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Recuerda M, Campagna L. How structural variants shape avian phenotypes: Lessons from model systems. Mol Ecol 2024:e17364. [PMID: 38651830 DOI: 10.1111/mec.17364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although recent advances in long-read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review the role of SVs in shaping phenotypes in avian model systems, and identify some general patterns in SV type, length and their associated traits. We found that most of the avian SVs so far identified are short indels in chickens, which are frequently associated with changes in body weight and plumage colouration. Overall, we found that relatively short SVs are more frequently detected, likely due to a combination of their prevalence compared to large SVs, and a detection bias, stemming primarily from the widespread use of short-read sequencing and associated analytical methods. SVs most commonly involve non-coding regions, especially introns, and when patterns of inheritance were reported, SVs associated primarily with dominant discrete traits. We summarise several examples of phenotypic convergence across different species, mediated by different SVs in the same or different genes and different types of changes in the same gene that can lead to various phenotypes. Complex rearrangements and supergenes, which can simultaneously affect and link several genes, tend to have pleiotropic phenotypic effects. Additionally, SVs commonly co-occur with single-nucleotide polymorphisms, highlighting the need to consider all types of genetic changes to understand the basis of phenotypic traits. We end by summarising expectations for when long-read technologies become commonly implemented in non-model birds, likely leading to an increase in SV discovery and characterisation. The growing interest in this subject suggests an increase in our understanding of the phenotypic effects of SVs in upcoming years.
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Affiliation(s)
- María Recuerda
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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2
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Redaelli S, Grati FR, Tritto V, Giannuzzi G, Recalcati MP, Sala E, Villa N, Crosti F, Roversi G, Malvestiti F, Zanatta V, Repetti E, Rodeschini O, Valtorta C, Catusi I, Romitti L, Martinoli E, Conconi D, Dalprà L, Lavitrano M, Riva P, Bentivegna A. Olfactory receptor genes and chromosome 11 structural aberrations: Players or spectators? HGG Adv 2024; 5:100261. [PMID: 38160254 PMCID: PMC10820794 DOI: 10.1016/j.xhgg.2023.100261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024] Open
Abstract
The largest multi-gene family in metazoans is the family of olfactory receptor (OR) genes. Human ORs are organized in clusters over most chromosomes and seem to include >0.1% the human genome. Because 369 out of 856 OR genes are mapped on chromosome 11 (HSA11), we sought to determine whether they mediate structural rearrangements involving this chromosome. To this aim, we analyzed 220 specimens collected during diagnostic procedures involving structural rearrangements of chromosome 11. A total of 222 chromosomal abnormalities were included, consisting of inversions, deletions, translocations, duplications, and one insertion, detected by conventional chromosome analysis and/or fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (array-CGH). We verified by bioinformatics and statistical approaches the occurrence of breakpoints in cytobands with or without OR genes. We found that OR genes are not involved in chromosome 11 reciprocal translocations, suggesting that different DNA motifs and mechanisms based on homology or non-homology recombination can cause chromosome 11 structural alterations. We also considered the proximity between the chromosomal territories of chromosome 11 and its partner chromosomes involved in the translocations by using the deposited Hi-C data concerning the possible occurrence of chromosome interactions. Interestingly, most of the breakpoints are located in regions highly involved in chromosome interactions. Further studies should be carried out to confirm the potential role of chromosome territories' proximity in promoting genome structural variation, so fundamental in our understanding of the molecular basis of medical genetics and evolutionary genetics.
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Affiliation(s)
- Serena Redaelli
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Francesca Romana Grati
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, Toma Advanced Biomedical Assays S.p.A. (ImpactLab), 21052 Busto Arsizio, Italy
| | - Viviana Tritto
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20122 Milan, Italy
| | | | - Maria Paola Recalcati
- IRCCS Istituto Auxologico Italiano, Medical Cytogenetics Laboratory, 20095 Cusano Milanino, Italy
| | - Elena Sala
- UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Nicoletta Villa
- UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Francesca Crosti
- UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Gaia Roversi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Francesca Malvestiti
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, Toma Advanced Biomedical Assays S.p.A. (ImpactLab), 21052 Busto Arsizio, Italy
| | - Valentina Zanatta
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, Toma Advanced Biomedical Assays S.p.A. (ImpactLab), 21052 Busto Arsizio, Italy
| | - Elena Repetti
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, Toma Advanced Biomedical Assays S.p.A. (ImpactLab), 21052 Busto Arsizio, Italy
| | - Ornella Rodeschini
- IRCCS Istituto Auxologico Italiano, Medical Cytogenetics Laboratory, 20095 Cusano Milanino, Italy
| | - Chiara Valtorta
- IRCCS Istituto Auxologico Italiano, Medical Cytogenetics Laboratory, 20095 Cusano Milanino, Italy
| | - Ilaria Catusi
- IRCCS Istituto Auxologico Italiano, Medical Cytogenetics Laboratory, 20095 Cusano Milanino, Italy
| | - Lorenza Romitti
- Pathology and Cytogenetics Laboratory, Clinical Pathology Department, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20162 Milan, Italy
| | - Emanuela Martinoli
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20122 Milan, Italy
| | - Donatella Conconi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Leda Dalprà
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; UC Medical Genetics, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Marialuisa Lavitrano
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Paola Riva
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20122 Milan, Italy
| | - Angela Bentivegna
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy.
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3
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Ament-Velásquez SL, Vogan AA, Wallerman O, Hartmann FE, Gautier V, Silar P, Giraud T, Johannesson H. High-Quality Genome Assemblies of 4 Members of the Podospora anserina Species Complex. Genome Biol Evol 2024; 16:evae034. [PMID: 38386982 PMCID: PMC10936905 DOI: 10.1093/gbe/evae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/29/2023] [Accepted: 02/17/2024] [Indexed: 02/24/2024] Open
Abstract
The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of 7 closely related species. In addition to P. anserina, high-quality genomic resources are available for 2 of these taxa. Here, we provide chromosome-level annotated assemblies of the 4 remaining species of the complex, as well as a comprehensive data set of annotated assemblies from a total of 28 Podospora genomes. We find that all 7 species have genomes of around 35 Mb arranged in 7 chromosomes that are mostly collinear and less than 2% divergent from each other at genic regions. We further attempt to resolve their phylogenetic relationships, finding significant levels of phylogenetic conflict as expected from a rapid and recent diversification.
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Affiliation(s)
- S Lorena Ament-Velásquez
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Comparative Genetics and Functional Genomics, Uppsala University, 752 37 Uppsala, Sweden
| | - Fanny E Hartmann
- Ecologie Systematique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91198 Gif-sur-Yvette, France
| | - Valérie Gautier
- Laboratoire Interdisciplinaire des Energies de Demain (LIED), Université de Paris Cité, F-75013 Paris, France
| | - Philippe Silar
- Laboratoire Interdisciplinaire des Energies de Demain (LIED), Université de Paris Cité, F-75013 Paris, France
| | - Tatiana Giraud
- Ecologie Systematique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91198 Gif-sur-Yvette, France
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
- The Royal Swedish Academy of Sciences, 114 18 Stockholm, Sweden
- Department of Ecology, Environmental and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
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4
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Kretschmer R, Santos de Souza M, Gunski RJ, Del Valle Garnero A, de Freitas TRO, Zefa E, Toma GA, Cioffi MDB, Herculano Corrêa de Oliveira E, O'Connor RE, Griffin DK. Understanding the chromosomal evolution in cuckoos (Aves, Cuculiformes): a journey through unusual rearrangements. Genome 2024. [PMID: 38346285 DOI: 10.1139/gen-2023-0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The Cuculiformes are a family of over 150 species that live in a range of habitats, such as forests, savannas, and deserts. Here, bacterial artificial chromosome (BAC) probes (75 from chicken and 14 from zebra finch macrochromosomes 1-10 +ZW and for microchromosomes 11-28 (except 16)) were used to investigate chromosome homologies between chicken and the squirrel cuckoo (Piaya cayana). In addition, repetitive DNA probes were applied to characterize the chromosome organization and to explore the role of these sequences in the karyotype evolution of P. cayana. We also applied BAC probes for chicken chromosome 17 and Z to the guira cuckoo (Guira guira) to test whether this species has an unusual Robertsonian translocation between a microchromosome and the Z chromosome, recently described in the smooth-billed ani (Crotophaga ani). Our results revealed extensive chromosome reorganization with inter- and intrachromosomal rearrangements in P. cayana, including a conspicuous chromosome size and heterochromatin polymorphism on chromosome pair 20. Furthermore, we confirmed that the Z-autosome Robertsonian translocation found in C. ani is also found in G. guira, not P. cayana. These findings suggest that this translocation occurred prior to the divergence between C. ani and G. guira, but after the divergence with P. cayana.
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Affiliation(s)
- Rafael Kretschmer
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul 97300-162, Brazil
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul 97300-162, Brazil
| | - Analía Del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul 97300-162, Brazil
| | | | - Edison Zefa
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil
| | - Gustavo Akira Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil
| | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará 67030-000, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Rebecca E O'Connor
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
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5
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de Oliveira TD, de Freitas TR. Investigating the evolutionary dynamics of diploid number variation in Ctenomys (Ctenomyidae, Rodentia). Genet Mol Biol 2024; 46:e20230180. [PMID: 38315881 PMCID: PMC10842476 DOI: 10.1590/1678-4685-gmb-2023-0180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024] Open
Abstract
Contrary to predictions from classical hybrid sterility models of chromosomal speciation, some organisms display high rates of karyotype variation. Ctenomys are the current mammals with the greatest interspecific and intraspecific chromosomal variation. A large number of species have been studied cytogenetically. The diploid numbers of chromosomes range from 2n = 10 to 2n = 70. Here, we analyzed karyotype evolution in Ctenomys using comparative phylogenetic methods. We found a strong phylogenetic signal with chromosome number. This refutes the chromosomal megaevolution model, which proposes the independent accumulation of multiple chromosomal rearrangements in each closely related species. We found that Brownian motion (BM) described the observed characteristic changes more thoroughly than the Ornstein-Uhlenbeck and Early-Burst models. This suggests that the evolution of chromosome numbers occurs by a random walk along phylogenetic clades. However, our data indicate that the BM model alone does not fully characterize the chromosomal evolution of Ctenomys.
