines
| | - Liming Li
- Department of Epidemiology and Biostatistics, Peking University Health Science Centre, Peking University, Beijing, China
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Andrea O Luk
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, Peking University Health Science Centre, Peking University, Beijing, China
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Mark A Pereira
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Jinxiu Shi
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Dong Mun Shin
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Wing Yee So
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Atsushi Takahashi
- Laboratory for Statistical and Translational Genetics, RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan
- Department of Genomic Medicine, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Brian Tomlinson
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Fuu-Jen Tsai
- Department of Medical Genetics and Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Yong-Bing Xiang
- State Key Laboratory of Oncogene and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kyungheon Yoon
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, Peking University Health Science Centre, Peking University, Beijing, China
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Liang Zhang
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michiya Igase
- Department of Anti-aging Medicine, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yoon Shin Cho
- Biomedical Science, Hallym University, Chuncheon, South Korea
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, UCLA School of Medicine, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ya-Xing Wang
- Beijing Institute of Ophthalmology, Ophthalmology and Visual Sciences Key Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wayne H H Sheu
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
- Division of Endocrinology and Metabolism, Department of Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | | | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kyong-Soo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Woon-Puay Koh
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Shiro Maeda
- Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Iona Y Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Juyoung Lee
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK.
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK.
| | - Bong-Jo Kim
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea.
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore.
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8
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Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR. Genome Res 2020; 30:724-735. [PMID: 32424072 PMCID: PMC7263195 DOI: 10.1101/gr.255273.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/17/2020] [Indexed: 12/20/2022]
Abstract
Despite the interest in characterizing genomic variation, the presence of large repeats at the breakpoints hinders the analysis of many structural variants. This is especially problematic for inversions, since there is typically no gain or loss of DNA. Here, we tested novel linkage-based droplet digital PCR (ddPCR) assays to study 20 inversions ranging from 3.1 to 742 kb flanked by inverted repeats (IRs) up to 134 kb long. Of those, we validated 13 inversions predicted by different genome-wide techniques. In addition, we obtained new experimental human population information across 95 African, European, and East Asian individuals for 16 inversions, including four already validated variants without high-throughput genotyping methods. Through comparison with previous data, independent replicates and both inversion breakpoints, we demonstrate that the technique is highly accurate and reproducible. Most studied inversions are widespread across continents, and their frequency is negatively correlated with genetic length. Moreover, all except two show clear signs of being recurrent, and we could better define the factors affecting recurrence levels and estimate the inversion rate across the genome. Finally, the generated genotypes have allowed us to check inversion functional effects, validating gene expression differences reported before for two inversions and finding new candidate associations. Therefore, the developed methodology makes it possible to screen these and other complex genomic variants quickly in a large number of samples for the first time, highlighting the importance of direct genotyping to assess their potential consequences and clinical implications.
