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Milani D, Gasparotto AE, Loreto V, Martí DA, Cabral-de-Mello DC. Chromosomal and genomic analysis suggests single origin and high molecular differentiation of the B chromosome of Abracris flavolineata. Genome 2024; 67:327-338. [PMID: 38723289 DOI: 10.1139/gen-2023-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Supernumerary chromosomes (B chromosomes) have been an intriguing subject of study. Our understanding of the molecular differentiation of B chromosomes from an interpopulation perspective remains limited, with most analyses involving chromosome banding and mapping of a few sequences. To gain insights into the molecular composition, origin, and evolution of B chromosomes, we conducted cytogenetic and next-generation sequencing analysis of the repeatome in the grasshopper Abracris flavolineata across various populations. Our results unveiled the presence of B chromosomes in two newly investigated populations and described new satellite DNA sequences. While we observed some degree of genetic connection among A. flavolineata populations, our comparative analysis of genomes with and without B chromosomes provided evidence of two new B chromosome variants. These variants exhibited distinct compositions of various repeat classes, including transposable elements and satellite DNAs. Based on shared repeats, their chromosomal location, and the C-positive heterochromatin content on the B chromosome, these variants likely share a common origin but have undergone distinct molecular differentiation processes, resulting in varying degrees of heterochromatinization. Our data serve as a detailed example of the dynamic and differentiated nature of B chromosome molecular content at the interpopulation level, even when they share a common origin.
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Affiliation(s)
- Diogo Milani
- Univ Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, São Paulo, Brazil
| | - Ana Elisa Gasparotto
- Univ Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, São Paulo, Brazil
| | - Vilma Loreto
- Univ Federal de Pernambuco (UFPE), Centro de Biociências, Departamento de Genética, Recife, Pernambuco, Brazil
| | | | - Diogo C Cabral-de-Mello
- Univ Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, São Paulo, Brazil
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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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Rajpal VR, Sharma S, Sehgal D, Sharma P, Wadhwa N, Dhakate P, Chandra A, Thakur RK, Deb S, Rama Rao S, Mir BA, Raina SN. Comprehending the dynamism of B chromosomes in their journey towards becoming unselfish. Front Cell Dev Biol 2023; 10:1072716. [PMID: 36684438 PMCID: PMC9846793 DOI: 10.3389/fcell.2022.1072716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Investigated for more than a century now, B chromosomes (Bs) research has come a long way from Bs being considered parasitic or neutral to becoming unselfish and bringing benefits to their hosts. B chromosomes exist as accessory chromosomes along with the standard A chromosomes (As) across eukaryotic taxa. Represented singly or in multiple copies, B chromosomes are largely heterochromatic but also contain euchromatic and organellar segments. Although B chromosomes are derived entities, they follow their species-specific evolutionary pattern. B chromosomes fail to pair with the standard chromosomes during meiosis and vary in their number, size, composition and structure across taxa and ensure their successful transmission through non-mendelian mechanisms like mitotic, pre-meiotic, meiotic or post-meiotic drives, unique non-disjunction, self-pairing or even imparting benefits to the host when they lack drive. B chromosomes have been associated with cellular processes like sex determination, pathogenicity, resistance to pathogens, phenotypic effects, and differential gene expression. With the advancements in B-omics research, novel insights have been gleaned on their functions, some of which have been associated with the regulation of gene expression of A chromosomes through increased expression of miRNAs or differential expression of transposable elements located on them. The next-generation sequencing and emerging technologies will further likely unravel the cellular, molecular and functional behaviour of these enigmatic entities. Amidst the extensive fluidity shown by B chromosomes in their structural and functional attributes, we perceive that the existence and survival of B chromosomes in the populations most likely seem to be a trade-off between the drive efficiency and adaptive significance versus their adverse effects on reproduction.
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Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, India,*Correspondence: Vijay Rani Rajpal, , ; Soom Nath Raina,
| | - Suman Sharma
- Department of Botany, Ramjas College, University of Delhi, Delhi, India
| | - Deepmala Sehgal
- Syngenta, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Prashansa Sharma
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | | | - Atika Chandra
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Rakesh Kr. Thakur
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Sohini Deb
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
| | - Satyawada Rama Rao
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
| | - Bilal Ahmad Mir
- Department of Botany, University of Kashmir, Srinagar, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India,*Correspondence: Vijay Rani Rajpal, , ; Soom Nath Raina,
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4
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Gutiérrez ML, Rodríguez-González R, Fuentes I, Gálvez-Prada F, Kovařík A, Garcia S. First Update to B-Chrom: A Database on B-Chromosomes. Methods Mol Biol 2023; 2703:227-236. [PMID: 37646949 DOI: 10.1007/978-1-0716-3389-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The supernumerary mostly dispensable B chromosomes are nuclear components of about 15% of eukaryotic phyla. For a long time, B chromosomes have been studied, generating an enormous bulk of knowledge, diluted in the vastness of the scientific literature. In order to provide better access to this information, we created B-chrom ( www.bchrom.csic.es ), an online database with comprehensive information on Bs for plants, animals, and fungi. It was released in 2017 and first updated in 2021, by adding 334 entries and 123 new species. Currently, the resource provides information for 2951 species coming from 3292 sources. During this time, the usefulness of this database has been proven by the number of visits (more than 207,000 since its release) and by the scientific community, having been cited in more than 60 publications until present. This chapter explains the database composition and tips on how to use it.