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Affiliation(s)
- Thays Duarte de Oliveira
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
| | - Thales R.O. de Freitas
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
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6
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Bravo‐Perez C, Cifuentes‐Riquelme R, Padilla J, de la Morena‐Barrio ME, Ortuño FJ, Garrido‐Rodríguez P, Amigo ML, Heras I, Vicente V, Lozano ML, Teruel‐Montoya R, de la Morena‐Barrio B, Corral J. The whole is greater than the sum of its parts: Long-read sequencing for solving clinical problems in haematology. J Cell Mol Med 2024; 28:e17961. [PMID: 38260950 PMCID: PMC10844759 DOI: 10.1111/jcmm.17961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 01/24/2024] Open
Affiliation(s)
- Carlos Bravo‐Perez
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de HemodonaciónUniversidad de Murcia, IMIB‐Pascual Parrilla, CIBERER‐ISCIIIMurciaSpain
| | - Rosa Cifuentes‐Riquelme
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de HemodonaciónUniversidad de Murcia, IMIB‐Pascual Parrilla, CIBERER‐ISCIIIMurciaSpain
| | - Jose Padilla
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de HemodonaciónUniversidad de Murcia, IMIB‐Pascual Parrilla, CIBERER‐ISCIIIMurciaSpain
| | - Maria E. de la Morena‐Barrio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de HemodonaciónUniversidad de Murcia, IMIB‐Pascual Parrilla, CIBERER‐ISCIIIMurciaSpain
| | - Francisco J. Ortuño
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de HemodonaciónUniversidad de Murcia, IMIB‐Pascual Parrilla, CIBERER‐ISCIIIMurciaSpain
| | - Pedro Garrido‐Rodríguez
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de HemodonaciónUniversidad de Murcia, IMIB‐Pascual Parrilla, CIBERER‐ISCIIIMurciaSpain
| | - Maria L. Amigo
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de HemodonaciónUniversidad de Murcia, IMIB‐Pascual Parrilla, CIBERER‐ISCIIIMurciaSpain
| | - Inmaculada Heras
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de HemodonaciónUniversidad de Murcia, IMIB‐Pascual Parrilla, CIBERER‐ISCIIIMurciaSpain
| | - Vicente Vicente
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de HemodonaciónUniversidad de Murcia, IMIB‐Pascual Parrilla, CIBERER‐ISCIIIMurciaSpain
| | - Maria L. Lozano
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de HemodonaciónUniversidad de Murcia, IMIB‐Pascual Parrilla, CIBERER‐ISCIIIMurciaSpain
| | - Raul Teruel‐Montoya
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de HemodonaciónUniversidad de Murcia, IMIB‐Pascual Parrilla, CIBERER‐ISCIIIMurciaSpain
| | - Belen de la Morena‐Barrio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de HemodonaciónUniversidad de Murcia, IMIB‐Pascual Parrilla, CIBERER‐ISCIIIMurciaSpain
| | - Javier Corral
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de HemodonaciónUniversidad de Murcia, IMIB‐Pascual Parrilla, CIBERER‐ISCIIIMurciaSpain
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7
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Villarreal P, O'Donnell S, Agier N, Muñoz-Guzman F, Benavides-Parra J, Urbina K, Peña TA, Solomon M, Nespolo RF, Fischer G, Varela C, Cubillos FA. Domestication signatures in the non-conventional yeast Lachancea cidri. mSystems 2024; 9:e0105823. [PMID: 38085042 PMCID: PMC10805023 DOI: 10.1128/msystems.01058-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/06/2023] [Indexed: 01/24/2024] Open
Abstract
Evaluating domestication signatures beyond model organisms is essential for a thorough understanding of the genotype-phenotype relationship in wild and human-related environments. Structural variations (SVs) can significantly impact phenotypes playing an important role in the physiological adaptation of species to different niches, including during domestication. A detailed characterization of the fitness consequences of these genomic rearrangements, however, is still limited in non-model systems, largely due to the paucity of direct comparisons between domesticated and wild isolates. Here, we used a combination of sequencing strategies to explore major genomic rearrangements in a Lachancea cidri yeast strain isolated from cider (CBS2950) and compared them to those in eight wild isolates from primary forests. Genomic analysis revealed dozens of SVs, including a large reciprocal translocation (~16 kb and 500 kb) present in the cider strain, but absent from all wild strains. Interestingly, the number of SVs was higher relative to single-nucleotide polymorphisms in the cider strain, suggesting a significant role in the strain's phenotypic variation. The set of SVs identified directly impacts dozens of genes and likely underpins the greater fermentation performance in the L. cidri CBS2950. In addition, the large reciprocal translocation affects a proline permease (PUT4) regulatory region, resulting in higher PUT4 transcript levels, which agrees with higher ethanol tolerance, improved cell growth when using proline, and higher amino acid consumption during fermentation. These results suggest that SVs are responsible for the rapid physiological adaptation of yeast to a human-related environment and demonstrate the key contribution of SVs in adaptive fermentative traits in non-model species.IMPORTANCEThe exploration of domestication signatures associated with human-related environments has predominantly focused on studies conducted on model organisms, such as Saccharomyces cerevisiae, overlooking the potential for comparisons across other non-Saccharomyces species. In our research, employing a combination of long- and short-read data, we found domestication signatures in Lachancea cidri, a non-model species recently isolated from fermentative environments in cider in France. The significance of our study lies in the identification of large array of major genomic rearrangements in a cider strain compared to wild isolates, which underly several fermentative traits. These domestication signatures result from structural variants, which are likely responsible for the phenotypic differences between strains, providing a rapid path of adaptation to human-related environments.
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Affiliation(s)
- Pablo Villarreal
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Samuel O'Donnell
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Nicolas Agier
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Felipe Muñoz-Guzman
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Jose Benavides-Parra
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Kami Urbina
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Millenium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Tomas A. Peña
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Mark Solomon
- The Australian Wine Research Institute, Glen Osmond, Adelaide, SA, Australia
| | - Roberto F. Nespolo
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Millenium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago, Chile
| | - Gilles Fischer
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Cristian Varela
- The Australian Wine Research Institute, Glen Osmond, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, Adelaide, SA, Australia
| | - Francisco A. Cubillos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Millenium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
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8
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Li J, Huang K, Ji H, Qian J, Lu H, Zhang Y, Russo A, Romero A, Urbanska EM, Tabbò F, Zhao X, Chu T. Efficacy of alectinib in lung adenocarcinoma patients with different anaplastic lymphoma kinase ( ALK) rearrangements and co-existing alterations-a retrospective cohort study. Transl Lung Cancer Res 2023; 12:2505-2519. [PMID: 38205204 PMCID: PMC10775000 DOI: 10.21037/tlcr-23-658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/16/2023] [Indexed: 01/12/2024]
Abstract
Background Alectinib significantly improves survival of non-small cell lung cancer (NSCLC) patients with anaplastic lymphoma kinase (ALK)-rearrangement. In this study, we analyzed the effects of different ALK rearrangements and co-mutations on the efficacy of alectinib. Methods Using the electronic medical record system, we reviewed in terms of clinical and pathological features patients with advanced (IIIB/IV stage) ALK-rearranged NSCLC at Shanghai Chest Hospital between January 2018 and December 2021 who were treated with alectinib in first or second line and were assessed for objective response rate (ORR), disease control rate (DCR), and progression-free survival (PFS). Results A total of 66 patients were enrolled in the study, and 17 types of ALK rearrangements were detected, of which five types of ALK rearrangements responded well to alectinib. We classified ALK-rearrangements into four main types, namely echinoderm microtubule-associated protein-like 4 (EML4)-ALK (E6:A20), EML4-ALK (E13:A20), EML4-ALK (E20:A20), and others. There was no significant difference in ORR and DCR of these types (ORR: 31.3% vs. 13.0% vs. 18.2% vs. 17.6%, P=0.575; DCR: 93.8% vs. 95.6% vs. 100.0% vs. 88.2%, P=0.627). The 3-year PFS rates were 25.0% (4/16) vs. 13.0% (3/23) vs. 27.3% (3/11) vs. 18.8% (3/16) for EML4-ALK (E6:A20), EML4-ALK (E13:A20), EML4-ALK (E20:A20), and others, respectively (P=0.725). The results of co-mutation analysis showed that the median PFS (mPFS) for patients with tumors harboring TP53 mutations was 30.4 months, significantly shorter than that of patients with tumors without co-mutations and whose mPFS was not mature (P=0.026). TSC1 co-mutation was also identified as a detrimental factor in outcome, with a DCR of 60% vs. 100% (P=0.031), mPFS of 30.4 months vs. not applicable (P=0.160) in patients with vs. those without this co-mutation, respectively. The efficacy of alectinib in patients with brain metastases is comparable to that in patients without distant organ metastases. There were two cases with specific fusion types that also responded to alectinib; namely, double ALK-rearrangements: EML4-ALK (E13:A20) and MSH2-ALK (M7:A20), and with a rare fusion partner, SPECC1L-ALK (S8:A20). Their PFS were 8.7 and 38.0 months, respectively. Conclusions In this study, the efficacy of alectinib in different types of ALK-rearrangements varied slightly. TP53 and TSC1 co-mutations were identified as detrimental factors affecting efficacy. This study provides references for the response to alectinib in patients with different types of ALK rearrangements and co-mutation.
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Affiliation(s)
- Jiaqi Li
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kuofang Huang
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Ji
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Healthcare-Associated Infection Management, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jialin Qian
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haijiao Lu
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanan Zhang
- Department of Exosome, 3D Medicines Inc., Shanghai, China
| | - Alessandro Russo
- Medical Oncology Unit, Department of Onco-Hematology, Papardo Hospital, Messina, Italy
| | - Atocha Romero
- Medical Oncology Department, Hospital Universitario Puerta de Hierro de Majadahonda, Madrid, Spain
| | - Edyta Maria Urbanska
- Department of Oncology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Fabrizio Tabbò
- Oncology Unit, Department of Medicine, Michele and Pietro Ferrero Hospital, Verduno, Italy
| | - Xiaoyu Zhao
- Department of Exosome, 3D Medicines Inc., Shanghai, China
| | - Tianqing Chu
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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9
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Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. How chromosomal inversions reorient the evolutionary process. J Evol Biol 2023; 36:1761-1782. [PMID: 37942504 DOI: 10.1111/jeb.14242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.
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Affiliation(s)
- Emma L Berdan
- Bioinformatics Core, Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Nicholas H Barton
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Roger Butlin
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Ecology and Evolutionary Biology, School of Bioscience, The University of Sheffield, Sheffield, UK
| | - Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Rui Faria
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Inês Fragata
- CHANGE - Global Change and Sustainability Institute/Animal Biology Department, cE3c - Center for Ecology, Evolution and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | | | - Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Martin Kapun
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
- Central Research Laboratories, Natural History Museum of Vienna, Vienna, Austria
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Claire Mérot
- UMR 6553 Ecobio, Université de Rennes, OSUR, CNRS, Rennes, France
| | - Esra Durmaz Mitchell
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Functional Genomics & Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anja M Westram
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Stephen W Schaeffer
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kerstin Johannesson
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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10
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Brockhoff G. Complementary Tumor Diagnosis by Single Cell-Based Cytogenetics Using Multi-marker Fluorescence In Situ Hybridization (mFISH). Curr Protoc 2023; 3:e942. [PMID: 37984366 DOI: 10.1002/cpz1.942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Multi-color (or multi-marker) fluorescence in situ hybridization (mFISH) is a well-established, valuable, complementary tool for prenatal and pathological (tumor) diagnosis. A variety of chromosomal abnormalities, such as partial or total chromosomal gains, losses, inversions, or translocations, which are considered to cause genetic syndromes, can relatively easily be detected on a cell-by-cell basis. Individual cells either in suspension (e.g., in the form of a cytological specimen derived from body fluids) or within a tissue (e.g., a solid tumor specimen or biopsy) can be quantitatively evaluated with respect to the chromosomal hybridization markers of interest (e.g., a gene or centromeric region) and with due consideration of cellular heterogeneity. FISH is helpful or even essential for the (sub-)classification, stratification, and unambiguous diagnosis of a number of malignant diseases and contributes to treatment decision in many cases. Here, the diagnostic power and limitations of typical FISH and mFISH approaches (except chromosome painting and RNA hybridization) are discussed, with special emphasis on tumor and single-cell diagnostics. Well-established and novel FISH protocols, the latter addressed to accelerate and flexibilize the preparation and hybridization of formalin-fixed and paraffin-embedded tissues, are provided. Moreover, guidelines and molecular aspects important for data interpretation are discussed. Finally, sophisticated multiplexed approaches and those that analyze very rare single-cell events, which are not yet implemented in diagnostic procedures, will be touched upon. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: (m)FISH applied to formaldehyde-fixed paraffin-embedded tissues Basic Protocol 2: (m)FISH applied to cytological specimens.
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Affiliation(s)
- Gero Brockhoff
- Department of Gynecology and Obstetrics, University Medical Center Regensburg, Regensburg, Germany
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11
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Huang Y, Guo X, Zhang K, Mandáková T, Cheng F, Lysak MA. The meso-octoploid Heliophila variabilis genome sheds a new light on the impact of polyploidization and diploidization on the diversity of the Cape flora. Plant J 2023; 116:446-466. [PMID: 37428465 DOI: 10.1111/tpj.16383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/05/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
Although the South African Cape flora is one of the most remarkable biodiversity hotspots, its high diversity has not been associated with polyploidy. Here, we report the chromosome-scale genome assembly of an ephemeral cruciferous species Heliophila variabilis (~334 Mb, n = 11) adapted to South African semiarid biomes. Two pairs of differently fractionated subgenomes suggest an allo-octoploid origin of the genome at least 12 million years ago. The ancestral octoploid Heliophila genome (2n = 8x = ~60) has probably originated through hybridization between two allotetraploids (2n = 4x = ~30) formed by distant, intertribal, hybridization. Rediploidization of the ancestral genome was marked by extensive reorganization of parental subgenomes, genome downsizing, and speciation events in the genus Heliophila. We found evidence for loss-of-function changes in genes associated with leaf development and early flowering, and over-retention and sub/neofunctionalization of genes involved in pathogen response and chemical defense. The genomic resources of H. variabilis will help elucidate the role of polyploidization and genome diploidization in plant adaptation to hot arid environments and origin of the Cape flora. The sequenced H. variabilis represents the first chromosome-scale genome assembly of a meso-octoploid representative of the mustard family.