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9
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Escouflaire C, Rebours E, Charles M, Orellana S, Cano M, Rivière J, Grohs C, Hayes H, Capitan A. Α de novo 3.8-Mb inversion affecting the EDA and XIST genes in a heterozygous female calf with generalized hypohidrotic ectodermal dysplasia. BMC Genomics 2019; 20:715. [PMID: 31533624 PMCID: PMC6749632 DOI: 10.1186/s12864-019-6087-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In mammals, hypohidrotic ectodermal dysplasia (HED) is a genetic disorder that is characterized by sparse hair, tooth abnormalities, and defects in cutaneous glands. Only four genes, EDA, EDAR, EDARADD and WNT10A account for more than 90% of HED cases, and EDA, on chromosome X, is involved in 50% of the cases. In this study, we explored an isolated case of a female Holstein calf with symptoms similar to HED. RESULTS Clinical examination confirmed the diagnosis. The affected female showed homogeneous hypotrichosis and oligodontia as previously observed in bovine EDAR homozygous and EDA hemizygous mutants. Under light microscopy, the hair follicles were thinner and located higher in the dermis of the frontal skin in the affected animal than in the control. Moreover, the affected animal showed a five-fold increase in the number of hair follicles and a four-fold decrease in the diameter of the pilary canals. Pedigree analysis revealed that the coefficient of inbreeding of the affected calf (4.58%) was not higher than the average population inbreeding coefficient (4.59%). This animal had ten ancestors in its paternal and maternal lineages. By estimating the number of affected cases that would be expected if any of these common ancestors carried a recessive mutation, we concluded that, if they existed, other cases of HED should have been reported in France, which is not the case. Therefore, we assumed that the causal mutation was dominant and de novo. By analyzing whole-genome sequencing data, we identified a large chromosomal inversion with breakpoints located in the first introns of the EDA and XIST genes. Genotyping by PCR-electrophoresis the case and its parents allowed us to demonstrate the de novo origin of this inversion. Finally, using various sources of information we present a body of evidence that supports the hypothesis that this mutation is responsible for a skewed inactivation of X, and that only the normal X can be inactivated. CONCLUSIONS In this article, we report a unique case of X-linked HED affected Holstein female calf with an assumed full inactivation of the normal X-chromosome, thus leading to a severe phenotype similar to that of hemizygous males.
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Affiliation(s)
- Clémentine Escouflaire
- INRA, GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,Allice, 75595, Paris, France.
| | - Emmanuelle Rebours
- INRA, GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Mathieu Charles
- INRA, GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,INRA, SIGENAE, GABI, 78350, Jouy-en-Josas, France
| | - Sébastien Orellana
- INRA, GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Margarita Cano
- INRA, GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Julie Rivière
- INRA, GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,INRA, Micalis Institute, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Cécile Grohs
- INRA, GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Hélène Hayes
- INRA, GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Aurélien Capitan
- INRA, GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,Allice, 75595, Paris, France.
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10
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Giner-Delgado C, Villatoro S, Lerga-Jaso J, Gayà-Vidal M, Oliva M, Castellano D, Pantano L, Bitarello BD, Izquierdo D, Noguera I, Olalde I, Delprat A, Blancher A, Lalueza-Fox C, Esko T, O'Reilly PF, Andrés AM, Ferretti L, Puig M, Cáceres M. Evolutionary and functional impact of common polymorphic inversions in the human genome. Nat Commun 2019; 10:4222. [PMID: 31530810 PMCID: PMC6748972 DOI: 10.1038/s41467-019-12173-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 08/27/2019] [Indexed: 12/21/2022] Open
Abstract
Inversions are one type of structural variants linked to phenotypic differences and adaptation in multiple organisms. However, there is still very little information about polymorphic inversions in the human genome due to the difficulty of their detection. Here, we develop a new high-throughput genotyping method based on probe hybridization and amplification, and we perform a complete study of 45 common human inversions of 0.1–415 kb. Most inversions promoted by homologous recombination occur recurrently in humans and great apes and they are not tagged by SNPs. Furthermore, there is an enrichment of inversions showing signatures of positive or balancing selection, diverse functional effects, such as gene disruption and gene-expression changes, or association with phenotypic traits. Therefore, our results indicate that the genome is more dynamic than previously thought and that human inversions have important functional and evolutionary consequences, making possible to determine for the first time their contribution to complex traits. Inversions are a little-studied type of genomic variation that could contribute to phenotypic traits. Here the authors characterize 45 common polymorphic inversions in human populations and investigate their evolutionary and functional impact.