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Affiliation(s)
- María Luisa Gutiérrez
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Roi Rodríguez-González
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Inés Fuentes
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
- Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Catalonia, Spain
| | | | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Sònia Garcia
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
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5
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Oliveira JIN, Cardoso AL, Wolf IR, de Oliveira RA, Martins C. First characterization of PIWI-interacting RNA clusters in a cichlid fish with a B chromosome. BMC Biol 2022; 20:204. [PMID: 36127679 PMCID: PMC9490952 DOI: 10.1186/s12915-022-01403-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND B chromosomes are extra elements found in several eukaryote species. Usually, they do not express a phenotype in the host. However, advances in bioinformatics over the last decades have allowed us to describe several genes and molecular functions related to B chromosomes. These advances enable investigations of the relationship between the B chromosome and the host to understand how this element has been preserved in genomes. However, considering that transposable elements (TEs) are highly abundant in this supernumerary chromosome, there is a lack of knowledge concerning the dynamics of TE control in B-carrying cells. Thus, the present study characterized PIWI-interacting RNA (piRNA) clusters and pathways responsible for silencing the mobilization of TEs in gonads of the cichlid fish Astatotilapia latifasciata carrying the B chromosome. RESULTS Through small RNA-seq and genome assembly, we predicted and annotated piRNA clusters in the A. latifasciata genome for the first time. We observed that these clusters had biased expression related to sex and the presence of the B chromosome. Furthermore, three piRNA clusters, named curupira, were identified in the B chromosome. Two of them were expressed exclusively in gonads of samples with the B chromosome. The composition of these curupira sequences was derived from LTR, LINE, and DNA elements, representing old and recent transposition events in the A. latifasciata genome and the B chromosome. The presence of the B chromosome also affected the expression of piRNA pathway genes. The mitochondrial cardiolipin hydrolase-like (pld6) gene is present in the B chromosome, as previously reported, and an increase in its expression was detected in gonads with the B chromosome. CONCLUSIONS Due to the high abundance of TEs in the B chromosome, it was possible to investigate the origin of piRNA from these jumping genes. We hypothesize that the B chromosome has evolved its own genomic guardians to prevent uncontrolled TE mobilization. Furthermore, we also detected an expression bias in the presence of the B chromosome over A. latifasciata piRNA clusters and pathway genes.
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Affiliation(s)
- Jordana Inácio Nascimento Oliveira
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Adauto Lima Cardoso
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Ivan Rodrigo Wolf
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Rogério Antônio de Oliveira
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
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6
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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; 12:2174. [PMID: 36077895 PMCID: PMC9454733 DOI: 10.3390/ani12172174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [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
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
| | - 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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7
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Cardoso AL, Venturelli NB, da Cruz I, de Sá Patroni FM, de Moraes D, de Oliveira RA, Benavente R, Martins C. Meiotic behavior, transmission and active genes of B chromosomes in the cichlid Astatotilapia latifasciata: new clues about nature, evolution and maintenance of accessory elements. Mol Genet Genomics 2022; 297:1151-1167. [PMID: 35704117 DOI: 10.1007/s00438-022-01911-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 05/24/2022] [Indexed: 12/23/2022]
Abstract
Supernumerary B chromosomes (Bs) are dispensable genetic elements widespread in eukaryotes and are poorly understood mainly in relation to mechanisms of maintenance and transmission. The cichlid Astatotilapia latifasciata can harbor Bs in a range of 0 (named B -) and 1-2 (named B +). The B in A. latifasciata is rich in several classes of repetitive DNA sequences, contains protein coding genes, and affects hosts in diverse ways, including sex-biased effects. To advance in the knowledge about the mechanisms of maintenance and transmission of B chromosomes in A. latifasciata, here, we studied the meiotic behavior in males and transmission rates of A. latifasciata B chromosome. We also analyzed structurally and functionally the predicted B chromosome copies of the cell cycle genes separin-like, tubb1-like and kif11-like. We identified in the meiotic structure relative to the B chromosome the presence of proteins associated with Synaptonemal Complex organization (SMC3, SYCP1 and SYCP3) and found that the B performs self-pairing. These data suggest that isochromosome formation was a step during B chromosome evolution and this element is in a stage of diversification of the two arms keeping the self-pairing behavior to protect the A chromosome complement of negative effects of recombination. Moreover, we observed no occurrence of B-drive and confirmed the presence of cell cycle genes copies in the B chromosome and their transcription in encephalon, muscle and gonads, which can indicates beneficial effects to hosts and contribute to B maintenance.
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Affiliation(s)
- Adauto Lima Cardoso
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Natália Bortholazzi Venturelli
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Irene da Cruz
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Fábio Malta de Sá Patroni
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Diogo de Moraes
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Rogério Antonio de Oliveira
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, Brazil
| | - Ricardo Benavente
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil.