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Affiliation(s)
- Yile Huang
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Xinyi Guo
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- Department of Experimental Biology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
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12
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Kavalco KF, Pasa R. Chromosomal Radiation: A model to explain karyotypic diversity in cryptic species. Genet Mol Biol 2023; 46:e20230116. [PMID: 37815421 PMCID: PMC10563172 DOI: 10.1590/1678-4685-gmb-2023-0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/22/2023] [Indexed: 10/11/2023] Open
Abstract
We present a concept that explains the pattern of occurrence of widely distributed organisms with large chromosomal diversity, large or small molecular divergence, and the insufficiency or absence of morphological identity. Our model is based on cytogenetic studies associated with molecular and biological data and can be applied to any lineage of sister species, chronospecies, or cryptic species. Through the evaluation of the karyotypic macrostructure, as the physical location of genes e satellites DNAs, in addition to phylogenetic reconstructions from mitochondrial and nuclear genes, per example, we have observed morphologically indistinguishable individuals presenting different locally fixed karyomorphs with phylogeographic discontinuity. The biological process behind this pattern is seen in many groups of cryptic species, in which variation lies mainly in the organization of their genomes but not necessarily in the ecosystems they inhabit or in their external morphology. It's similar to the processes behind other events observed in the distribution of lineages. In this work, we explore the hypothesis of a process analogous to ecological-evolutionary radiation, which we called Chromosomal Radiation. Chromosomal Radiation can be adaptive or non-adaptive and applied to different groups of organisms.
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Affiliation(s)
- Karine Frehner Kavalco
- Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, Laboratório de Genética Ecológica e Evolutiva (LaGEEvo), Campus Rio Paranaíba, Rio Paranaíba, MG, Brazil
- Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, Laboratório de Bioinformática e Genômica, Campus Rio Paranaíba, Rio Paranaíba, MG, Brazil
| | - Rubens Pasa
- Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, Laboratório de Genética Ecológica e Evolutiva (LaGEEvo), Campus Rio Paranaíba, Rio Paranaíba, MG, Brazil
- Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, Laboratório de Bioinformática e Genômica, Campus Rio Paranaíba, Rio Paranaíba, MG, Brazil
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13
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Yu X, Qin M, Qu M, Jiang Q, Guo S, Chen Z, Shen Y, Fu G, Fei Z, Huang H, Gao L, Yao X. Genomic analyses reveal dead-end hybridization between two deeply divergent kiwifruit species rather than homoploid hybrid speciation. Plant J 2023; 115:1528-1543. [PMID: 37258460 DOI: 10.1111/tpj.16336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/02/2023]
Abstract
Despite the importance of hybridization in evolution, the evolutionary consequence of homoploid hybridizations in plants remains poorly understood. Specially, homoploid hybridization events have been rarely documented due to a lack of genomic resources and methodological limitations. Actinidia zhejiangensis was suspected to have arisen from hybridization of Actinidia eriantha and Actinidia hemsleyana or Actinidia rufa. However, this species was very rare in nature and exhibited sympatric distribution with its potential parent species, which implied it might be a spontaneous hybrid of ongoing homoploid hybridization. Here, we illustrate the dead-end homoploid hybridization and genomic basis of isolating barriers between A. eriantha and A. hemsleyana through whole genome sequencing and population genomic analyses. Chromosome-scale genome assemblies of A. zhejiangensis and A. hemsleyana were generated. The chromosomes of A. zhejiangensis are confidently assigned to the two haplomes, and one of them originates from A. eriantha and the other originates from A. hemsleyana. Whole genome resequencing data reveal that A. zhejiangensis are mainly F1 hybrids of A. hemsleyana and A. eriantha and gene flow initiated about 0.98 million years ago, implying both strong genetic barriers and ongoing hybridization between these two deeply divergent kiwifruit species. Five inversions containing genes involved in pollen germination and pollen tube growth might account for the fertility breakdown of hybrids between A. hemsleyana and A. eriantha. Despite its distinct morphological traits and long recurrent hybrid origination, A. zhejiangensis does not initiate speciation. Collectively, our study provides new insights into homoploid hybridization in plants and provides genomic resources for evolutionary and functional genomic studies of kiwifruit.
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Affiliation(s)
- Xiaofen Yu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Mengyun Qin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minghao Qu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Quan Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sumin Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Zhenghai Chen
- Forest Resources Monitoring Center of Zhejiang Province, Hangzhou, Zhejiang, 310020, China
| | - Yufang Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Guodong Fu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, 14853, USA
| | - Hongwen Huang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, 332900, China
| | - Lei Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
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14
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Coelho MA, Ianiri G, David-Palma M, Theelen B, Goyal R, Narayanan A, Lorch JM, Sanyal K, Boekhout T, Heitman J. Frequent transitions in mating-type locus chromosomal organization in Malassezia and early steps in sexual reproduction. Proc Natl Acad Sci U S A 2023; 120:e2305094120. [PMID: 37523560 PMCID: PMC10410736 DOI: 10.1073/pnas.2305094120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/28/2023] [Indexed: 08/02/2023] Open
Abstract
Fungi in the basidiomycete genus Malassezia are the most prevalent eukaryotic microbes resident on the skin of human and other warm-blooded animals and have been implicated in skin diseases and systemic disorders. Analysis of Malassezia genomes revealed that key adaptations to the skin microenvironment have a direct genomic basis, and the identification of mating/meiotic genes suggests a capacity to reproduce sexually, even though no sexual cycle has yet been observed. In contrast to other bipolar or tetrapolar basidiomycetes that have either two linked mating-type-determining (MAT) loci or two MAT loci on separate chromosomes, in Malassezia species studied thus far the two MAT loci are arranged in a pseudobipolar configuration (linked on the same chromosome but capable of recombining). By generating additional chromosome-level genome assemblies, and an improved Malassezia phylogeny, we infer that the pseudobipolar arrangement was the ancestral state of this group and revealed six independent transitions to tetrapolarity, seemingly driven by centromere fission or translocations in centromere-flanking regions. Additionally, in an approach to uncover a sexual cycle, Malassezia furfur strains were engineered to express different MAT alleles in the same cell. The resulting strains produce hyphae reminiscent of early steps in sexual development and display upregulation of genes associated with sexual development as well as others encoding lipases and a protease potentially relevant for pathogenesis of the fungus. Our study reveals a previously unseen genomic relocation of mating-type loci in fungi and provides insight toward the identification of a sexual cycle in Malassezia, with possible implications for pathogenicity.
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Affiliation(s)
- Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso86100, Italy
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht3584 CT, The Netherlands
| | - Rohit Goyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru560064, India
| | - Aswathy Narayanan
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru560064, India
| | - Jeffrey M. Lorch
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI53711
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru560064, India
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht3584 CT, The Netherlands
- College of Science, King Saud University, Riyadh11451, Saudi Arabia
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
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15
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Sozzoni M, Ferrer Obiol J, Formenti G, Tigano A, Paris JR, Balacco JR, Jain N, Tilley T, Collins J, Sims Y, Wood J, Benowitz-Fredericks ZM, Field KA, Seyoum E, Gatt MC, Léandri-Breton DJ, Nakajima C, Whelan S, Gianfranceschi L, Hatch SA, Elliott KH, Shoji A, Cecere JG, Jarvis ED, Pilastro A, Rubolini D. A Chromosome-Level Reference Genome for the Black-Legged Kittiwake (Rissa tridactyla), a Declining Circumpolar Seabird. Genome Biol Evol 2023; 15:evad153. [PMID: 37590950 PMCID: PMC10457150 DOI: 10.1093/gbe/evad153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/19/2023] Open
Abstract
Amidst the current biodiversity crisis, the availability of genomic resources for declining species can provide important insights into the factors driving population decline. In the early 1990s, the black-legged kittiwake (Rissa tridactyla), a pelagic gull widely distributed across the arctic, subarctic, and temperate zones, suffered a steep population decline following an abrupt warming of sea surface temperature across its distribution range and is currently listed as Vulnerable by the International Union for the Conservation of Nature. Kittiwakes have long been the focus for field studies of physiology, ecology, and ecotoxicology and are primary indicators of fluctuating ecological conditions in arctic and subarctic marine ecosystems. We present a high-quality chromosome-level reference genome and annotation for the black-legged kittiwake using a combination of Pacific Biosciences HiFi sequencing, Bionano optical maps, Hi-C reads, and RNA-Seq data. The final assembly spans 1.35 Gb across 32 chromosomes, with a scaffold N50 of 88.21 Mb and a BUSCO completeness of 97.4%. This genome assembly substantially improves the quality of a previous draft genome, showing an approximately 5× increase in contiguity and a more complete annotation. Using this new chromosome-level reference genome and three more chromosome-level assemblies of Charadriiformes, we uncover several lineage-specific chromosome fusions and fissions, but find no shared rearrangements, suggesting that interchromosomal rearrangements have been commonplace throughout the diversification of Charadriiformes. This new high-quality genome assembly will enable population genomic, transcriptomic, and phenotype-genotype association studies in a widely studied sentinel species, which may provide important insights into the impacts of global change on marine systems.
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Affiliation(s)
- Marcella Sozzoni
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Joan Ferrer Obiol
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
| | - Anna Tigano
- Department of Biology, Queen’s University, Kingston, Ontario, Canada
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Josephine R Paris
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Jennifer R Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
| | - Nivesh Jain
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
| | - Tatiana Tilley
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
| | - Joanna Collins
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Ying Sims
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Jonathan Wood
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Kenneth A Field
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Eyuel Seyoum
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Marie Claire Gatt
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Don-Jean Léandri-Breton
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
- Centre d’Études Biologiques de Chizé (CEBC), UMR 7372 - CNRS & Université de La Rochelle, Villiers-en-Bois, France
| | - Chinatsu Nakajima
- Department of Life and Environmental Science, University of Tsukuba, Tsukuba, Japan
| | - Shannon Whelan
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
| | | | - Scott A Hatch
- Institute for Seabird Research and Conservation, Anchorage, Alaska, USA
| | - Kyle H Elliott
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
| | - Akiko Shoji
- Department of Life and Environmental Science, University of Tsukuba, Tsukuba, Japan
| | | | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | | | - Diego Rubolini
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Water Research Institute, IRSA-CNR, Brugherio, Monza and Brianza, Italy
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16
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Assaf N, Chakhachiro Z. Intrachromosomal amplification 21: A driver of acute myeloid leukemia? EJHaem 2023; 4:857-858. [PMID: 37601843 PMCID: PMC10435686 DOI: 10.1002/jha2.730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/22/2023] [Accepted: 05/26/2023] [Indexed: 08/22/2023]
Affiliation(s)
- Nada Assaf
- Department of Pathology and Laboratory Medicine American University of Beirut Medical Center Beirut Lebanon
| | - Zaher Chakhachiro
- Department of Pathology and Laboratory Medicine American University of Beirut Medical Center Beirut Lebanon
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17
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Sassi FDMC, Deon GA, Sember A, Liehr T, Oyakawa OT, Moreira Filho O, Bertollo LAC, Vicari MR, Cioffi MDB. Turnover of multiple sex chromosomes in Harttia catfish (Siluriformes, Loricariidae): a glimpse from whole chromosome painting. Front Genet 2023; 14:1226222. [PMID: 37576550 PMCID: PMC10421700 DOI: 10.3389/fgene.2023.1226222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
The remarkable fish biodiversity encompasses also great sex chromosome variability. Harttia catfish belong to Neotropical models for karyotype and sex chromosome research. Some species possess one of the three male-heterogametic sex chromosome systems, XY, X1X2Y or XY1Y2, while other members of the genus have yet uncharacterized modes of sex determination. Particularly the XY1Y2 multiple sex chromosome system shows a relatively low incidence among vertebrates, and it has not been yet thoroughly investigated. Previous research suggested two independent X-autosome fusions in Harttia which led to the emergence of XY1Y2 sex chromosome system in three of its species. In this study, we investigated evolutionary trajectories of synteny blocks involved in this XY1Y2 system by probing six Harttia species with whole chromosome painting (WCP) probes derived from the X (HCA-X) and the chromosome 9 (HCA-9) of H. carvalhoi. We found that both painting probes hybridize to two distinct chromosome pairs in Amazonian species, whereas the HCA-9 probe paints three chromosome pairs in H. guianensis, endemic to Guyanese drainages. These findings demonstrate distinct evolutionary fates of mapped synteny blocks and thereby elevated karyotype dynamics in Harttia among the three evolutionary clades.
