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Ferree PM, Blagojević J, Houben A, Martins C, Trifonov VA, Vujošević M. What is a B chromosome? Early definitions revisited. G3 (BETHESDA, MD.) 2024; 14:jkae068. [PMID: 38626314 DOI: 10.1093/g3journal/jkae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 03/19/2024] [Indexed: 04/18/2024]
Abstract
Since the discovery of B chromosomes, multiple different definitions of these selfish genetic elements have been put forth. We reconsidered early definitions in light of recently published studies. While there are many characteristics that vary among different B chromosomes, such as their evolutionary origins, size, segregation behaviors, gene content, and function, there is one defining trait of all B chromosomes: they are nonessential for the organism. The points raised here may be useful for framing future B chromosome studies and help guide the categorization of new chromosomal elements that are uncovered in genomic studies.
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Affiliation(s)
- Patrick M Ferree
- Department of Natural Sciences, Pitzer College, Scripps College, Claremont, CA 91711, USA
| | - Jelena Blagojević
- Institute for Biological Research "Siniša Stanković" - National Institute for the Republic of Serbia, University of Belgrade, Belgrade 11060, Serbia
| | - Andreas Houben
- Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland 06466, Germany
| | - Cesar Martins
- Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP 18618-689, Brazil
| | - Vladimir A Trifonov
- Research Institute for Limnology, University of Innsbruck, Mondsee A-5310, Austria
| | - Mladen Vujošević
- Institute for Biological Research "Siniša Stanković" - National Institute for the Republic of Serbia, University of Belgrade, Belgrade 11060, Serbia
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Oliveira JIN, Cabral-de-Mello DC, Valente GT, Martins C. Transcribing the enigma: the B chromosome as a territory of uncharted RNAs. Genetics 2024; 227:iyae026. [PMID: 38513121 DOI: 10.1093/genetics/iyae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/10/2024] [Indexed: 03/23/2024] Open
Abstract
B chromosomes are supernumerary elements found in several groups of eukaryotes, including fungi, plants, and animals. Typically, these chromosomes either originate from their hosts through errors in meiosis or interspecifically through horizontal transfer. While many B chromosomes are primarily heterochromatic and possess a low number of coding genes, these additional elements are still capable of transcribing sequences and exerting influence on the expression of host genes. How B chromosomes escape elimination and which impacts can be promoted in the cell always intrigued the cytogeneticists. In pursuit of understanding the behavior and functional impacts of these extra elements, cytogenetic studies meet the advances of molecular biology, incorporating various techniques into investigating B chromosomes from a functional perspective. In this review, we present a timeline of studies investigating B chromosomes and RNAs, highlighting the advances and key findings throughout their history. Additionally, we identified which RNA classes are reported in the B chromosomes and emphasized the necessity for further investigation into new perspectives on the B chromosome functions. In this context, we present a phylogenetic tree that illustrates which branches either report B chromosome presence or have functional RNA studies related to B chromosomes. We propose investigating other unexplored RNA classes and conducting functional analysis in conjunction with cytogenetic studies to enhance our understanding of the B chromosome from an RNA perspective.