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8
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Gatto KP, Timoshevskaya N, Smith JJ, Lourenço LB. Sequencing of laser captured Z and W chromosomes of the tocantins paradoxical frog (Pseudis tocantins) provides insights on repeatome and chromosomal homology. J Evol Biol 2022; 35:1659-1674. [PMID: 35642451 DOI: 10.1111/jeb.14027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/06/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022]
Abstract
Pseudis tocantins is the only frog species of the hylid genus Pseudis that possesses highly heteromorphic sex chromosomes. Z and W chromosomes of Ps. tocantins differ in size, morphology, position of the nucleolar organizer region (NOR) and the amount and distribution of heterochromatin. A chromosomal inversion and heterochromatin amplification on the W chromosome were previously inferred to be involved in the evolution of this sex chromosome pair. Despite these findings, knowledge related to the molecular composition of the large heterochromatic band of this W chromosome is restricted to the PcP190 satellite DNA, and no data are available regarding the gene content of either the W or the Z chromosome of Ps. tocantins. Here, we sequenced microdissected Z and W chromosomes of this species to further resolve their molecular composition. Comparative genomic analysis suggests that Ps. tocantins sex chromosomes are likely homologous to chromosomes 4 and 10 of Xenopus tropicalis. Analyses of the repetitive DNA landscape in the Z and W assemblies allowed for the identification of several transposable elements and putative satellite DNA sequences. Finally, some transposable elements from the W assembly were found to be highly diverse and divergent from elements found elsewhere in the genome, suggesting a rapid amplification of these elements on the W chromosome.
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Affiliation(s)
- Kaleb Pretto Gatto
- Laboratory of Chromosome Studies, Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, Brazil.,Laboratory of Herpetology and Aquaculture Center, Department of Zoology, Institute of Biosciences, São Paulo State University, Rio Claro, Brazil
| | - Nataliya Timoshevskaya
- Department of Biology, College of Arts and Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Jeramiah J Smith
- Department of Biology, College of Arts and Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Luciana Bolsoni Lourenço
- Laboratory of Chromosome Studies, Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, Brazil
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9
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Kocher TD, Behrens KA, Conte MA, Aibara M, Mrosso HDJ, Green ECJ, Kidd MR, Nikaido M, Koblmüller S. New Sex Chromosomes in Lake Victoria Cichlid Fishes (Cichlidae: Haplochromini). Genes (Basel) 2022; 13:804. [PMID: 35627189 PMCID: PMC9141883 DOI: 10.3390/genes13050804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/19/2022] Open
Abstract
African cichlid fishes harbor an extraordinary diversity of sex-chromosome systems. Within just one lineage, the tribe Haplochromini, at least 6 unique sex-chromosome systems have been identified. Here we focus on characterizing sex chromosomes in cichlids from the Lake Victoria basin. In Haplochromis chilotes, we identified a new ZW system associated with the white blotch color pattern, which shows substantial sequence differentiation over most of LG16, and is likely to be present in related species. In Haplochromis sauvagei, we found a coding polymorphism in amh that may be responsible for an XY system on LG23. In Pundamilia nyererei, we identified a feminizing effect of B chromosomes together with XY- and ZW-patterned differentiation on LG23. In Haplochromis latifasciatus, we identified a duplication of amh that may be present in other species of the Lake Victoria superflock. We further characterized the LG5-14 XY system in Astatotilapia burtoni and identified the oldest stratum on LG14. This species also showed ZW differentiation on LG2. Finally, we characterized an XY system on LG7 in Astatoreochromis alluaudi. This report brings the number of distinct sex-chromosome systems in haplochromine cichlids to at least 13, and highlights the dynamic evolution of sex determination and sex chromosomes in this young lineage.
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Affiliation(s)
- Thomas D. Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA; (K.A.B.); (M.A.C.)
| | - Kristen A. Behrens
- Department of Biology, University of Maryland, College Park, MD 20742, USA; (K.A.B.); (M.A.C.)
| | - Matthew A. Conte
- Department of Biology, University of Maryland, College Park, MD 20742, USA; (K.A.B.); (M.A.C.)
| | - Mitsuto Aibara
- Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; (M.A.); (M.N.)
| | - Hillary D. J. Mrosso
- Mwanza Fisheries Research Center, Tanzania Fisheries Research Institute (TAFIRI), Mwanza P.O. Box 475, Tanzania;
| | - Elizabeth C. J. Green
- Department of Biology and Chemistry, Texas A&M International University, Laredo, TX 78041, USA; (E.C.J.G.); (M.R.K.)
| | - Michael R. Kidd
- Department of Biology and Chemistry, Texas A&M International University, Laredo, TX 78041, USA; (E.C.J.G.); (M.R.K.)
| | - Masato Nikaido
- Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; (M.A.); (M.N.)