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Affiliation(s)
| | - Geize Aparecida Deon
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, Jena, Germany
| | | | - Orlando Moreira Filho
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Luiz Antonio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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18
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Coelho MA, Ianiri G, David-Palma M, Theelen B, Goyal R, Narayanan A, Lorch JM, Sanyal K, Boekhout T, Heitman J. Frequent transitions in mating-type locus chromosomal organization in Malassezia and early steps in sexual reproduction. bioRxiv 2023:2023.03.25.534224. [PMID: 36993584 PMCID: PMC10055393 DOI: 10.1101/2023.03.25.534224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Fungi in the basidiomycete genus Malassezia are the most prevalent eukaryotic microbes resident on the skin of human and other warm-blooded animals and have been implicated in skin diseases and systemic disorders. Analysis of Malassezia genomes revealed that key adaptations to the skin microenvironment have a direct genomic basis, and the identification of mating/meiotic genes suggests a capacity to reproduce sexually, even though no sexual cycle has yet been observed. In contrast to other bipolar or tetrapolar basidiomycetes that have either two linked mating-type-determining ( MAT ) loci or two MAT loci on separate chromosomes, in Malassezia species studied thus far the two MAT loci are arranged in a pseudobipolar configuration (linked on the same chromosome but capable of recombining). By incorporating newly generated chromosome-level genome assemblies, and an improved Malassezia phylogeny, we infer that the pseudobipolar arrangement was the ancestral state of this group and revealed six independent transitions to tetrapolarity, seemingly driven by centromere fission or translocations in centromere- flanking regions. Additionally, in an approach to uncover a sexual cycle, Malassezia furfur strains were engineered to express different MAT alleles in the same cell. The resulting strains produce hyphae reminiscent of early steps in sexual development and display upregulation of genes associated with sexual development as well as others encoding lipases and a protease potentially relevant for pathogenesis of the fungus. Our study reveals a previously unseen genomic relocation of mating-type loci in fungi and provides insight towards the discovery of a sexual cycle in Malassezia , with possible implications for pathogenicity. Significance Statement Malassezia , the dominant fungal group of the mammalian skin microbiome, is associated with numerous skin disorders. Sexual development and yeast-to-hyphae transitions, governed by genes at two mating-type ( MAT ) loci, are thought to be important for fungal pathogenicity. However, Malassezia sexual reproduction has never been observed. Here, we used chromosome-level assemblies and comparative genomics to uncover unforeseen transitions in MAT loci organization within Malassezia , possibly related with fragility of centromeric-associated regions. Additionally, by expressing different MAT alleles in the same cell, we show that Malassezia can undergo hyphal development and this phenotype is associated with increased expression of key mating genes along with other genes known to be virulence factors, providing a possible connection between hyphal development, sexual reproduction, and pathogenicity.
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Affiliation(s)
- Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso 86100, Italy
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, The Netherlands
| | - Rohit Goyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Aswathy Narayanan
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Jeffrey M. Lorch
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, The Netherlands
- College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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19
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Ravagni S, Sanchez-Donoso I, Jiménez-Blasco I, Andrade P, Puigcerver M, Chorão Guedes A, Godinho R, Gonçalves D, Leitão M, Leonard JA, Rodríguez-Teijeiro JD, Vilà C. Evolutionary history of an island endemic, the Azorean common quail. Mol Ecol 2023. [PMID: 37212202 DOI: 10.1111/mec.16997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/23/2023]
Abstract
Oceanic islands are characterized by conditions that favour diversification into endemic lineages that can be very different from their mainland counterparts. This can be the result of fast phenotypic divergence due to drift or the result of slower adaptation to local conditions. This uniqueness can obscure their evolutionary history. Here we used morphological, stable isotope, genetic and genomic data to characterize common quails (Coturnix coturnix) in the Azores archipelago and assess the divergence from neighbouring common quail populations. Historical documents suggested that these quails could have a recent origin associated with the arrival of humans in the last centuries. Our results show that Azorean quails constitute a well-differentiated lineage with small size and dark throat pigmentation that has lost the migratory ability and that diverged from mainland quail lineages more than 0.8 mya, contrary to the notion of a recent human-mediated arrival. Even though some Azorean quails carry an inversion that affects 115 Mbp of chromosome 1 and that has been associated with the loss of the migratory behaviour in other common quail populations, half of the analysed individuals do not have that inversion and still do not migrate. The long coexistence and evolution in isolation in the Azores of two chromosomal variants (with and without the inversion) is best explained by balancing selection. Thus, a unique and long evolutionary history led to the island endemic that we know today, C. c. conturbans.
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Affiliation(s)
- Sara Ravagni
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Ines Sanchez-Donoso
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Irene Jiménez-Blasco
- IrBio and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Spain
| | - Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Manel Puigcerver
- IrBio and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Spain
| | - Ana Chorão Guedes
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - David Gonçalves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Manuel Leitão
- Direção Regional dos Recursos Florestais, Ponta Delgada, Portugal
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | | | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
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20
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Yoosefzadeh Najafabadi M, Hesami M, Rajcan I. Unveiling the Mysteries of Non-Mendelian Heredity in Plant Breeding. Plants (Basel) 2023; 12:1956. [PMID: 37653871 PMCID: PMC10221147 DOI: 10.3390/plants12101956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 07/30/2023]
Abstract
Mendelian heredity is the cornerstone of plant breeding and has been used to develop new varieties of plants since the 19th century. However, there are several breeding cases, such as cytoplasmic inheritance, methylation, epigenetics, hybrid vigor, and loss of heterozygosity (LOH), where Mendelian heredity is not applicable, known as non-Mendelian heredity. This type of inheritance can be influenced by several factors besides the genetic architecture of the plant and its breeding potential. Therefore, exploring various non-Mendelian heredity mechanisms, their prevalence in plants, and the implications for plant breeding is of paramount importance to accelerate the pace of crop improvement. In this review, we examine the current understanding of non-Mendelian heredity in plants, including the mechanisms, inheritance patterns, and applications in plant breeding, provide an overview of the various forms of non-Mendelian inheritance (including epigenetic inheritance, cytoplasmic inheritance, hybrid vigor, and LOH), explore insight into the implications of non-Mendelian heredity in plant breeding, and the potential it holds for future research.
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Affiliation(s)
| | | | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.Y.N.); (M.H.)
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21
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Demin DE, Murashko MM, Uvarova AN, Stasevich EM, Shyrokova EY, Gorlachev GE, Zaretsky AR, Korneev KV, Ustiugova AS, Tkachenko EA, Kostenko VV, Tatosyan KA, Sheetikov SA, Spirin PV, Kuprash DV, Schwartz AM. Adversary of DNA integrity: A long non-coding RNA stimulates driver oncogenic chromosomal rearrangement in human thyroid cells. Int J Cancer 2023; 152:1452-1462. [PMID: 36510744 DOI: 10.1002/ijc.34396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/01/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022]
Abstract
The flurry of publications devoted to the functions of long non-coding RNAs (lncRNAs) published in the last decade leaves no doubt about the exceptional importance of lncRNAs in various areas including tumor biology. However, contribution of lncRNAs to the early stages of oncogenesis remains poorly understood. In this study we explored a new role for lncRNAs: stimulation of specific chromosomal rearrangements upon DNA damage. We demonstrated that lncRNA CASTL1 (ENSG00000269945) stimulates the formation of the CCDC6-RET inversion (RET/PTC1) in human thyroid cells subjected to radiation or chemical DNA damage. Facilitation of chromosomal rearrangement requires lncRNA to contain regions complementary to the introns of both CCDC6 and RET genes as deletion of these regions deprives CASTL1 of the ability to stimulate the gene fusion. We found that CASTL1 expression is elevated in tumors with CCDC6-RET fusion which is the most frequent rearrangement in papillary thyroid carcinoma. Our results open a new venue for the studies of early oncogenesis in various tumor types, especially those associated with physical or chemical DNA damage.
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Affiliation(s)
- Denis Eriksonovich Demin
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Matvey Mikhailovich Murashko
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Aksinya Nicolaevna Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Mikhailovna Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena Yurievna Shyrokova
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia.,Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Andrew Rostislavovich Zaretsky
- Department of Molecular Technologies, Research Institute of Translational Medicine, N. I. Pirogov Russian National Research Medical University of the Ministry of Health of the Russian Federation
| | - Kirill Viktorovich Korneev
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,National Research Center for Hematology, Moscow, Russia
| | - Alina Sergeevna Ustiugova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena Andreevna Tkachenko
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Valentina Vitalevna Kostenko
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Karina Aleksandrovna Tatosyan
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Saveliy Andreevich Sheetikov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,National Research Center for Hematology, Moscow, Russia
| | - Pavel Vladimirovich Spirin
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry Vladimirovich Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anton Markovich Schwartz
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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22
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Korobkova VA, Bespalova LA, Yanovsky AS, Chernook AG, Kroupin PY, Arkhipov AV, Yurkina AI, Nazarova LA, Mudrova AA, Voropaeva AD, Puzyrnaya OY, Agaeva EV, Karlov GI, Divashuk MG. Permanent Spreading of 1RS.1AL and 1RS.1BL Translocations in Modern Wheat Breeding. Plants (Basel) 2023; 12:1205. [PMID: 36986893 PMCID: PMC10051305 DOI: 10.3390/plants12061205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
Wheat-rye translocations 1RS.1BL and 1RS.1AL are used in bread wheat breeding worldwide because a short arm of rye chromosome 1 (1RS) when introgressed into the wheat genome confers resistance to diseases, pests and better performance under drought-stress conditions. However, in durum wheat genotypes, these translocations occur only in experimental lines, although their advantages could enhance the potential of this crop. P.P. Lukyanenko National Grain Centre (NGC) has successfully developed commercially competitive cultivars of bread and durum wheat demanded by many agricultural producers in the South of Russia for decades. Here, 94 accessions of bread and 343 accessions of durum wheat, representing lines and cultivars from collection, competitive variety trials and breeding nursery developed at NGC were screened for 1RS using PCR markers and genomic in situ hybridization. The 1RS.1BL and 1RS.1AL translocations were detected in 38 and 6 bread wheat accessions, respectively. None of the durum wheat accessions showed translocation, despite the fact that some of them had 1RS.1BL donors in their pedigree. The absence of translocations in the studied durum wheat germplasm can be caused by the negative selection of 1RS carriers at different stages of the breeding process due to low quality and difficulties in transferring rye chromatin through wheat gametes.
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Affiliation(s)
- Varvara A. Korobkova
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Ludmila A. Bespalova
- P.P. Lukyanenko National Grain Centre, Department of Breeding and Seed Production of Wheat and Triticale, Central Estate of KNIISH, 350012 Krasnodar, Russia
| | - Aleksey S. Yanovsky
- P.P. Lukyanenko National Grain Centre, Department of Breeding and Seed Production of Wheat and Triticale, Central Estate of KNIISH, 350012 Krasnodar, Russia
| | | | - Pavel Yu. Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Andrey V. Arkhipov
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Anna I. Yurkina
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Lubov A. Nazarova
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Aleksandra A. Mudrova
- P.P. Lukyanenko National Grain Centre, Department of Breeding and Seed Production of Wheat and Triticale, Central Estate of KNIISH, 350012 Krasnodar, Russia
| | - Anastasiya D. Voropaeva
- P.P. Lukyanenko National Grain Centre, Department of Breeding and Seed Production of Wheat and Triticale, Central Estate of KNIISH, 350012 Krasnodar, Russia
| | - Olga Yu. Puzyrnaya
- P.P. Lukyanenko National Grain Centre, Department of Breeding and Seed Production of Wheat and Triticale, Central Estate of KNIISH, 350012 Krasnodar, Russia
| | - Elena V. Agaeva
- P.P. Lukyanenko National Grain Centre, Department of Breeding and Seed Production of Wheat and Triticale, Central Estate of KNIISH, 350012 Krasnodar, Russia
| | - Gennady I. Karlov
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Mikhail G. Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
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23
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Tavares MG, Teixeira GA. Cytogenetic characterization of solitary wasp Ancistrocerus flavomarginatus (Brèthes, 1906) (Hymenoptera, Vespidae) with insights into the chromosomal evolution in the genus. Genome 2023; 66:62-67. [PMID: 36645884 DOI: 10.1139/gen-2022-0095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cytogenetic studies have enabled the characterization of the chromosomal macrostructure and microstructure and have contributed to the understanding of the evolution of wasp karyotypes. However, studies on Eumeninae solitary wasps are scarce. In this study, we characterized the karyotype of Ancistrocerus flavomarginatus (Brèthes, 1906) and compared it with previous data from other Ancistrocerus (Wesmael, 1836) species to shed light on the chromosomal diversity of the genus. A chromosome number of 2n = 24 in females and n = 12 in males was observed. Comparing the A. flavomarginatus karyotype with that of another Ancistrocerus species showed variations in the morphology of some chromosomal pairs. The presence of two larger chromosome pairs, almost entirely heterochromatic, and the predominance of subtelocentric chromosomes with heterochromatic short arms in A. flavomarginatus support the occurrence of fissions in Ancistrocerus. A single site of ribosomal genes was observed in A. flavomarginatus, in addition to a size polymorphism of these rDNA clusters between the homologues of some analyzed females. This polymorphism may originate from duplications/deletions due to unequal crossing-over or amplification via transposable elements. The (GA)15 microsatellite is located exclusively in euchromatic regions. Our data show that different rearrangements seem to shape chromosomal evolution in Ancistrocerus species.