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Affiliation(s)
- Carla Giner-Delgado
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Sergi Villatoro
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Jon Lerga-Jaso
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Magdalena Gayà-Vidal
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain.,CIBIO/InBIO Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Vairão, Distrito do Porto, 4485-661, Portugal
| | - Meritxell Oliva
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - David Castellano
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Lorena Pantano
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Bárbara D Bitarello
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Saxony, 04103, Germany
| | - David Izquierdo
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Isaac Noguera
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Iñigo Olalde
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, 08003, Spain
| | - Alejandra Delprat
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Antoine Blancher
- Laboratoire d'immunologie, CHU de Toulouse, IFB Hôpital Purpan, Toulouse, 31059, France.,Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Université Paul Sabatier (UPS), Toulouse, 31024, France
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, 08003, Spain
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia
| | - Paul F O'Reilly
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Saxony, 04103, Germany.,UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, OX3 7LF, UK
| | - Marta Puig
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Mario Cáceres
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain. .,ICREA, Barcelona, 08010, Spain.
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11
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Dorajoo R, Chang X, Gurung RL, Li Z, Wang L, Wang R, Beckman KB, Adams-Haduch J, M Y, Liu S, Meah WY, Sim KS, Lim SC, Friedlander Y, Liu J, van Dam RM, Yuan JM, Koh WP, Khor CC, Heng CK. Loci for human leukocyte telomere length in the Singaporean Chinese population and trans-ethnic genetic studies. Nat Commun 2019; 10:2491. [PMID: 31171785 PMCID: PMC6554354 DOI: 10.1038/s41467-019-10443-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/09/2019] [Indexed: 01/02/2023] Open
Abstract
Genetic factors underlying leukocyte telomere length (LTL) may provide insights into telomere homeostasis, with direct links to disease susceptibility. Genetic evaluation of 23,096 Singaporean Chinese samples identifies 10 genome-wide loci (P < 5 × 10-8). Several of these contain candidate genes (TINF2, PARP1, TERF1, ATM and POT1) with potential roles in telomere biology and DNA repair mechanisms. Meta-analyses with additional 37,505 European individuals reveals six more genome-wide loci, including associations at MPHOSPH6, NKX2-3 and TYMS. We demonstrate that longer LTL associates with protection against respiratory disease mortality [HR = 0.854(0.804-0.906), P = 1.88 × 10-7] in the Singaporean Chinese samples. We further show that the LTL reducing SNP rs7253490 associates with respiratory infections (P = 7.44 × 10-4) although this effect may not be strongly mediated through LTL. Our data expands on the genetic basis of LTL and may indicate on a potential role of LTL in immune competence.
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Affiliation(s)
- Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Xuling Chang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, 119074, Singapore
| | - Resham Lal Gurung
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, 768828, Singapore
| | - Zheng Li
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Ling Wang
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Renwei Wang
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Kenneth B Beckman
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jennifer Adams-Haduch
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Yiamunaa M
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, 768828, Singapore
| | - Sylvia Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, 768828, Singapore
| | - Wee Yang Meah
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Kar Seng Sim
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Su Chi Lim
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, 768828, Singapore
- Diabetes Centre, Khoo Teck Puat Hospital, Singapore, 768828, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549, Singapore
| | - Yechiel Friedlander
- School of Public Health and Community Medicine, Hebrew University of Jerusalem, Jerusalem, 12272, Israel
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Woon-Puay Koh
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549, Singapore
- Health Systems and Services Research, Duke-NUS Medical School Singapore, Singapore, 169857, Singapore
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore.
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore.
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, 119074, Singapore.
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12
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Cheng C, Tan JC, Hahn MW, Besansky NJ. Systems genetic analysis of inversion polymorphisms in the malaria mosquito Anopheles gambiae. Proc Natl Acad Sci U S A 2018; 115:E7005-E7014. [PMID: 29987007 PMCID: PMC6064990 DOI: 10.1073/pnas.1806760115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inversion polymorphisms in the African malaria vector Anopheles gambiae segregate along climatic gradients of aridity. Despite indirect evidence of their adaptive significance, little is known of the phenotypic targets of selection or the underlying genetic mechanisms. Here we adopt a systems genetics approach to explore the interaction of two inversions on opposite arms of chromosome 2 with gender, climatic conditions, and one another. We measure organismal traits and transcriptional profiles in 8-d-old adults of both sexes and four alternative homokaryotypic classes reared under two alternative climatic regimes. We show that karyotype strongly influences both organismal traits and transcriptional profiles but that the strength and direction of the effects depend upon complex interactions with gender and environmental conditions and between inversions on independent arms. Our data support the suppressed recombination model for the role of inversions in local adaptation, and-supported by transcriptional and physiological measurements following perturbation with the drug rapamycin-suggest that one mechanism underlying their adaptive role may be the maintenance of energy homeostasis.