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Affiliation(s)
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Guilherme T Valente
- Applied Biotechnology Laboratory, Clinical Hospital of Botucatu Medical School, Botucatu 18618-687, Brazil
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
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3
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Silva DMZA, Castro JP, Goes CAG, Utsunomia R, Vidal MR, Nascimento CN, Lasmar LF, Paim FG, Soares LB, Oliveira C, Porto-Foresti F, Artoni RF, Foresti F. B Chromosomes in Psalidodon scabripinnis (Characiformes, Characidae) Species Complex. Animals (Basel) 2022; 12:ani12172174. [PMID: 36077895 PMCID: PMC9454733 DOI: 10.3390/ani12172174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/19/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary For more than a century, B chromosomes have been investigated in several eukaryotic species. These supernumerary genomic elements behave as parasites or provide fitness benefits to the hosts. They are mostly composed of repetitive DNA, but they also have protein-coding genes. B chromosomes are associated with differential gene expression and phenotypic effects. This makes them one of the most interesting genomic elements to investigate. Fish species of the Psalidodon genus harbor a great diversity of B chromosomes. Recent studies showed they share a common ancestor, persisting in the genus for a long time and enduring speciation processes. In the Psalidodon scabripinnis species complex, B chromosomes express their own genes, mostly related to cell cycle and gonad differentiation. Moreover, these B chromosomes are associated with functional effects, e.g., cell cycle extension. Here, we review the current knowledge regarding these elements in the P. scabripinnis species complex and propose a chromosome speciation model facilitated by the B chromosome manipulation of the cell machinery. Abstract B chromosomes are extra-genomic components of cells found in individuals and in populations of some eukaryotic organisms. They have been described since the first observations of chromosomes, but several aspects of their biology remain enigmatic. Despite being present in hundreds of fungi, plants, and animal species, only a small number of B chromosomes have been investigated through high-throughput analyses, revealing the remarkable mechanisms employed by these elements to ensure their maintenance. Populations of the Psalidodon scabripinnis species complex exhibit great B chromosome diversity, making them a useful material for various analyses. In recent years, important aspects of their biology have been revealed. Here, we review these studies presenting a comprehensive view of the B chromosomes in the P. scabripinnis complex and a new hypothesis regarding the role of the B chromosome in the speciation process.
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Affiliation(s)
- Duílio M. Z. A. Silva
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
- Correspondence:
| | - Jonathan P. Castro
- Post-Graduate Program in Evolutionary Genetics and Molecular Biology, Department of Genetics and Evolution, Federal University of Sao Carlos, Sao Carlos 13565-905, SP, Brazil
- Laboratory of Evolutionary Genetics, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
| | - Caio A. G. Goes
- Laboratory of Fish Genetics, Department of Biological Sciences, Faculty of Sciences, São Paulo State University, Bauru 17033-360, SP, Brazil
| | - Ricardo Utsunomia
- Laboratory of Fish Genetics, Department of Biological Sciences, Faculty of Sciences, São Paulo State University, Bauru 17033-360, SP, Brazil
- Laboratory of Fish Genetics, Department of Genetics, Institute of Biological Sciences and Health, Federal Rural University of Rio de Janeiro, Seropedica 23890-000, RJ, Brazil
| | - Mateus R. Vidal
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Cristiano N. Nascimento
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Lucas F. Lasmar
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Fabilene G. Paim
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Letícia B. Soares
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Claudio Oliveira
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Fábio Porto-Foresti
- Laboratory of Fish Genetics, Department of Biological Sciences, Faculty of Sciences, São Paulo State University, Bauru 17033-360, SP, Brazil
| | - Roberto F. Artoni
- Post-Graduate Program in Evolutionary Genetics and Molecular Biology, Department of Genetics and Evolution, Federal University of Sao Carlos, Sao Carlos 13565-905, SP, Brazil
- Laboratory of Evolutionary Genetics, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
| | - Fausto Foresti
- Laboratory of Biology and Genetics of Fishes, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu 18618-970, SP, Brazil
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Goes CAG, Silva DMZDA, Utsunomia R, Nascimento NFD, Yasui GS, Senhorini JA, Hashimoto DT, Artoni RF, Foresti F, Porto-Foresti F. Sex-Dependent Inheritance of B Chromosomes in Psalidodon paranae (Teleostei, Characiformes) Revealed by Directed Crossings. Zebrafish 2021; 18:363-368. [PMID: 34935496 DOI: 10.1089/zeb.2021.0053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
B chromosomes are additional dispensable elements to the standard chromosomal set of an organism. In most cases, their transmission differs from Mendelian patterns, leading to their accumulation or extinction. The present study aimed to describe, for the first time, the transmission pattern of B chromosome in a population of Psalidodon paranae through directed crosses, as well as to analyze the populational dynamics of B chromosome. Our results revealed the possible elimination of B chromosome in crossings where only females were B-carriers, with a mean transmission rate (kB) of 0.149; however, kB was significantly higher in crossings involving male B-carriers (kB = 0.328-0.450). Moreover, we observed an increase in the frequency of B chromosomes in the natural population of P. paranae in the last two decades. These apparently contradictory results can make sense if the B chromosome provides adaptive advantages to their carriers. Here, we observed a differential transmission of B chromosomes in each sex of parental individuals, with higher transmission rates in crossing involving males B-carriers, in addition to describe the temporal changes of B chromosome frequency in P. paranae.