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria;
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10
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Boudichevskaia A, Fiebig A, Kumke K, Himmelbach A, Houben A. Rye B chromosomes differently influence the expression of A chromosome-encoded genes depending on the host species. Chromosome Res 2022; 30:335-349. [PMID: 35781770 PMCID: PMC9771852 DOI: 10.1007/s10577-022-09704-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/16/2022] [Accepted: 06/16/2022] [Indexed: 01/25/2023]
Abstract
The B chromosome (B) is a dispensable component of the genome in many species. To evaluate the impact of Bs on the transcriptome of the standard A chromosomes (A), comparative RNA-seq analyses of rye and wheat anthers with and without additional rye Bs were conducted. In both species, 5-6% of the A-derived transcripts across the entire genomes were differentially expressed in the presence of 2Bs. The GO term enrichment analysis revealed that Bs influence A chromosome encoded processes like "gene silencing"; "DNA methylation or demethylation"; "chromatin silencing"; "negative regulation of gene expression, epigenetic"; "post-embryonic development"; and "chromosome organization." 244 B chromosome responsive A-located genes in + 2B rye and + B wheat shared the same biological function. Positively correlated with the number of Bs, 939 and 1391 B-specific transcripts were identified in + 2B and + 4B wheat samples, respectively. 85% of B-transcripts in + 2B were also found in + 4B transcriptomes. 297 B-specific transcripts were identified in + 2B rye, and 27% were common to the B-derived transcripts identified in + B wheat. Bs encode mobile elements and housekeeping genes, but most B-transcripts were without detectable similarity to known genes. Some of these genes are involved in cell division-related functions like Nuf2 and might indicate their importance in maintaining Bs. The transcriptome analysis provides new insights into the complex interrelationship between standard A chromosomes and supernumerary B chromosomes.
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Affiliation(s)
- Anastassia Boudichevskaia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany.
- KWS SAAT SE & Co. KGaA, 37574, Einbeck, Germany.
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Katrin Kumke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany.
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11
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B Chromosomes’ Sequences in Yellow-Necked Mice Apodemus flavicollis—Exploring the Transcription. Life (Basel) 2021; 12:life12010050. [PMID: 35054443 PMCID: PMC8781039 DOI: 10.3390/life12010050] [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: 11/22/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 11/17/2022] Open
Abstract
B chromosomes (Bs) are highly polymorphic additional chromosomes in the genomes of many species. Due to the dispensability of Bs and the lack of noticeable phenotypic effects in their carriers, they were considered genetically inert for a long time. Recent studies on Bs in Apodemus flavicollis revealed their genetic composition, potential origin, and spatial organization in the interphase nucleus. Surprisingly, the genetic content of Bs in this species is preserved in all studied samples, even in geographically distinct populations, indicating its biological importance. Using RT-PCR we studied the transcription activity of three genes (Rraga, Haus6, and Cenpe) previously identified on Bs in A. flavicollis. We analysed mRNA isolated from spleen tissues of 34 animals harboring different numbers of Bs (0–3).The products of transcriptional activity of the analysed sequences differ in individuals with and without Bs. We recorded B-genes and/or genes from the standard genome in the presence of Bs, showing sex-dependent higher levels of transcriptional activity. Furthermore, the transcriptional activity of Cenpe varied with the age of the animals differently in the group with and without Bs. With aging, the amount of product was only found to significantly decrease in B carriers. The potential biological significance of all these differences is discussed in the paper.
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12
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Johnson Pokorná M, Reifová R. Evolution of B Chromosomes: From Dispensable Parasitic Chromosomes to Essential Genomic Players. Front Genet 2021; 12:727570. [PMID: 34956308 PMCID: PMC8695967 DOI: 10.3389/fgene.2021.727570] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
B chromosomes represent additional chromosomes found in many eukaryotic organisms. Their origin is not completely understood but recent genomic studies suggest that they mostly arise through rearrangements and duplications from standard chromosomes. They can occur in single or multiple copies in a cell and are usually present only in a subset of individuals in the population. Because B chromosomes frequently show unstable inheritance, their maintenance in a population is often associated with meiotic drive or other mechanisms that increase the probability of their transmission to the next generation. For all these reasons, B chromosomes have been commonly considered to be nonessential, selfish, parasitic elements. Although it was originally believed that B chromosomes had little or no effect on an organism's biology and fitness, a growing number of studies have shown that B chromosomes can play a significant role in processes such as sex determination, pathogenicity and resistance to pathogens. In some cases, B chromosomes became an essential part of the genome, turning into new sex chromosomes or germline-restricted chromosomes with important roles in the organism's fertility. Here, we review such cases of "cellular domestication" of B chromosomes and show that B chromosomes can be important genomic players with significant evolutionary impact.
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Affiliation(s)
- Martina Johnson Pokorná
- Department of Zoology, Charles University, Prague, Czech Republic.,Department of Ecology, Charles University, Prague, Czech Republic.,Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Radka Reifová
- Department of Zoology, Charles University, Prague, Czech Republic
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13
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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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14
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Zadesenets KS, Rubtsov NB. B Chromosomes in Free-Living Flatworms of the Genus Macrostomum (Platyhelminthes, Macrostomorpha). Int J Mol Sci 2021; 22:13617. [PMID: 34948412 PMCID: PMC8708343 DOI: 10.3390/ijms222413617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 11/17/2022] Open
Abstract
B chromosomes (Bs) or supernumerary chromosomes are extra chromosomes in the species karyotype that can vary in its copy number. Bs are widespread in eukaryotes. Usually, the Bs of specimens collected from natural populations are the object of the B chromosome studies. We applied another approach analyzing the Bs in animals maintained under the laboratory conditions as lines and cultures. In this study, three species of the Macrostomum genus that underwent a recent whole-genome duplication (WGD) were involved. In laboratory lines of M. lignano and M. janickei, the frequency of Bs was less than 1%, while in the laboratory culture of M. mirumnovem, it was nearer 30%. Their number in specimens of the culture varied from 1 to 14. Mosaicism on Bs was discovered in parts of these animals. We analyzed the distribution of Bs among the worms of the laboratory cultures during long-term cultivation, the transmission rates of Bs in the progeny obtained from crosses of worms with different numbers of Bs, and from self-fertilized isolated worms. The DNA content of the Bs in M. mirumnovem was analyzed with the chromosomal in situ suppression (CISS) hybridization of microdissected DNA probes derived from A chromosomes (As). Bs mainly consisted of repetitive DNA. The cytogenetic analysis also revealed the divergence and high variation in large metacentric chromosomes (LMs) containing numerous regions enriched for repeats. The possible mechanisms of the appearance and evolution of Bs and LMs in species of the Macrostomum genus were also discussed.