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Affiliation(s)
- Changde Cheng
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - John C Tan
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Computer Science, Indiana University, Bloomington, IN 47405
| | - Nora J Besansky
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556;
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
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13
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Roesti M. Varied Genomic Responses to Maladaptive Gene Flow and Their Evidence. Genes (Basel) 2018; 9:E298. [PMID: 29899287 PMCID: PMC6027369 DOI: 10.3390/genes9060298] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/17/2018] [Accepted: 05/30/2018] [Indexed: 12/02/2022] Open
Abstract
Adaptation to a local environment often occurs in the face of maladaptive gene flow. In this perspective, I discuss several ideas on how a genome may respond to maladaptive gene flow during adaptation. On the one hand, selection can build clusters of locally adaptive alleles at fortuitously co-localized loci within a genome, thereby facilitating local adaptation with gene flow ('allele-only clustering'). On the other hand, the selective pressure to link adaptive alleles may drive co-localization of the actual loci relevant for local adaptation within a genome through structural genome changes or an evolving intra-genomic crossover rate ('locus clustering'). While the expected outcome is, in both cases, a higher frequency of locally adaptive alleles in some genome regions than others, the molecular units evolving in response to gene flow differ (i.e., alleles versus loci). I argue that, although making this distinction is important, we commonly lack the critical empirical evidence to do so. This is mainly because many current approaches are biased towards detecting local adaptation in genome regions with low crossover rates. The importance of low-crossover genome regions for adaptation with gene flow, such as in co-localizing relevant loci within a genome, thus remains unclear. Future empirical investigations should address these questions by making use of comparative genomics, where multiple de novo genome assemblies from species evolved under different degrees of genetic exchange are compared. This research promises to advance our understanding of how a genome adapts to maladaptive gene flow, thereby promoting adaptive divergence and reproductive isolation.
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Affiliation(s)
- Marius Roesti
- Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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14
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Artemov GN, Bondarenko SM, Naumenko AN, Stegniy VN, Sharakhova MV, Sharakhov IV. Partial-arm translocations in evolution of malaria mosquitoes revealed by high-coverage physical mapping of the Anopheles atroparvus genome. BMC Genomics 2018; 19:278. [PMID: 29688842 PMCID: PMC5914054 DOI: 10.1186/s12864-018-4663-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/12/2018] [Indexed: 02/06/2023] Open
Abstract
Background Malaria mosquitoes have had a remarkable stability in the number of chromosomes in their karyotype (2n = 6) during 100 million years of evolution. Moreover, autosomal arms were assumed to maintain their integrity even if their associations with each other changed via whole-arm translocations. Here we use high-coverage comparative physical genome mapping of three Anopheles species to test the extent of evolutionary conservation of chromosomal arms in malaria mosquitoes. Results In this study, we developed a physical genome map for Anopheles atroparvus, one of the dominant malaria vectors in Europe. Using fluorescence in situ hybridization (FISH) of DNA probes with the ovarian nurse cell polytene chromosomes and synteny comparison, we anchored 56 genomic scaffolds to the An. atroparvus chromosomes. The obtained physical map represents 89.6% of the An. atroparvus genome. This genome has the second highest mapping coverage among Anophelinae assemblies after An. albimanus, which has 98.2% of the genome assigned to its chromosomes. A comparison of the An. atroparvus, An. albimanus, and An. gambiae genomes identified partial-arm translocations between the autosomal arms that break down the integrity of chromosome elements in evolution affecting the structure of the genetic material in the pericentromeric regions. Unlike An. atroparvus and An. albimanus, all chromosome elements of An. gambiae are fully syntenic with chromosome elements of the putative ancestral Anopheles karyotype. We also detected nonrandom distribution of large conserved synteny blocks and confirmed a higher rate of inversion fixation in the X chromosome compared with autosomes. Conclusions Our study demonstrates the power of physical mapping for understanding the genome evolution in malaria mosquitoes. The results indicate that syntenic relationships among chromosome elements of Anopheles species have not been fully preserved because of multiple partial-arm translocations. Electronic supplementary material The online version of this article (10.1186/s12864-018-4663-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gleb N Artemov
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk, 634050, Russia
| | - Semen M Bondarenko
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk, 634050, Russia
| | - Anastasia N Naumenko
- Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA, 24061, USA
| | - Vladimir N Stegniy
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk, 634050, Russia
| | - Maria V Sharakhova
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk, 634050, Russia. .,Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA, 24061, USA.