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Affiliation(s)
- Caio Augusto Gomes Goes
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho," Bauru, Brazil
| | | | - Ricardo Utsunomia
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | | | - George Shigueki Yasui
- Centro nacional de Pesquisa e Conservação da Biota Aquática Continental (CEPTA-ICMBIO), Pirassununga, Brazil
| | - José Augusto Senhorini
- Centro nacional de Pesquisa e Conservação da Biota Aquática Continental (CEPTA-ICMBIO), Pirassununga, Brazil
| | - Diogo Teruo Hashimoto
- Centro de Aquicultura da UNESP, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Jaboticabal, Brazil
| | - Roberto Ferreira Artoni
- Departamento de Biologia Estrutural, Molecular e Genética, Setor de Ciências Biológicas e da Saúde, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Fausto Foresti
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Botucatu, Brazil
| | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho," Bauru, Brazil
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Silva DMZDA, Araya-Jaime C, Yamashita M, Vidal MR, Oliveira C, Porto-Foresti F, Artoni RF, Foresti F. Meiotic self-pairing of the Psalidodon (Characiformes, Characidae) iso-B chromosome: A successful perpetuation mechanism. Genet Mol Biol 2021; 44:e20210084. [PMID: 34617950 PMCID: PMC8495774 DOI: 10.1590/1678-4685-gmb-2021-0084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 08/14/2021] [Indexed: 11/22/2022] Open
Abstract
B chromosomes are non-essential additional genomic elements present in several animal and plant species. In fishes, species of the genus Psalidodon (Characiformes, Characidae) harbor great karyotype diversity, and multiple populations carry different types of non-essential B chromosomes. This study analyzed how the dispensable supernumerary B chromosome of Psalidodon paranae behaves during meiosis to overcome checkpoints and express its own meiosis-specific genes. We visualized the synaptonemal complexes of P. paranae individuals with zero, one, or two B chromosomes using immunodetection with anti-medaka SYCP3 antibody and fluorescence in situ hybridization with a (CA)15 microsatellite probe. Our results showed that B chromosomes self-pair in cells containing only one B chromosome. In cells with two identical B chromosomes, these elements remain as separate synaptonemal complexes or close self-paired elements in the nucleus territory. Overall, we reveal that B chromosomes can escape meiotic silencing of unsynapsed chromatin through a self-pairing process, allowing expression of their own genes to facilitate regular meiosis resulting in fertile individuals. This behavior, also seen in other congeneric species, might be related to their maintenance throughout the evolutionary history of Psalidodon.
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Affiliation(s)
| | - Cristian Araya-Jaime
- Universidad de La Serena, Instituto de Investigación
Multidisciplinar en Ciencia y Tecnología, La Serena, Chile
- Universidad de La Serena, Departamento de Biología, Laboratorio de
Genética y Citogenética Vegetal, La Serena, Chile
| | - Masakane Yamashita
- Hokkaido University, Faculty of Science, Department of Biological
Sciences, Laboratory of Reproductive & Developmental Biology, Sapporo,
Japan
| | - Mateus Rossetto Vidal
- Universidade Estadual Paulista (UNESP), Instituto de Biociências de
Botucatu, Departamento de Biologia Estrutural e Funcional, Botucatu, SP,
Brazil
| | - Claudio Oliveira
- Universidade Estadual Paulista (UNESP), Instituto de Biociências de
Botucatu, Departamento de Biologia Estrutural e Funcional, Botucatu, SP,
Brazil
| | - Fábio Porto-Foresti
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências,
Departamento de Ciências Biológicas, Bauru, SP, Brazil
| | - Roberto Ferreira Artoni
- Universidade Federal de São Carlos (UFSCAR), Departamento de
Genética e Evolução, São Carlos, SP, Brazil
- Universidade Estadual de Ponta Grossa (UEPG), Departamento de
Biologia Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | - Fausto Foresti
- Universidade Estadual Paulista (UNESP), Instituto de Biociências de
Botucatu, Departamento de Biologia Estrutural e Funcional, Botucatu, SP,
Brazil
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Dos Santos LP, Francisco CM, Campos Júnior EO, Castro JP, Utsunomia R, Morelli S, Porto-Foresti F, Foresti F, Artoni RF. Chromosomal Instability and Origin of B Chromosomes in the Amazonian Glass Tetra Moenkhausia oligolepis (Günther, 1864) (Characiformes, Characidae). Cytogenet Genome Res 2021; 161:249-256. [PMID: 34433167 DOI: 10.1159/000517091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/28/2021] [Indexed: 11/19/2022] Open