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Affiliation(s)
- Kira S. Zadesenets
- The Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
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15
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A supernumerary "B-sex" chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus. Curr Biol 2021; 31:4800-4809.e9. [PMID: 34496222 DOI: 10.1016/j.cub.2021.08.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/30/2021] [Accepted: 08/09/2021] [Indexed: 01/30/2023]
Abstract
Sex chromosomes are generally derived from a pair of classical type-A chromosomes, and relatively few alternative models have been proposed up to now.1,2 B chromosomes (Bs) are supernumerary and dispensable chromosomes with non-Mendelian inheritance found in many plant and animal species3,4 that have often been considered as selfish genetic elements that behave as genome parasites.5,6 The observation that in some species Bs can be either restricted or predominant in one sex7-14 raised the interesting hypothesis that Bs could play a role in sex determination.15 The characterization of putative B master sex-determining (MSD) genes, however, has not yet been provided to support this hypothesis. Here, in Astyanax mexicanus cavefish originating from Pachón cave, we show that Bs are strongly male predominant. Based on a high-quality genome assembly of a B-carrying male, we characterized the Pachón cavefish B sequence and found that it contains two duplicated loci of the putative MSD gene growth differentiation factor 6b (gdf6b). Supporting its role as an MSD gene, we found that the Pachón cavefish gdf6b gene is expressed specifically in differentiating male gonads, and that its knockout induces male-to-female sex reversal in B-carrying males. This demonstrates that gdf6b is necessary for triggering male sex determination in Pachón cavefish. Altogether these results bring multiple and independent lines of evidence supporting the conclusion that the Pachón cavefish B is a "B-sex" chromosome that contains duplicated copies of the gdf6b gene, which can promote male sex determination in this species.
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16
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Milani D, Ruiz-Ruano FJ, Camacho JPM, Cabral-de-Mello DC. Out of patterns, the euchromatic B chromosome of the grasshopper Abracris flavolineata is not enriched in high-copy repeats. Heredity (Edinb) 2021; 127:475-483. [PMID: 34482369 PMCID: PMC8551250 DOI: 10.1038/s41437-021-00470-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 02/07/2023] Open
Abstract
In addition to the normal set of standard (A) chromosomes, some eukaryote species harbor supernumerary (B) chromosomes. In most cases, B chromosomes show differential condensation with respect to A chromosomes and display dark C-bands of heterochromatin, and some of them are highly enriched in repetitive DNA. Here we perform a comprehensive NGS (next-generation sequencing) analysis of the repeatome in the grasshopper Abracris flavolineata aimed at uncovering the molecular composition and origin of its B chromosome. Our results have revealed that this B chromosome shows a DNA repeat content highly similar to the DNA repeat content observed for euchromatic (non-C-banded) regions of A chromosomes. Moreover, this B chromosome shows little enrichment for high-copy repeats, with only a few elements showing overabundance in B-carrying individuals compared to the 0B individuals. Consequently, the few satellite DNAs (satDNAs) mapping on the B chromosome were mostly restricted to its centromeric and telomeric regions, and they displayed much smaller bands than those observed on the A chromosomes. Our data support the intraspecific origin of the B chromosome from the longest autosome by misdivision, isochromosome formation, and additional restructuring, with accumulation of specific repeats in one or both B chromosome arms, yielding a submetacentric B. Finally, the absence of B-specific satDNAs, which are frequent in other species, along with its euchromatic nature, suggest that this B chromosome arose recently and might still be starting a heterochromatinization process. On this basis, it could be a good model to investigate the initial steps of B chromosome evolution.
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Affiliation(s)
- Diogo Milani
- Departamento de Biologia Geral e Aplicada, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo, Brazil
| | - Francisco J Ruiz-Ruano
- Evolutionary Biology Centre, Department of Organismal Biology - Systematic Biology, Uppsala University, Uppsala, Sweden
- Norwich Research Park, School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Juan Pedro M Camacho
- Departamento de Genética, Facultad de Ciencias, UGR - Univ de Granada, Granada, Spain
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo, Brazil.
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17
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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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18
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Araya-Jaime C, Palma-Rojas C, Lam N, Von Brand E. Cytogenetics from the Dock: A New Postmortem Protocol Makes It Possible to Obtain Cytogenetic Preparations from Marine Fish. Zebrafish 2021; 18:326-329. [PMID: 34491117 DOI: 10.1089/zeb.2021.0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cytogenetic studies in marine fish are scarce, and elemental cytogenetic information is available for not >2% of the species. Traditional cytogenetic methods require living individuals for their application, making the analysis of marine ichthyofauna very difficult. In this study, we present a detailed new protocol to obtain cytogenetic preparations from marine fish, through access to specimens in postmortem condition. The application of this protocol made it possible to access elemental cytogenetic information (diploid number) in six native species of the South Pacific Ocean, representative of five orders. In this way, we provide a new low-cost methodological tool for focused or large-scale cytogenetic analysis, both in economically important, native, or threatened species.