| | - Igor V Sharakhov
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk, 634050, Russia. .,Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA, 24061, USA.
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15
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Luteijn RD, Drexler I, Smith GL, Lebbink RJ, Wiertz EJHJ. Mutagenic repair of double-stranded DNA breaks in vaccinia virus genomes requires cellular DNA ligase IV activity in the cytosol. J Gen Virol 2018; 99:790-804. [PMID: 29676720 PMCID: PMC7614823 DOI: 10.1099/jgv.0.001034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Poxviruses comprise a group of large dsDNA viruses that include members relevant to human and animal health, such as variola virus, monkeypox virus, cowpox virus and vaccinia virus (VACV). Poxviruses are remarkable for their unique replication cycle, which is restricted to the cytoplasm of infected cells. The independence from the host nucleus requires poxviruses to encode most of the enzymes involved in DNA replication, transcription and processing. Here, we use the CRISPR/Cas9 genome engineering system to induce DNA damage to VACV (strain Western Reserve) genomes. We show that targeting CRISPR/Cas9 to essential viral genes limits virus replication efficiently. Although VACV is a strictly cytoplasmic pathogen, we observed extensive viral genome editing at the target site; this is reminiscent of a non-homologous end-joining DNA repair mechanism. This pathway was not dependent on the viral DNA ligase, but critically involved the cellular DNA ligase IV. Our data show that DNA ligase IV can act outside of the nucleus to allow repair of dsDNA breaks in poxvirus genomes. This pathway might contribute to the introduction of mutations within the genome of poxviruses and may thereby promote the evolution of these viruses.
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Affiliation(s)
- Rutger David Luteijn
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Present address: Department of Molecular and Cell Biology, University of California, Berkeley, USA
| | - Ingo Drexler
- Institute for Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | | | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emmanuel J H J Wiertz
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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16
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Rao S, Ghani M, Guo Z, Deming Y, Wang K, Sims R, Mao C, Yao Y, Cruchaga C, Stephan DA, Rogaeva E. An APOE-independent cis-eSNP on chromosome 19q13.32 influences tau levels and late-onset Alzheimer's disease risk. Neurobiol Aging 2018; 66:178.e1-178.e8. [PMID: 29395286 DOI: 10.1016/j.neurobiolaging.2017.12.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/18/2017] [Accepted: 12/27/2017] [Indexed: 10/18/2022]
Abstract
Although multiple susceptibility loci for late-onset Alzheimer's disease (LOAD) have been identified, a large portion of the genetic risk for this disease remains unexplained. LOAD risk may be associated with single-nucleotide polymorphisms responsible for changes in gene expression (eSNPs). To detect eSNPs associated with LOAD, we integrated data from LOAD genome-wide association studies and expression quantitative trait loci using Sherlock (a Bayesian statistical method). We identified a cis-regulatory eSNP (rs2927438) located on chromosome 19q13.32, for which subsequent analyses confirmed the association with both LOAD risk and the expression level of several nearby genes. Importantly, rs2927438 may represent an APOE-independent LOAD eSNP according to the weak linkage disequilibrium of rs2927438 with the 2 polymorphisms (rs7412 and rs429358) defining the APOE-ε2, -ε3, and -ε4 alleles. Furthermore, rs2927438 does not influence chromatin interaction events at the APOE locus or cis-regulation of APOE expression. Further exploratory analysis revealed that rs2927438 is significantly associated with tau levels in the cerebrospinal fluid. Our findings suggest that rs2927438 may confer APOE-independent risk for LOAD.