Abstract
B chromosomes occur in different species of the small characid fishes of the genus Moenkhausia. These supernumerary elements, that do not recombine with chromosomes of the standard A complement and follow their own evolutionary mechanism vary in number, morphology, and distribution. Here, we show karyotypic data of individuals of 2 populations of Moenkhausia oligolepis of the Brazilian Amazon (Pedro Correia and Taboquinha streams, Tocantins river basin), both with a diploid number of 50 chromosomes and karyotypic formula of 10m + 32sm + 8a. In addition to the normal complement, we also observed the occurrence of B chromosomes in the 2 populations with intra- and interindividual variation ranging from 0 to 10 Bs, independent of sex. The C-banding pattern evidenced heterochromatic blocks located mainly in the pericentromeric region of the chromosomes, while the B chromosomes appeared euchromatic. Silver-stained nucleolus organizer regions were identified in multiples sites, and some of these blocks were positive when stained with chromomycin A3. The karyotype analysis and the application of whole-chromosome painting in populations of M. oligolepis reinforce the conservation of the basal diploid number for the genus, as well as the evolutionary tendency in these fishes to carry B chromosomes. Both populations turned out to be in different stages of stability and expansion of their B chromosomes. We further suggest that the origin of these chromosomes is due to the formation of isochromosomes. Here, we identified a pair of complement A chromosomes involved in this process.
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Affiliation(s)
| | - Carine M Francisco
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Brazil
| | - Edimar O Campos Júnior
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Brazil
| | - Jonathan P Castro
- Post-Graduate Program in Evolutionary Biology, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Ricardo Utsunomia
- Department of Genetics, Institute of Biological and Health Sciences, ICBS, Federal Rural University of Rio de Janeiro, Seropédica, Brazil
| | - Sandra Morelli
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Brazil
| | - Fábio Porto-Foresti
- Department of Biological Sciences, Faculty of Sciences, Paulista State University (UNESP), Bauru, Brazil
| | - Fausto Foresti
- Department of Structural and Functional Biology, Botucatu Biosciences Institute, Paulista State University (UNESP), Botucatu, Brazil
| | - Roberto F Artoni
- Post-Graduate Program in Evolutionary Biology, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Ponta Grossa, Brazil
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Satellite DNA Is an Inseparable Fellow Traveler of B Chromosomes. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:85-102. [PMID: 34386873 DOI: 10.1007/978-3-030-74889-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Next-Generation Sequencing (NGS) has revealed that B chromosomes in several species are enriched in repetitive DNA, mostly satellite DNA (satDNA). This raises the question of whether satDNA is important to B chromosomes for functional reasons or else its abundance on Bs is simply a consequence of properties of B chromosomes such as their dispensability and late replication. Here we review current knowledge in this respect and contextualize it within the frame of practical difficulties to perform this kind of research, the most important being the absence of good full genome sequencing for B-carrying species, which is an essential requisite to ascertain the intragenomic origin of B chromosomes. Our review analysis on 16 species revealed that 38% of them showed B-specific satDNAs whereas only one of them (6%) carried an inter-specifically originated B chromosome. This shows that B-specific satDNA families can eventually evolve in intraspecifically arisen B chromosomes. Finally, the possibility of satDNA accumulation on B chromosomes for functional reasons is exemplified by B chromosomes in rye, as they contain B-specific satDNAs which are transcribed and occupy chromosome locations where they might facilitate the kind of drive shown by this B chromosome during pollen grain mitosis.
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