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Affiliation(s)
- Mara Garcia Tavares
- Laboratory of Insect Cytogenetics, Department of General Biology, CCB, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Gisele Amaro Teixeira
- Laboratory of Insect Cytogenetics, Department of General Biology, CCB, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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24
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Barnes EJ, Eide CA, Kaempf A, Bottomly D, Romine KA, Wilmot B, Saunders D, McWeeney SK, Tognon CE, Druker BJ. Secondary fusion proteins as a mechanism of BCR::ABL1 kinase-independent resistance in chronic myeloid leukaemia. Br J Haematol 2023; 200:323-328. [PMID: 36264026 PMCID: PMC9851972 DOI: 10.1111/bjh.18515] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/14/2022] [Accepted: 10/02/2022] [Indexed: 01/22/2023]
Abstract
Drug resistance in chronic myeloid leukaemia (CML) may occur via mutations in the causative BCR::ABL1 fusion or BCR::ABL1-independent mechanisms. We analysed 48 patients with BCR::ABL1-independent resistance for the presence of secondary fusion genes by RNA sequencing. We identified 10 of the most frequently detected secondary fusions in 21 patients. Validation studies, cell line models, gene expression analysis and drug screening revealed differences with respect to proliferation rate, differentiation and drug sensitivity. Notably, expression of RUNX1::MECOM led to resistance to ABL1 tyrosine kinase inhibitors in vitro. These results suggest secondary fusions contribute to BCR::ABL1-independent resistance and may be amenable to combined therapies.
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MESH Headings
- Humans
- Fusion Proteins, bcr-abl/metabolism
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Mutation
- Cell Line
- Drug Resistance, Neoplasm/genetics
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Affiliation(s)
- Evan J Barnes
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Christopher A Eide
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Andy Kaempf
- Biostatistics Shared Resource, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Daniel Bottomly
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Kyle A Romine
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Beth Wilmot
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Dominick Saunders
- Flow Cytometry Shared Resource, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Shannon K McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Cristina E Tognon
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Brian J Druker
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
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25
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Corrêa de Sousa RP, Dos Santos JLA, Silva-Oliveira GC, Furo IDO, de Oliveira EHC, Vallinoto M. Characterization of a new cytotype and ocurrence of a B microchromosome in two spot astyanax, Astyanax bimaculatus Linnaeus, 1758 (Characiformes: Characidae). J Fish Biol 2023; 102:520-524. [PMID: 36321966 DOI: 10.1111/jfb.15265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Although Astyanax bimaculatus is the most representative species of the genus in the Amazon region, there are no cytogenetic studies of A. bimaculatus species in Amazon region. Thus, we aimed to analyse the chromosome complements of specimens from this area using classic and molecular cytogenetic approaches. The results revealed the existence of a distinct cytotype and this is the first report of the occurrence of a B microchromosome in the species. Overall, these data indicate that the karyotypic evolution of this species is complex, involving the occurrence of chromosomal rearrangements.
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Affiliation(s)
| | | | | | | | - Edivaldo Herculano Corrêa de Oliveira
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
- Laboratório de Culturas de Células e Citogenética, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Marcelo Vallinoto
- Laboratório de Evolução, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Brazil
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Laboratório associado, Universidade do Porto, Vairão, Portugal
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26
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de Moraes RLR, Sassi FDMC, Marinho MMF, Ráb P, Porto JIR, Feldberg E, Cioffi MDB. Small Body, Large Chromosomes: Centric Fusions Shaped the Karyotype of the Amazonian Miniature Fish Nannostomus anduzei (Characiformes, Lebiasinidae). Genes (Basel) 2023; 14:192. [PMID: 36672933 PMCID: PMC9858914 DOI: 10.3390/genes14010192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Miniature refers to species with extraordinarily small adult body size when adult and can be found within all major metazoan groups. It is considered that miniature species have experienced severe alteration of numerous morphological traits during evolution. For a variety of reasons, including severe labor concerns during collecting, chromosomal acquisition, and taxonomic issues, miniature fishes are neglected and understudied. Since some available studies indicate possible relationship between diploid chromosome number (2n) and body size in fishes, we aimed to study one of the smallest Neotropical fish Nannostomus anduzei (Teleostei, Characiformes, Lebiasinidae), using both conventional (Giemsa staining, C-banding) and molecular cytogenetic methods (FISH mapping of rDNAs, microsatellites, and telomeric sequences). Our research revealed that N. anduzei possesses one of the lowest diploid chromosome numbers (2n = 22) among teleost fishes, and its karyotype is entirely composed of large metacentric chromosomes. All chromosomes, except for pair number 11, showed an 18S rDNA signal in the pericentromeric region. 5S rDNA signals were detected in the pericentromeric regions of chromosome pair number 1 and 6, displaying synteny to 18S rDNA signals. Interstitial telomeric sites (ITS) were identified in the centromeric region of pairs 6 and 8, indicating that centric fusions played a significant role in karyotype evolution of studied species. Our study provides further evidence supporting the trend of diploid chromosome number reduction along with miniaturization of adult body size in fishes.
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Affiliation(s)
- Renata Luiza Rosa de Moraes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
| | - Francisco de Menezes Cavalcante Sassi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
| | - Manoela Maria Ferreira Marinho
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Cidade Universitária, Castelo Branco, João Pessoa 58051-900, PB, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Jorge Ivan Rebelo Porto
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil
| | - Eliana Feldberg
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
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27
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Prazdnikov DV. Chromosome complements of Channalucius and C.striata from Phu Quoc Island and karyotypic evolution in snakehead fishes (Actinopterygii, Channidae). Comp Cytogenet 2023; 17:1-12. [PMID: 36761446 PMCID: PMC9836404 DOI: 10.3897/compcytogen.v17.i1.94943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Snakehead fishes of the family Channidae are obligatory air-breathers freshwater predators, the vast majority of which belong to the genus Channa Scopoli, 1777. Channa species are characterized by high karyotypic diversity due to various types of chromosomal rearrangements. It is assumed that, in addition to the lifestyle, fragmentation and isolation of snakehead populations contribute to an increase in karyotypic diversity. However, the chromosome complements of many isolated populations of widespread Channa species remain unknown, and the direction of karyotype transformations is poorly understood. This paper describes the previously unstudied karyotypes of Channalucius (Cuvier, 1831) and C.striata (Bloch, 1793) from Phu Quoc Island and analyzes the trends of karyotypic evolution in the genus Channa. In C.lucius, the karyotypes are differed in the number of chromosome arms (2n = 48, NF = 50 and 51), while in C.striata, the karyotypes are differed in the diploid chromosome number (2n = 44 and 43, NF = 48). A comparative cytogenetic analysis showed that the main trend of karyotypic evolution of Channa species is associated with a decrease in the number of chromosomes and an increase in the number of chromosome arms, mainly due to fusions and pericentric inversions. The data obtained support the assumption that fragmentation and isolation of populations, especially of continental islands, contribute to the karyotypic diversification of snakeheads and are of interest for further cytogenetic studies of Channidae.
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Affiliation(s)
- Denis V Prazdnikov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russia Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Moscow Russia
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28
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de Groot D, Spanjaard A, Hogenbirk MA, Jacobs H. Chromosomal Rearrangements and Chromothripsis: The Alternative End Generation Model. Int J Mol Sci 2023; 24:ijms24010794. [PMID: 36614236 PMCID: PMC9821053 DOI: 10.3390/ijms24010794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 01/04/2023] Open
Abstract
Chromothripsis defines a genetic phenomenon where up to hundreds of clustered chromosomal rearrangements can arise in a single catastrophic event. The phenomenon is associated with cancer and congenital diseases. Most current models on the origin of chromothripsis suggest that prior to chromatin reshuffling numerous DNA double-strand breaks (DSBs) have to exist, i.e., chromosomal shattering precedes rearrangements. However, the preference of a DNA end to rearrange in a proximal accessible region led us to propose chromothripsis as the reaction product of successive chromatin rearrangements. We previously coined this process Alternative End Generation (AEG), where a single DSB with a repair-blocking end initiates a domino effect of rearrangements. Accordingly, chromothripsis is the end product of this domino reaction taking place in a single catastrophic event.
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Affiliation(s)
- Daniel de Groot
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Aldo Spanjaard
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Marc A. Hogenbirk
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Agendia NV, Radarweg 60, 1043 NT Amsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Correspondence: ; Tel.: +31-20-512-2065
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29
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Rhiel M, Geiger K, Andrieux G, Rositzka J, Boerries M, Cathomen T, Cornu TI. T-CAST: An optimized CAST-Seq pipeline for TALEN confirms superior safety and efficacy of obligate-heterodimeric scaffolds. Front Genome Ed 2023; 5:1130736. [PMID: 36890979 PMCID: PMC9986454 DOI: 10.3389/fgeed.2023.1130736] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
Transcription activator-like effector nucleases (TALENs) are programmable nucleases that have entered the clinical stage. Each subunit of the dimer consists of a DNA-binding domain composed of an array of TALE repeats fused to the catalytically active portion of the FokI endonuclease. Upon DNA-binding of both TALEN arms in close proximity, the FokI domains dimerize and induce a staggered-end DNA double strand break. In this present study, we describe the implementation and validation of TALEN-specific CAST-Seq (T-CAST), a pipeline based on CAST-Seq that identifies TALEN-mediated off-target effects, nominates off-target sites with high fidelity, and predicts the TALEN pairing conformation leading to off-target cleavage. We validated T-CAST by assessing off-target effects of two promiscuous TALENs designed to target the CCR5 and TRAC loci. Expression of these TALENs caused high levels of translocations between the target sites and various off-target sites in primary T cells. Introduction of amino acid substitutions to the FokI domains, which render TALENs obligate-heterodimeric (OH-TALEN), mitigated the aforementioned off-target effects without loss of on-target activity. Our findings highlight the significance of T-CAST to assess off-target effects of TALEN designer nucleases and to evaluate mitigation strategies, and advocate the use of obligate-heterodimeric TALEN scaffolds for therapeutic genome editing.