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Affiliation(s)
- Cristian Araya-Jaime
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile.,Laboratorio de Genética y Citogenética Vegetal, Departamento de Biología, Universidad de La Serena, La Serena, Chile
| | - Claudio Palma-Rojas
- Laboratorio de Genética y Citogenética Vegetal, Departamento de Biología, Universidad de La Serena, La Serena, Chile
| | - Natalia Lam
- Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Elisabeth Von Brand
- Departamento de Biología Marina Facultad de Ciencias del Mar, Universidad Católica del Norte Sede Coquimbo, Coquimbo, Chile
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19
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Ding M, Li XY, Zhu ZX, Chen JH, Lu M, Shi Q, Wang Y, Li Z, Zhao X, Wang T, Du WX, Miao C, Yao TZ, Wang MT, Zhang XJ, Wang ZW, Zhou L, Gui JF. Genomic anatomy of male-specific microchromosomes in a gynogenetic fish. PLoS Genet 2021; 17:e1009760. [PMID: 34491994 PMCID: PMC8448357 DOI: 10.1371/journal.pgen.1009760] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 09/17/2021] [Accepted: 08/09/2021] [Indexed: 11/19/2022] Open
Abstract
Unisexual taxa are commonly considered short-lived as the absence of meiotic recombination is supposed to accumulate deleterious mutations and hinder the creation of genetic diversity. However, the gynogenetic gibel carp (Carassius gibelio) with high genetic diversity and wide ecological distribution has outlived its predicted extinction time of a strict unisexual reproduction population. Unlike other unisexual vertebrates, males associated with supernumerary microchromosomes have been observed in gibel carp, which provides a unique system to explore the rationales underlying male occurrence in unisexual lineage and evolution of unisexual reproduction. Here, we identified a massively expanded satellite DNA cluster on microchromosomes of hexaploid gibel carp via comparing with the ancestral tetraploid crucian carp (Carassius auratus). Based on the satellite cluster, we developed a method for single chromosomal fluorescence microdissection and isolated three male-specific microchromosomes in a male metaphase cell. Genomic anatomy revealed that these male-specific microchromosomes contained homologous sequences of autosomes and abundant repetitive elements. Significantly, several potential male-specific genes with transcriptional activity were identified, among which four and five genes displayed male-specific and male-biased expression in gonads, respectively, during the developmental period of sex determination. Therefore, the male-specific microchromosomes resembling common features of sex chromosomes may be the main driving force for male occurrence in gynogenetic gibel carp, which sheds new light on the evolution of unisexual reproduction.
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Affiliation(s)
- Miao Ding
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi-Xuan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Hui Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- ShenZhen People’s Hospital, Shenzhen, China
| | - Meng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qian Shi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Xuan Du
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun Miao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tian-Zi Yao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming-Tao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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20
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Abstract
Female meiotic drive is the phenomenon where a selfish genetic element alters chromosome segregation during female meiosis to segregate to the egg and transmit to the next generation more frequently than Mendelian expectation. While several examples of female meiotic drive have been known for many decades, a molecular understanding of the underlying mechanisms has been elusive. Recent advances in this area in several model species prompts a comparative re-examination of these drive systems. In this review, we compare female meiotic drive of several animal and plant species, highlighting pertinent similarities.
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Affiliation(s)
- Frances E. Clark
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Takashi Akera
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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21
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The B Chromosomes of Prochilodus lineatus (Teleostei, Characiformes) Are Highly Enriched in Satellite DNAs. Cells 2021; 10:cells10061527. [PMID: 34204462 PMCID: PMC8235050 DOI: 10.3390/cells10061527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/07/2021] [Accepted: 06/11/2021] [Indexed: 12/18/2022] Open
Abstract
B or supernumerary chromosomes are dispensable elements that are widely present in numerous eukaryotes. Due to their non-recombining nature, there is an evident tendency for repetitive DNA accumulation in these elements. Thus, satellite DNA plays an important role in the evolution and diversification of B chromosomes and can provide clues regarding their origin. The characiform Prochilodus lineatus was one of the first discovered fish species bearing B chromosomes, with all populations analyzed so far showing one to nine micro-B chromosomes and exhibiting at least three morphological variants (Ba, Bsm, and Bm). To date, a single satellite DNA is known to be located on the B chromosomes of this species, but no information regarding the differentiation of the proposed B-types is available. Here, we characterized the satellitome of P. lineatus and mapped 35 satellite DNAs against the chromosomes of P. lineatus, of which six were equally located on all B-types and this indicates a similar genomic content. In addition, we describe, for the first time, an entire population without B chromosomes.