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Affiliation(s)
- Shuquan Rao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Mahdi Ghani
- Tanz Centre for Research in Neurodegenerative Diseases, and Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Zhiyun Guo
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Kesheng Wang
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN, USA
| | - Rebecca Sims
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Canquan Mao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Yao Yao
- Department of Fundamental Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Dietrich A Stephan
- Department of Human Genetics, Graduate School of Public Health, Pittsburgh, PA, USA
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, and Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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17
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Puerma E, Orengo DJ, Aguadé M. Inversion evolutionary rates might limit the experimental identification of inversion breakpoints in non-model species. Sci Rep 2017; 7:17281. [PMID: 29222501 PMCID: PMC5722822 DOI: 10.1038/s41598-017-17650-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/29/2017] [Indexed: 11/09/2022] Open
Abstract
Chromosomal inversions are structural changes that alter gene order but generally not gene content in the affected region. In Drosophila, extensive cytological studies revealed the widespread character of inversion polymorphism, with evidence for its adaptive character. In Drosophila subobscura, polymorphism affects both its four large autosomal elements and its X (A) chromosome. The characterization of eight of these autosomal inversions breakpoints revealed that most of them originated through the staggered-breaks mechanism. Here, we have performed chromosomal walks to identify the breakpoints of two X-chromosome widely distributed inversions -A2 and A1- of D. subobscura. Inversion A2 is considered a warm-adapted arrangement that exhibits parallel latitudinal clines in the species ancestral distribution area and in both American subcontinents, whereas inversion A1 is only present in the Palearctic region where it presents an east-west cline. The duplication detected at the A2 inversion breakpoints is consistent with its origin by the staggered-breaks mechanism. Inversion A1 breakpoints could not be molecularly identified even though they could be narrowly delimited. This result points to chromosome walking limitations when using as a guide the genome of other species. Limitations stem from the rate of evolution by paracentric inversions, which in Drosophila is highest for the X chromosome.
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Affiliation(s)
- Eva Puerma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
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18
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Basak AK, Chatterjee T, Ghosh SK, Chakravarty A. Impacts of dietary exposure to sodium or potassium salts of nitrate and nitrite on the development of Drosophila melanogaster. Interdiscip Toxicol 2017; 10:70-78. [PMID: 30123041 PMCID: PMC6096860 DOI: 10.1515/intox-2017-0012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 10/25/2017] [Indexed: 12/27/2022] Open
Abstract
The effects of four food additives, namely sodium nitrite (NaNO2), sodium nitrate (NaNO3), potassium nitrite (KNO2), and potassium nitrate (KNO3), on animal development were evaluated by using Drosophila melanogster, a model organism. Adult male and female flies were allowed to breed in culture medium, each containing one of 4 concentrations, i.e.10, 20, 30 or 40 mM of the above mentioned salts. The concentration of 40 mM, NaNO2 and KNO2 completely arrested the development of the flies. Of the different concentrations of the four salts tested, exposure of flies to 30 mM NaNO2 exhibited only significant delays in the initial appearances of third instar larvae, pupae and young adults, along with huge reduction in the number of pupae and young adults compared to controls. Rearrangements like inversions, deletion looping, regional shrinking, as well as highly enlarged puffing, etc. were also observed in the polytene chromosomes of the third instar larvae exposed to 30 mM NaNO2. Developmental outcomes of the flies exposed to varying concentrations of NaNO3 and KNO3 did not differ significantly from the controls. Owing to the extensive genetic homology between Drosophila and human and the successful uses of this fly as models in developmental and toxicological studies, we speculate that the experimental results exhibited by this organism in our study strongly advocate for abstaining from the dietary use of NaNO2 and KNO2 during human pregnancies to avoid possible negative developmental outcomes.