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Affiliation(s)
- Manuel Rhiel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany
| | - Kerstin Geiger
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany.,Ph.D. Program, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julia Rositzka
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Comprehensive Cancer Center Freiburg (CCCF), Medical Center-University of Freiburg, Freiburg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tatjana I Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
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30
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Shaskolskiy B, Kravtsov D, Kandinov I, Dementieva E, Gryadunov D. Genomic Diversity and Chromosomal Rearrangements in Neisseria gonorrhoeae and Neisseria meningitidis. Int J Mol Sci 2022; 23:ijms232415644. [PMID: 36555284 PMCID: PMC9778887 DOI: 10.3390/ijms232415644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/18/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Chromosomal rearrangements in N. gonorrhoeae and N. meningitidis were studied with the determination of mobile elements and their role in rearrangements. The results of whole-genome sequencing and de novo genome assembly for 50 N. gonorrhoeae isolates collected in Russia were compared with 96 genomes of N. gonorrhoeae and 138 genomes of N. meningitidis from the databases. Rearrangement events with the determination of the coordinates of syntenic blocks were analyzed using the SibeliaZ software v.1.2.5, the minimum number of events that allow one genome to pass into another was calculated using the DCJ-indel model using the UniMoG program v.1.0. Population-level analysis revealed a stronger correlation between changes in the gene order and phylogenetic proximity for N. meningitidis in contrast to N. gonorrhoeae. Mobile elements were identified, including Correa elements; Spencer-Smith elements (in N. gonorrhoeae); Neisserial intergenic mosaic elements; IS elements of IS5, IS30, IS110, IS1595 groups; Nf1-Nf3 prophages; NgoФ1-NgoФ9 prophages; and Mu-like prophages Pnm1, Pnm2, MuMenB (in N. meningitidis). More than 44% of the observed rearrangements most likely occurred with the participation of mobile elements, including prophages. No differences were found between the Russian and global N. gonorrhoeae population both in terms of rearrangement events and in the number of transposable elements in genomes.
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31
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García-Ríos E, Guillamón JM. Genomic Adaptations of Saccharomyces Genus to Wine Niche. Microorganisms 2022; 10:microorganisms10091811. [PMID: 36144411 PMCID: PMC9500811 DOI: 10.3390/microorganisms10091811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Wine yeast have been exposed to harsh conditions for millennia, which have led to adaptive evolutionary strategies. Thus, wine yeasts from Saccharomyces genus are considered an interesting and highly valuable model to study human-drive domestication processes. The rise of whole-genome sequencing technologies together with new long reads platforms has provided new understanding about the population structure and the evolution of wine yeasts. Population genomics studies have indicated domestication fingerprints in wine yeast, including nucleotide variations, chromosomal rearrangements, horizontal gene transfer or hybridization, among others. These genetic changes contribute to genetically and phenotypically distinct strains. This review will summarize and discuss recent research on evolutionary trajectories of wine yeasts, highlighting the domestication hallmarks identified in this group of yeast.
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Affiliation(s)
- Estéfani García-Ríos
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, 46980 Paterna, Spain
- Department of Science, Universidad Internacional de Valencia-VIU, Pintor Sorolla 21, 46002 Valencia, Spain
- Correspondence:
| | - José Manuel Guillamón
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, 46980 Paterna, Spain
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32
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Abstract
Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
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Affiliation(s)
- Anja M Westram
- ISTA (Institute of Science and Technology Austria), Klosterneuburg, Austria.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.,Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Roger Butlin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Nick Barton
- ISTA (Institute of Science and Technology Austria), Klosterneuburg, Austria
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33
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Malhotra N, Seshasayee ASN. Replication-Dependent Organization Constrains Positioning of Long DNA Repeats in Bacterial Genomes. Genome Biol Evol 2022; 14:6625829. [PMID: 35776426 PMCID: PMC9297083 DOI: 10.1093/gbe/evac102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 01/29/2023] Open
Abstract
Bacterial genome organization is primarily driven by chromosomal replication from a single origin of replication. However, chromosomal rearrangements, which can disrupt such organization, are inevitable in nature. Long DNA repeats are major players mediating rearrangements, large and small, via homologous recombination. Since changes to genome organization affect bacterial fitness-and more so in fast-growing than slow-growing bacteria-and are under selection, it is reasonable to expect that genomic positioning of long DNA repeats is also under selection. To test this, we identified identical DNA repeats of at least 100 base pairs across ∼6,000 bacterial genomes and compared their distribution in fast- and slow-growing bacteria. We found that long identical DNA repeats are distributed in a non-random manner across bacterial genomes. Their distribution differs in the overall number, orientation, and proximity to the origin of replication, between fast- and slow-growing bacteria. We show that their positioning-which might arise from a combination of the processes that produce repeats and selection on rearrangements that recombination between repeat elements might cause-permits less disruption to the replication-dependent genome organization of bacteria compared with random suggesting it as a major constraint to positioning of long DNA repeats.
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34
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Abstract
Background selection (BGS), the effect that purifying selection exerts on sites linked to deleterious alleles, is expected to be ubiquitous across eukaryotic genomes. The effects of BGS reflect the interplay of the rates and fitness effects of deleterious mutations with recombination. A fundamental assumption of BGS models is that recombination rates are invariant over time. However, in some lineages, recombination rates evolve rapidly, violating this central assumption. Here, we investigate how recombination rate evolution affects genetic variation under BGS. We show that recombination rate evolution modifies the effects of BGS in a manner similar to a localized change in the effective population size, potentially leading to underestimation or overestimation of the genome-wide effects of selection. Furthermore, we find evidence that recombination rate evolution in the ancestors of modern house mice may have impacted inferences of the genome-wide effects of selection in that species.
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Affiliation(s)
- Tom R. Booker
- Department of Zoology, University of British Columbia, Vancouver Campus, Vancouver, BC, Canada
| | - Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, WI, USA
| | - Anna Tigano
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, Canada
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35
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Zhang WP, Cao L, Lin XR, Ding YM, Liang Y, Zhang DY, Pang EL, Renner SS, Bai WN. Dead-End Hybridization in Walnut Trees Revealed by Large-Scale Genomic Sequence Data. Mol Biol Evol 2022; 39:msab308. [PMID: 34687315 PMCID: PMC8760940 DOI: 10.1093/molbev/msab308] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Although hybridization plays a large role in speciation, some unknown fraction of hybrid individuals never reproduces, instead remaining as genetic dead-ends. We investigated a morphologically distinct and culturally important Chinese walnut, Juglans hopeiensis, suspected to have arisen from hybridization of Persian walnut (J. regia) with Asian butternuts (J. cathayensis, J. mandshurica, and hybrids between J. cathayensis and J. mandshurica). Based on 151 whole-genome sequences of the relevant taxa, we discovered that all J. hopeiensis individuals are first-generation hybrids, with the time for the onset of gene flow estimated as 370,000 years, implying both strong postzygotic barriers and the presence of J. regia in China by that time. Six inversion regions enriched for genes associated with pollen germination and pollen tube growth may be involved in the postzygotic barriers that prevent sexual reproduction in the hybrids. Despite its long-recurrent origination and distinct traits, J. hopeiensis does not appear on the way to speciation.
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Affiliation(s)
- Wei-Ping Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lei Cao
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xin-Rui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ya-Mei Ding
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yu Liang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Er-Li Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO, USA
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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36
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Prouteau A, Mottier S, Primot A, Cadieu E, Bachelot L, Botherel N, Cabillic F, Houel A, Cornevin L, Kergal C, Corre S, Abadie J, Hitte C, Gilot D, Lindblad-Toh K, André C, Derrien T, Hedan B. Canine Oral Melanoma Genomic and Transcriptomic Study Defines Two Molecular Subgroups with Different Therapeutical Targets. Cancers (Basel) 2022; 14:cancers14020276. [PMID: 35053440 PMCID: PMC8774001 DOI: 10.3390/cancers14020276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 02/05/2023] Open
Abstract
Simple Summary In humans, mucosal melanoma (MM) is a rare and aggressive cancer. The canine model is frequently and spontaneously affected by MM, thus facilitating the collection of samples and the study of its genetic bases. Thanks to an integrative genomic and transcriptomic analysis of 32 canine MM samples, we identified two molecular subgroups of MM with a different microenvironment and structural variant (SV) content. We demonstrated that SVs are associated with recurrently amplified regions, and identified new candidate oncogenes (TRPM7, GABPB1, and SPPL2A) for MM. Our findings suggest the existence of two MM molecular subgroups that could benefit from dedicated therapies, such as immune checkpoint inhibitors or targeted therapies, for both human and veterinary medicine. Abstract Mucosal melanoma (MM) is a rare, aggressive clinical cancer. Despite recent advances in genetics and treatment, the prognosis of MM remains poor. Canine MM offers a relevant spontaneous and immunocompetent model to decipher the genetic bases and explore treatments for MM. We performed an integrative genomic and transcriptomic analysis of 32 canine MM samples, which identified two molecular subgroups with a different microenvironment and structural variant (SV) content. The overexpression of genes related to the microenvironment and T-cell response was associated with tumors harboring a lower content of SVs, whereas the overexpression of pigmentation-related pathways and oncogenes, such as TERT, was associated with a high SV burden. Using whole-genome sequencing, we showed that focal amplifications characterized complex chromosomal rearrangements targeting oncogenes, such as MDM2 or CDK4, and a recurrently amplified region on canine chromosome 30. We also demonstrated that the genes TRPM7, GABPB1, and SPPL2A, located in this CFA30 region, play a role in cell proliferation, and thus, may be considered as new candidate oncogenes for human MM. Our findings suggest the existence of two MM molecular subgroups that may benefit from dedicated therapies, such as immune checkpoint inhibitors or targeted therapies, for both human and veterinary medicine.
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Affiliation(s)
- Anais Prouteau
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Stephanie Mottier
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Aline Primot
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Edouard Cadieu
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Laura Bachelot
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Nadine Botherel
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Florian Cabillic
- Laboratoire de Cytogénétique et Biologie Cellulaire, CHU de Rennes, INSERM, INRA, University of Rennes 1, Nutrition Metabolisms and Cancer, 35000 Rennes, France; (F.C.); (L.C.)
| | - Armel Houel
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Laurence Cornevin
- Laboratoire de Cytogénétique et Biologie Cellulaire, CHU de Rennes, INSERM, INRA, University of Rennes 1, Nutrition Metabolisms and Cancer, 35000 Rennes, France; (F.C.); (L.C.)
| | - Camille Kergal
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Sébastien Corre
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Jérôme Abadie
- Laboniris, Department of Biology, Pathology and Food Sciences, Oniris, 44300 Nantes, France;
| | - Christophe Hitte
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - David Gilot
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA;
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Catherine André
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Thomas Derrien
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
- Correspondence: (T.D.); (B.H.); Tel.: +33-2-23-23-43-19 (B.H.)
| | - Benoit Hedan
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
- Correspondence: (T.D.); (B.H.); Tel.: +33-2-23-23-43-19 (B.H.)
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Koltsova AS, Efimova OA, Malysheva OV, Osinovskaya NS, Liehr T, Al-Rikabi A, Shved NY, Sultanov IY, Chiryaeva OG, Yarmolinskaya MI, Polenov NI, Kunitsa VV, Kakhiani MI, Tral TG, Tolibova GK, Bespalova ON, Kogan IY, Glotov AS, Baranov VS, Pendina AA. Cytogenomic Profile of Uterine Leiomyoma: In Vivo vs. In Vitro Comparison. Biomedicines 2021; 9:1777. [PMID: 34944592 DOI: 10.3390/biomedicines9121777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/15/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
We performed a comparative cytogenomic analysis of cultured and uncultured uterine leiomyoma (UL) samples. The experimental approach included karyotyping, aCGH, verification of the detected chromosomal abnormalities by metaphase and interphase FISH, MED12 mutation analysis and telomere measurement by Q-FISH. An abnormal karyotype was detected in 12 out of 32 cultured UL samples. In five karyotypically abnormal ULs, MED12 mutations were found. The chromosomal abnormalities in ULs were present mostly by complex rearrangements, including chromothripsis. In both karyotypically normal and abnormal ULs, telomeres were ~40% shorter than in the corresponding myometrium, being possibly prerequisite to chromosomal rearrangements. The uncultured samples of six karyotypically abnormal ULs were checked for the detected chromosomal abnormalities through interphase FISH with individually designed DNA probe sets. All chromosomal abnormalities detected in cultured ULs were found in corresponding uncultured samples. In all tumors, clonal spectra were present by the karyotypically abnormal cell clone/clones which coexisted with karyotypically normal ones, suggesting that chromosomal abnormalities acted as drivers, rather than triggers, of the neoplastic process. In vitro propagation did not cause any changes in the spectrum of the cell clones, but altered their ratio compared to uncultured sample. The alterations were unique for every UL. Compared to its uncultured counterpart, the frequency of chromosomally abnormal cells in the cultured sample was higher in some ULs and lower in others. To summarize, ULs are characterized by both inter- and intratumor genetic heterogeneity. Regardless of its MED12 status, a tumor may be comprised of clones with and without chromosomal abnormalities. In contrast to the clonal spectrum, which is unique and constant for each UL, the clonal frequency demonstrates up or down shifts under in vitro conditions, most probably determined by the unequal ability of cells with different genetic aberrations to exist outside the body.