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22
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Ma W, Liu Z, Beier S, Houben A, Carpentier S. Identification of rye B chromosome-associated peptides by mass spectrometry. THE NEW PHYTOLOGIST 2021; 230:2179-2185. [PMID: 33503271 DOI: 10.1111/nph.17238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
B chromosomes (Bs) are supernumerary dispensable components of the standard genome (A chromosomes, As) that have been found in many eukaryotes. So far, it is unkown whether the B-derived transcripts translate to proteins or if the host proteome is changed due to the presence of Bs. Comparative mass spectrometry was performed using the protein samples isolated from shoots of rye plants with and without Bs. We aimed to identify B-associated peptides and analyzed the effects of Bs on the total proteome. Our comparative proteome analysis demonstrates that the presence of rye Bs affects the total proteome including different biological function processes. We found 319 of 16 776 quantified features in at least three out of five +B plants but not in 0B plants; 31 of 319 features were identified as B-associated peptide features. According to our data mining, one B-specific protein fragment showed similarity to a glycine-rich RNA binding protein which differed from its A-paralogue by two amino acid insertions. Our result represents a milestone in B chromosome research, because this is the first report to demonstrate the existence of Bs changing the proteome of the host.
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Affiliation(s)
- Wei Ma
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - ZhaoJun Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
- School of Life Sciences Life, Science Center Weihenstephan, Crop Physiology, Technical University Munich, Alte Akademie 12, Freising, 85354, Germany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - Sebastien Carpentier
- Department of Biosystems, KU Leuven, Willem Decroylaan 42, 2455-3001 Leuven, Belgium
- SYBIOMA, KULeuven, Herestraat 49, Leuven, 3000, Belgium
- Genetic Resources, Bioversity International, Willem Decroylaan 42, 2455-3001 Leuven, Belgium
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Nascimento-Oliveira JI, Fantinatti BEA, Wolf IR, Cardoso AL, Ramos E, Rieder N, de Oliveira R, Martins C. Differential expression of miRNAs in the presence of B chromosome in the cichlid fish Astatotilapia latifasciata. BMC Genomics 2021; 22:344. [PMID: 33980143 PMCID: PMC8117508 DOI: 10.1186/s12864-021-07651-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND B chromosomes (Bs) are extra elements observed in diverse eukaryotes, including animals, plants and fungi. Although Bs were first identified a century ago and have been studied in hundreds of species, their biology is still enigmatic. Recent advances in omics and big data technologies are revolutionizing the B biology field. These advances allow analyses of DNA, RNA, proteins and the construction of interactive networks for understanding the B composition and behavior in the cell. Several genes have been detected on the B chromosomes, although the interaction of B sequences and the normal genome remains poorly understood. RESULTS We identified 727 miRNA precursors in the A. latifasciata genome, 66% which were novel predicted sequences that had not been identified before. We were able to report the A. latifasciata-specific miRNAs and common miRNAs identified in other fish species. For the samples carrying the B chromosome (B+), we identified 104 differentially expressed (DE) miRNAs that are down or upregulated compared to samples without B chromosome (B-) (p < 0.05). These miRNAs share common targets in the brain, muscle and gonads. These targets were used to construct a protein-protein-miRNA network showing the high interaction between the targets of differentially expressed miRNAs in the B+ chromosome samples. Among the DE-miRNA targets there are protein-coding genes reported for the B chromosome that are present in the protein-protein-miRNA network. Additionally, Gene Ontology (GO) terms related to nuclear matrix organization and response to stimulus are exclusive to DE miRNA targets of B+ samples. CONCLUSIONS This study is the first to report the connection of B chromosomes and miRNAs in a vertebrate species. We observed that the B chromosome impacts the miRNAs expression in several tissues and these miRNAs target several mRNAs involved with important biological processes.
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Affiliation(s)
- Jordana Inácio Nascimento-Oliveira
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | | | - Ivan Rodrigo Wolf
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Adauto Lima Cardoso
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Erica Ramos
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Nathalie Rieder
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
| | - Rogerio de Oliveira
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
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Abstract
Chromosome size and morphology vary within and among species, but little is known about the proximate or ultimate causes of these differences. Cichlid fish species in the tribe Oreochromini share an unusual giant chromosome that is ∼3 times longer than the other chromosomes. This giant chromosome functions as a sex chromosome in some of these species. We test two hypotheses of how this giant sex chromosome may have evolved. The first hypothesis proposes that it evolved by accumulating repetitive elements as recombination was reduced around a dominant sex determination locus, as suggested by canonical models of sex chromosome evolution. An alternative hypothesis is that the giant sex chromosome originated via the fusion of an autosome with a highly repetitive B chromosome, one of which carried a sex determination locus. We test these hypotheses using comparative analysis of chromosome-scale cichlid and teleost genomes. We find that the giant sex chromosome consists of three distinct regions based on patterns of recombination, gene and transposable element content, and synteny to the ancestral autosome. The WZ sex determination locus encompasses the last ∼105 Mb of the 134-Mb giant chromosome. The last 47 Mb of the giant chromosome shares no obvious homology to any ancestral chromosome. Comparisons across 69 teleost genomes reveal that the giant sex chromosome contains unparalleled amounts of endogenous retroviral elements, immunoglobulin genes, and long noncoding RNAs. The results favor the B chromosome fusion hypothesis for the origin of the giant chromosome.