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Affiliation(s)
- Ashim Kumar Basak
- Dept. of Molecular Biology, Institute of Genetic Engineering, 30 Thakurhat Road, Kolkata-700128, West Bengal, India
| | - Tridip Chatterjee
- Dept. of Molecular Biology, Institute of Genetic Engineering, 30 Thakurhat Road, Kolkata-700128, West Bengal, India
- Dept. of Human Genetics, Institute of Genetic Medicine and Genomic Science, 30A Thakurhat Road, Kolkata-700128, West Bengal, India
| | - Swapan Kumar Ghosh
- Molecular Mycopathology Lab, Department of Botany, R K Mission VC College, Rahara, Kolkata 700118, India
| | - Amit Chakravarty
- Dept. of Molecular Biology, Institute of Genetic Engineering, 30 Thakurhat Road, Kolkata-700128, West Bengal, India
- Dept. of Human Genetics, Institute of Genetic Medicine and Genomic Science, 30A Thakurhat Road, Kolkata-700128, West Bengal, India
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19
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Vicente-Salvador D, Puig M, Gayà-Vidal M, Pacheco S, Giner-Delgado C, Noguera I, Izquierdo D, Martínez-Fundichely A, Ruiz-Herrera A, Estivill X, Aguado C, Lucas-Lledó JI, Cáceres M. Detailed analysis of inversions predicted between two human genomes: errors, real polymorphisms, and their origin and population distribution. Hum Mol Genet 2017; 26:567-581. [PMID: 28025331 DOI: 10.1093/hmg/ddw415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/05/2016] [Indexed: 12/11/2022] Open
Abstract
The growing catalogue of structural variants in humans often overlooks inversions as one of the most difficult types of variation to study, even though they affect phenotypic traits in diverse organisms. Here, we have analysed in detail 90 inversions predicted from the comparison of two independently assembled human genomes: the reference genome (NCBI36/HG18) and HuRef. Surprisingly, we found that two thirds of these predictions (62) represent errors either in assembly comparison or in one of the assemblies, including 27 misassembled regions in HG18. Next, we validated 22 of the remaining 28 potential polymorphic inversions using different PCR techniques and characterized their breakpoints and ancestral state. In addition, we determined experimentally the derived allele frequency in Europeans for 17 inversions (DAF = 0.01-0.80), as well as the distribution in 14 worldwide populations for 12 of them based on the 1000 Genomes Project data. Among the validated inversions, nine have inverted repeats (IRs) at their breakpoints, and two show nucleotide variation patterns consistent with a recurrent origin. Conversely, inversions without IRs have a unique origin and almost all of them show deletions or insertions at the breakpoints in the derived allele mediated by microhomology sequences, which highlights the importance of mechanisms like FoSTeS/MMBIR in the generation of complex rearrangements in the human genome. Finally, we found several inversions located within genes and at least one candidate to be positively selected in Africa. Thus, our study emphasizes the importance of careful analysis and validation of large-scale genomic predictions to extract reliable biological conclusions.
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Affiliation(s)
- David Vicente-Salvador
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Marta Puig
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Magdalena Gayà-Vidal
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Sarai Pacheco
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Carla Giner-Delgado
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, (Barcelona), Spain
| | - Isaac Noguera
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - David Izquierdo
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | | | - Aurora Ruiz-Herrera
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.,Departament de Biologia Celular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Xavier Estivill
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Aguado
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - José Ignacio Lucas-Lledó
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.,Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Paterna (València), Spain and
| | - Mario Cáceres
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.,ICREA, Barcelona, Spain
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