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Teixeira GA, Barros LAC, de Aguiar HJAC, Lopes DM. Distribution of GC-rich heterochromatin and ribosomal genes in three fungus-farming ants (Myrmicinae, Attini, Attina): insights on chromosomal evolution. Comp Cytogenet 2021; 15:413-428. [PMID: 34904051 PMCID: PMC8639600 DOI: 10.3897/compcytogen.v15.i4.73769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/11/2021] [Indexed: 06/14/2023]
Abstract
Cytogenetic studies on fungus-farming ants have shown remarkable karyotype diversity, suggesting different chromosomal rearrangements involved in karyotype evolution in some genera. A notable cytogenetic characteristic in this ant group is the presence of GC-rich heterochromatin in the karyotypes of some ancient and derivative species. It was hypothesized that this GC-rich heterochromatin may have a common origin in fungus-farming ants, and the increase in species studied is important for understanding this question. In addition, many genera within the subtribe Attina have few or no cytogenetically studied species; therefore, the processes that shaped their chromosomal evolution remain obscure. Thus, in this study, we karyotyped, through classical and molecular cytogenetic techniques, the fungus-farming ants Cyphomyrmextransversus Emery, 1894, Sericomyrmexmaravalhas Ješovnik et Schultz, 2017, and Mycetomoelleriusrelictus (Borgmeier, 1934), to provide insights into the chromosomal evolution in these genera and to investigate the presence the GC-rich heterochromatin in these species. Cyphomyrmextransversus (2n = 18, 10m + 2sm + 6a) and S.maravalhas (2n = 48, 28m + 20sm) showed karyotypes distinct from other species from their genera. Mycetomoelleriusrelictus (2n = 20, 20m) presented the same karyotype as the colonies previously studied. Notably, C.transversus presented the lowest chromosomal number for the genus and a distinct karyotype from the other two previously observed for this species, showing the existence of a possible species complex and the need for its taxonomic revision. Chromosomal banding data revealed GC-rich heterochromatin in all three species, which increased the number of genera with this characteristic, supporting the hypothesis of a common origin of GC-rich heterochromatin in Attina. Although a single chromosomal pair carries rDNA genes in all studied species, the positions of these rDNA clusters varied. The rDNA genes were located in the intrachromosomal region in C.transversus and M.relictus, and in the terminal region of S.maravalhas. The combination of our molecular cytogenetic data and observations from previous studies corroborates that a single rDNA site located in the intrachromosomal region is a plesiomorphic condition in Attina. In addition, cytogenetic data obtained suggest centric fission events in Sericomyrmex Mayr, 1865, and the occurrence of inversions as the origin of the location of the ribosomal genes in M.relictus and S.maravalhas. This study provides new insights into the chromosomal evolution of fungus-farming ants.
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Affiliation(s)
- Gisele Amaro Teixeira
- Programa de Pós-graduação em Biologia Celular e Estrutural, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Luísa Antônia Campos Barros
- Universidade Federal do Amapá, Campus Binacional, n°3051, Bairro Universidade, 68980-000, Oiapoque, Amapá, Brazil
| | | | - Denilce Meneses Lopes
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
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Kartavtseva IV, Sheremetyeva IN, Pavlenko MV. Intraspecies multiple chromosomal variations including rare tandem fusion in the Russian Far Eastern endemic evoron vole Alexandromysevoronensis (Rodentia, Arvicolinae). Comp Cytogenet 2021; 15:393-411. [PMID: 34900116 PMCID: PMC8629904 DOI: 10.3897/compcytogen.v15.i4.67112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/23/2021] [Indexed: 06/01/2023]
Abstract
The vole Alexandromysevoronensis (Kovalskaya et Sokolov, 1980) with its two chromosomal races, "Evoron" (2n = 38-41, NF = 54-59) and "Argi" (2n = 34, 36, 37, NF = 51-56) is the endemic vole found in the Russian Far East. For the "Argi" chromosomal race, individuals from two isolated populations in mountain regions were investigated here for the first time using GTG-, GTC-, NOR methods. In the area under study, 8 new karyotype variants have been registered. The karyotype with 2n = 34 has a rare tandem fusion of three autosomes: two biarmed (Mev6 and Mev7) and one acrocentric (Mev14) to form a large biarmed chromosome (Mev6/7/14), all of which reveal a heterozygous state. For A.evoronensis, the variation in the number of chromosomes exceeded the known estimate of 2n = 34, 36 and amounted to 2n = 34, 36, 38-41. The combination of all the variations of chromosomes for the species made it possible to describe 20 variants of the A.evoronensis karyotype, with 11 chromosomes being involved in multiple structural rearrangements. In the "Evoron" chromosomal race 4 chromosomes (Mev1, Mev4, Mev17, and Mev18) and in the "Argi" chromosomal race 9 chromosomes (Mev6, Mev7, Mev14, Mev13, Mev11, Mev15, Mev17, Mev18, and Mev19) were observed. Tandem and Robertsonian rearrangements (Mev17/18 and Mev17.18) were revealed in both chromosomal races "Evoron" and "Argi".
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Affiliation(s)
- Irina V. Kartavtseva
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Irina N. Sheremetyeva
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Marina V. Pavlenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of Sciences, Vladivostok 690022, Russia
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Federico C, Bruno F, Ragusa D, Clements CS, Brancato D, Henry MP, Bridger JM, Tosi S, Saccone S. Chromosomal Rearrangements and Altered Nuclear Organization: Recent Mechanistic Models in Cancer. Cancers (Basel) 2021; 13:5860. [PMID: 34831011 DOI: 10.3390/cancers13225860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/09/2021] [Accepted: 11/19/2021] [Indexed: 01/07/2023] Open
Abstract
Simple Summary New methodologies and technologies developed in the last few decades have highlighted the precise spatial organization of the genome into the cell nucleus, with chromatin architecture playing a central role in controlling several genome functions. Genes are expressed in a well-defined way and at a well-defined time during cell differentiation, and alterations in genome organization can lead to genetic diseases, such as cancers. Here we review how the genome is organized in the cell nucleus and the evidence of genome misorganization leading to cancer diseases. Abstract The last decade has seen significant progress in understanding how the genome is organized spatially within interphase nuclei. Recent analyses have confirmed earlier molecular cytogenetic studies on chromosome positioning within interphase nuclei and provided new information about the topologically associated domains (TADs). Examining the nuances of how genomes are organized within interphase nuclei will provide information fundamental to understanding gene regulation and expression in health and disease. Indeed, the radial spatial positioning of individual gene loci within nuclei has been associated with up- and down-regulation of specific genes, and disruption of normal genome organization within nuclei will result in compromised cellular health. In cancer cells, where reorganization of the nuclear architecture may occur in the presence of chromosomal rearrangements such as translocations, inversions, or deletions, gene repositioning can change their expression. To date, very few studies have focused on radial gene positioning and the correlation to gene expression in cancers. Further investigations would improve our understanding of the biological mechanisms at the basis of cancer and, in particular, in leukemia initiation and progression, especially in those cases where the molecular consequences of chromosomal rearrangements are still unclear. In this review, we summarize the main milestones in the field of genome organization in the nucleus and the alterations to this organization that can lead to cancer diseases.
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Kretschmer R, Franz I, de Souza MS, Garnero ADV, Gunski RJ, de Oliveira EHC, O’Connor RE, Griffin DK, de Freitas TRO. Cytogenetic Evidence Clarifies the Phylogeny of the Family Rhynchocyclidae (Aves: Passeriformes). Cells 2021; 10:2650. [PMID: 34685630 PMCID: PMC8534115 DOI: 10.3390/cells10102650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
The phylogenetic position and taxonomic status of Rhynchocyclidae (Aves: Passeriformes) have been the subject of debate since their first description. In most models, Rhynchocyclidae represents a subfamily-level taxon placed within the Tyrant Flycatchers (Tyrannidae). Considering that this classification does not include cytotaxonomic characters, we tested the hypothesis that the chromosome organization of Rhynchocyclidae members differs from that of Tyrannidae. Hence, we selected two species, Tolmomyias sulphurescens, and Pitangus sulphuratus, representing Rhynchocyclidae and Tyrannidae, respectively. Results revealed a diploid number (2n) of 60 in T. sulphurescens and 2n = 80 in P. sulphuratus, indicating significant chromosomal differences. Chromosome mapping of Gallus gallus (GGA) and Taeniopygia guttata bacterial artificial chromosome (BAC) corresponding to chromosomes GGA1-28 (except 16) revealed that the genome evolution of T. sulphurescens involved extensive chromosome fusions of macrochromosomes and microchromosomes. On the other hand, P. sulphuratus retained the ancestral pattern of organization of macrochromosomes (except the centric fission involving GGA1) and microchromosomes. In conclusion, comparing our results with previous studies in Tyrant Flycatchers and allies indicates that P. sulphuratus has similar karyotypes to other Tyrannidae members. However, T. sulphurescens does not resemble the Tyrannidae family, reinforcing family status to the clade named Rhynchocyclidae.
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Affiliation(s)
- Rafael Kretschmer
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (R.E.O.)
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil;
| | - Ismael Franz
- Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil;
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (M.S.d.S.); (A.D.V.G.); (R.J.G.)
| | - Analía Del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (M.S.d.S.); (A.D.V.G.); (R.J.G.)
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (M.S.d.S.); (A.D.V.G.); (R.J.G.)
| | - Edivaldo Herculano Corrêa de Oliveira
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, PA, Brazil;
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
| | - Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (R.E.O.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (R.E.O.)
| | - Thales Renato Ochotorena de Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil;
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Abstract
With more than 70,000 living species, vertebrates have a huge impact on the field of biology and research, including karyotype evolution. One prominent aspect of many vertebrate karyotypes is the enigmatic occurrence of tiny and often cytogenetically indistinguishable microchromosomes, which possess distinctive features compared to macrochromosomes. Why certain vertebrate species carry these microchromosomes in some lineages while others do not, and how they evolve remain open questions. New studies have shown that microchromosomes exhibit certain unique characteristics of genome structure and organization, such as high gene densities, low heterochromatin levels, and high rates of recombination. Our review focuses on recent concepts to expand current knowledge on the dynamic nature of karyotype evolution in vertebrates, raising important questions regarding the evolutionary origins and ramifications of microchromosomes. We introduce the basic karyotypic features to clarify the size, shape, and morphology of macro- and microchromosomes and report their distribution across different lineages. Finally, we characterize the mechanisms of different evolutionary forces underlying the origin and evolution of microchromosomes.
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Affiliation(s)
- Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
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Hanson SJ, Cinnéide EÓ, Salzberg LI, Wolfe KH, McGowan J, Fitzpatrick DA, Matlin K. Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex. G3 (Bethesda) 2021; 11:jkab211. [PMID: 34849824 PMCID: PMC8496258 DOI: 10.1093/g3journal/jkab211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/11/2021] [Indexed: 11/13/2022]
Abstract
The methylotrophic yeast Ogataea polymorpha has long been a useful system for recombinant protein production, as well as a model system for methanol metabolism, peroxisome biogenesis, thermotolerance, and nitrate assimilation. It has more recently become an important model for the evolution of mating-type switching. Here, we present a population genomics analysis of 47 isolates within the O. polymorpha species complex, including representatives of the species O. polymorpha, Ogataea parapolymorpha, Ogataea haglerorum, and Ogataea angusta. We found low levels of nucleotide sequence diversity within the O. polymorpha species complex and identified chromosomal rearrangements both within and between species. In addition, we found that one isolate is an interspecies hybrid between O. polymorpha and O. parapolymorpha and present evidence for loss of heterozygosity following hybridization.
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Affiliation(s)
- Sara J Hanson
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
| | - Eoin Ó Cinnéide
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Letal I Salzberg
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Kenneth H Wolfe
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Kate Matlin
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
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Lysak MA, Weiss-Schneeweiss H. Editorial: Chromosomal Evolution in Plants. Front Plant Sci 2021; 12:726330. [PMID: 34394175 PMCID: PMC8360229 DOI: 10.3389/fpls.2021.726330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Martin A. Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
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Li A, Wang J, Sun K, Wang S, Zhao X, Wang T, Xiong L, Xu W, Qiu L, Shang Y, Liu R, Wang S, Lu Y. Two reference-quality sea snake genomes reveal their divergent evolution of adaptive traits and venom systems. Mol Biol Evol 2021; 38:4867-4883. [PMID: 34320652 PMCID: PMC8557462 DOI: 10.1093/molbev/msab212] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
True sea snakes (Hydrophiini) are among the last and most successful clades of vertebrates that show secondary marine adaptation, exhibiting diverse phenotypic traits and lethal venom systems. To better understand their evolution, we generated the first chromosome-level genomes of two representative Hydrophiini snakes, Hydrophis cyanocinctus and H. curtus. Through comparative genomics we identified a great expansion of the underwater olfaction-related V2R gene family, consisting of more than 1,000 copies in both snakes. A series of chromosome rearrangements and genomic structural variations were recognized, including large inversions longer than 30 megabase (Mb) on sex chromosomes which potentially affect key functional genes associated with differentiated phenotypes between the two species. By integrating multiomics we found a significant loss of the major weapon for elapid predation, three-finger toxin genes, which displayed a dosage effect in H. curtus. These genetic changes may imply mechanisms that drove the divergent evolution of adaptive traits including prey preferences between the two closely related snakes. Our reference-quality sea snake genomes also enrich the repositories for addressing important issues on the evolution of marine tetrapods, and provide a resource for discovering marine-derived biological products.
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Affiliation(s)
- An Li
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.,School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Junjie Wang
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Kuo Sun
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Shuocun Wang
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Xin Zhao
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Tingfang Wang
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Liyan Xiong
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Weiheng Xu
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Lei Qiu
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Yan Shang
- Department of Respiratory and Critical Care Medicine, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Runhui Liu
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Sheng Wang
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Yiming Lu
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.,School of Pharmacy, Second Military Medical University, Shanghai, 200433, China.,School of Medicine, Shanghai University, Shanghai, 200444, China
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46
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Connallon T, Olito C. Natural selection and the distribution of chromosomal inversion lengths. Mol Ecol 2021; 31:3627-3641. [PMID: 34297880 DOI: 10.1111/mec.16091] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 11/28/2022]
Abstract
Chromosomal inversions contribute substantially to genome evolution, yet the processes governing their evolutionary dynamics remain poorly understood. Theory suggests that a readily measurable property of inversions-their length-can potentially affect their evolutionary fates. Emerging data on the lengths of polymorphic and fixed inversions may therefore provide clues to the evolutionary processes promoting inversion establishment. However, formal predictions for the distribution of inversion lengths remain incomplete, making empirical patterns difficult to interpret. We model the relation between inversion length and establishment probability for four inversion types: (1) neutral, (2) underdominant, (3) directly beneficial, and (4) indirectly beneficial, with selection favouring the latter because they capture locally adapted alleles at migration-selection balance and suppress recombination between them. We also consider how deleterious mutations affect the lengths of established inversions. We show that length distributions of common polymorphic and fixed inversions systematically differ among inversion types. Small rearrangements contribute the most to genome evolution under neutral and underdominant scenarios of selection, with the lengths of neutral inversion substitutions increasing, and those of underdominant substitutions decreasing, with effective population size. Among directly beneficial inversions, small rearrangements are preferentially fixed, whereas intermediate-to-large inversions are maintained as balanced polymorphisms via associative overdominance. Finally, inversions established under the local adaptation scenario are predominantly intermediate-to-large. Such inversions remain polymorphic or approach fixation within the local populations where they are favoured. Our models clarify how inversion length distributions relate to processes of inversion establishment, providing a platform for testing how natural selection shapes the evolution of genome structure.
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Affiliation(s)
- Tim Connallon
- School of Biological Sciences and Centre for Geometric Biology, Monash University, Clayton, Victoria, Australia
| | - Colin Olito
- Department of Biology, Section for Evolutionary Ecology, Lund University, Lund, Sweden
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Zhang S, Lei C, Wu J, Xiao M, Zhou J, Zhu S, Fu J, Lu D, Sun X, Xu C. A comprehensive and universal approach for embryo testing in patients with different genetic disorders. Clin Transl Med 2021; 11:e490. [PMID: 34323405 PMCID: PMC8265165 DOI: 10.1002/ctm2.490] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/01/2021] [Accepted: 06/20/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND In vitro fertilization (IVF) with preimplantation genetic testing (PGT) has markedly improved clinical pregnancy outcomes for carriers of gene mutations or chromosomal structural rearrangements by the selection of embryos free of disease-causing genes and chromosome abnormalities. However, for detecting whole or segmental chromosome aneuploidies, gene variants or balanced chromosome rearrangements in the same embryo require separate procedures, and none of the existing detection platforms is universal for all patients with different genetic disorders. METHODS Here, we report a cost-effective, family-based haplotype phasing approach that can simultaneously evaluate multiple genetic variants, including monogenic disorders, aneuploidy, and balanced chromosome rearrangements in the same embryo with a single test. A total of 12 monogenic diseases carrier couples and either of them carried chromosomal rearrangements were enrolled simultaneously in this present study. Genome-wide genotyping was performed with single-nucleotide polymorphism (SNP)-array, and aneuploidies were analyzed through SNP allele frequency and Log R ratio. Parental haplotypes were phased by an available genotype from a close relative, and the embryonic genome-wide haplotypes were determined through family haplotype linkage analysis (FHLA). Disease-causing genes and chromosomal rearrangements were detected by haplotypes located within the 2 Mb region covering the targeted genes or breakpoint regions. RESULTS Twelve blastocysts were thawed, and then transferred into the uterus of female patients. Nine pregnancies had reached the second trimester and five healthy babies have been born. Fetus validation results, performed with the amniotic fluid or umbilical cord blood samples, were consistent with those at the blastocyst stage diagnosed by PGT. CONCLUSIONS We demonstrate that SNP-based FHLA enables the accurate genetic detection of a wide spectrum of monogenic diseases and chromosome abnormalities in embryos, preventing the transfer of parental genetic abnormalities to the fetus. This method can be implemented as a universal platform for embryo testing in patients with different genetic disorders.
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Affiliation(s)
- Shuo Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Caixia Lei
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Junping Wu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Min Xiao
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Jing Zhou
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Saijuan Zhu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Jing Fu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life ScienceFudan UniversityShanghaiChina
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family PlanningScience and Technology Research InstituteChongqingChina
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Congjian Xu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
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48
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Murashko MM, Stasevich EM, Schwartz AM, Kuprash DV, Uvarova AN, Demin DE. The Role of RNA in DNA Breaks, Repair and Chromosomal Rearrangements. Biomolecules 2021; 11:biom11040550. [PMID: 33918762 PMCID: PMC8069526 DOI: 10.3390/biom11040550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 12/28/2022] Open
Abstract
Incorrect reparation of DNA double-strand breaks (DSB) leading to chromosomal rearrangements is one of oncogenesis's primary causes. Recently published data elucidate the key role of various types of RNA in DSB formation, recognition and repair. With growing interest in RNA biology, increasing RNAs are classified as crucial at the different stages of the main pathways of DSB repair in eukaryotic cells: nonhomologous end joining (NHEJ) and homology-directed repair (HDR). Gene mutations or variation in expression levels of such RNAs can lead to local DNA repair defects, increasing the chromosome aberration frequency. Moreover, it was demonstrated that some RNAs could stimulate long-range chromosomal rearrangements. In this review, we discuss recent evidence demonstrating the role of various RNAs in DSB formation and repair. We also consider how RNA may mediate certain chromosomal rearrangements in a sequence-specific manner.
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Affiliation(s)
- Matvey Mikhailovich Murashko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Ekaterina Mikhailovna Stasevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Anton Markovich Schwartz
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
- Moscow Institute of Physics and Technology, Department of Molecular and Biological Physics, 141701 Moscow, Russia
| | - Dmitriy Vladimirovich Kuprash
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Aksinya Nicolaevna Uvarova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Denis Eriksonovich Demin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
- Correspondence:
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Kretschmer R, de Souza MS, Furo IDO, Romanov MN, Gunski RJ, Garnero ADV, de Freitas TRO, de Oliveira EHC, O’Connor RE, Griffin DK. Interspecies Chromosome Mapping in Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes (Aves): Cytogenomic Insight into Microchromosome Organization and Karyotype Evolution in Birds. Cells 2021; 10:cells10040826. [PMID: 33916942 PMCID: PMC8067558 DOI: 10.3390/cells10040826] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 01/18/2023] Open
Abstract
Interchromosomal rearrangements involving microchromosomes are rare events in birds. To date, they have been found mostly in Psittaciformes, Falconiformes, and Cuculiformes, although only a few orders have been analyzed. Hence, cytogenomic studies focusing on microchromosomes in species belonging to different bird orders are essential to shed more light on the avian chromosome and karyotype evolution. Based on this, we performed a comparative chromosome mapping for chicken microchromosomes 10 to 28 using interspecies BAC-based FISH hybridization in five species, representing four Neoaves orders (Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes). Our results suggest that the ancestral microchromosomal syntenies are conserved in Pteroglossus inscriptus (Piciformes), Ramphastos tucanus tucanus (Piciformes), and Trogon surrucura surrucura (Trogoniformes). On the other hand, chromosome reorganization in Phalacrocorax brasilianus (Suliformes) and Hydropsalis torquata (Caprimulgiformes) included fusions involving both macro- and microchromosomes. Fissions in macrochromosomes were observed in P. brasilianus and H. torquata. Relevant hypothetical Neognathae and Neoaves ancestral karyotypes were reconstructed to trace these rearrangements. We found no interchromosomal rearrangement involving microchromosomes to be shared between avian orders where rearrangements were detected. Our findings suggest that convergent evolution involving microchromosomal change is a rare event in birds and may be appropriate in cytotaxonomic inferences in orders where these rearrangements occurred.
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Affiliation(s)
- Rafael Kretschmer
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91509-900 Rio Grande do Sul, Brazil;
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, 97300-162 Rio Grande do Sul, Brazil; (M.S.d.S.); (R.J.G.); (A.d.V.G.)
| | - Ivanete de Oliveira Furo
- Laboratório de Reprodução Animal, LABRAC, Universidade Federal Rural da Amazônia, UFRA, Parauapebas, 68515-000 Pará, Brazil;
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, 97300-162 Rio Grande do Sul, Brazil; (M.S.d.S.); (R.J.G.); (A.d.V.G.)
| | - Analía del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, 97300-162 Rio Grande do Sul, Brazil; (M.S.d.S.); (R.J.G.); (A.d.V.G.)
| | | | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, 67030-000 Pará, Brazil;
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, 66075-110 Pará, Brazil
| | - Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
- Correspondence: ; Tel.: +44-1227-823022
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50
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Roy U, Raghavan SC. Deleterious point mutations in T-cell acute lymphoblastic leukemia: Mechanistic insights into leukemogenesis. Int J Cancer 2021; 149:1210-1220. [PMID: 33634864 DOI: 10.1002/ijc.33527] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/11/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is characterized by the leukemogenic transformation of immature T cells, which accumulate an array of genetic and epigenetic lesions, leading to a sustained proliferation of abnormal T cells. Genetic alterations in the DNA repair genes, protooncogenes, transcription factors, and epigenetic modifiers have been studied in the past decade using next-generation sequencing and high-resolution copy number arrays. While other genomic lesions like chromosomal rearrangements, inversions, insertions, and gene fusions have been well studied at functional level, the mechanism of generation of driver mutations in T-ALL is the subject of current investigation. Novel oncogenic mutations in the TP53, BRCA2, PTEN, IL7R, RAS, NOTCH1, ETV6, BCL11B, WT1, DNMT3A, PRC2, PHF6, USP7, KDM6A and an array of other genes disrupt the genetic and epigenetic homeostasis in T-ALL. In this review, we have summarized the mechanistic role of deleterious driver mutations in T-ALL initiation and progression. We speculate that the formation of non-B DNA structures could be one of the primary reasons for the occurrence of different genomic lesions seen in T-ALL, which warrants further investigation. Understanding the mechanism behind the genesis of oncogenic mutations will pave the way to develop targeted therapies that can improve the overall survival and treatment outcome.
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Affiliation(s)
- Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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