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Affiliation(s)
- Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Frances E Clark
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Reade B Roberts
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Luohao Xu
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Qi Zhou
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
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25
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Silva DMZDA, Ruiz-Ruano FJ, Utsunomia R, Martín-Peciña M, Castro JP, Freire PP, Carvalho RF, Hashimoto DT, Suh A, Oliveira C, Porto-Foresti F, Artoni RF, Foresti F, Camacho JPM. Long-term persistence of supernumerary B chromosomes in multiple species of Astyanax fish. BMC Biol 2021; 19:52. [PMID: 33740955 PMCID: PMC7976721 DOI: 10.1186/s12915-021-00991-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/24/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Eukaryote genomes frequently harbor supernumerary B chromosomes in addition to the "standard" A chromosome set. B chromosomes are thought to arise as byproducts of genome rearrangements and have mostly been considered intraspecific oddities. However, their evolutionary transcendence beyond species level has remained untested. RESULTS Here we reveal that the large metacentric B chromosomes reported in several fish species of the genus Astyanax arose in a common ancestor at least 4 million years ago. We generated transcriptomes of A. scabripinnis and A. paranae 0B and 1B individuals and used these assemblies as a reference for mapping all gDNA and RNA libraries to quantify coverage differences between B-lacking and B-carrying genomes. We show that the B chromosomes of A. scabripinnis and A. paranae share 19 protein-coding genes, of which 14 and 11 were also present in the B chromosomes of A. bockmanni and A. fasciatus, respectively. Our search for B-specific single-nucleotide polymorphisms (SNPs) identified the presence of B-derived transcripts in B-carrying ovaries, 80% of which belonged to nobox, a gene involved in oogenesis regulation. Importantly, the B chromosome nobox paralog is expressed > 30× more than the A chromosome paralog. This indicates that the normal regulation of this gene is altered in B-carrying females, which could potentially facilitate B inheritance at higher rates than Mendelian law prediction. CONCLUSIONS Taken together, our results demonstrate the long-term survival of B chromosomes despite their lack of regular pairing and segregation during meiosis and that they can endure episodes of population divergence leading to species formation.
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Affiliation(s)
- Duílio Mazzoni Zerbinato de Andrade Silva
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | - Francisco J Ruiz-Ruano
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden.
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK.
| | - Ricardo Utsunomia
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, UNESP, Campus de Bauru, Bauru, SP, 17033-360, Brazil
| | | | - Jonathan Pena Castro
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCAR, São Carlos, SP, 13565-905, Brazil
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, UEPG, Ponta Grossa, PR, 84030-900, Brazil
| | - Paula Paccielli Freire
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, USP, São Paulo, SP, 05508-900, Brazil
| | - Robson Francisco Carvalho
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | - Diogo T Hashimoto
- Centro de Aquicultura, Universidade Estadual Paulista, UNESP, Campus Jaboticabal, Jaboticabal, SP, 14884-900, Brazil
| | - Alexander Suh
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, UNESP, Campus de Bauru, Bauru, SP, 17033-360, Brazil
| | - Roberto Ferreira Artoni
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCAR, São Carlos, SP, 13565-905, Brazil
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, UEPG, Ponta Grossa, PR, 84030-900, Brazil
| | - Fausto Foresti
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
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Bednářová M, Karafiátová M, Hřibová E, Bartoš J. B Chromosomes in Genus Sorghum (Poaceae). PLANTS (BASEL, SWITZERLAND) 2021; 10:505. [PMID: 33803087 PMCID: PMC8001295 DOI: 10.3390/plants10030505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 12/30/2022]
Abstract
B chromosomes (Bs) are supernumerary dispensable genomic elements that have been reported in several thousand eukaryotic species. Since their discovery, Bs have been subjected to countless studies aiming at the clarification of their origin, composition, and influence on the carriers. Despite these efforts, we still have very limited knowledge of the processes that led to the emergence of Bs, the mechanisms of their transmission, and the effects of Bs on the hosts. In the last decade, sophisticated molecular methods, including next-generation sequencing, have provided powerful tool to help answer some of these questions, but not many species have received much attention yet. In this review, we summarize the currently available information about Bs in the genus Sorghum, which has so far been on the periphery of scientific interest. We present an overview of the occurrence and characteristics of Bs in various Sorghum species, discuss the possible mechanisms involved in their maintenance and elimination, and outline hypotheses of the origin of Bs in this genus.
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Affiliation(s)
| | | | | | - Jan Bartoš
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic; (M.B.); (M.K.); (E.H.)
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27
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Felicetti D, Haerter CAG, Baumgärtner L, Paiz LM, Takagui FH, Margarido VP, Blanco DR, Feldberg E, da Silva M, Lui RL. A New Variant B Chromosome in Auchenipteridae: The Role of (GATA)n and (TTAGGG)n Sequences in Understanding the Evolution of Supernumeraries in Trachelyopterus. Cytogenet Genome Res 2021; 161:70-81. [PMID: 33601372 DOI: 10.1159/000513107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/20/2020] [Indexed: 11/19/2022] Open
Abstract
Basic and molecular cytogenetic techniques were carried out in 3 Neotropical region populations of catfishes, two of Trachelyopterus galeatus (one from the marshlands of Paraguay River basin and another from Lago Catalão, Amazon River basin) and one of Trachelyopterus porosus, a sympatric population to T. galeatus from the Amazon River basin. This study aimed to describe and understand the structure and evolution of Trachelyopterus B chromosomes, mainly through physical mapping of repetitive elements. A diploid number of 58 chromosomes was found for all individuals, as well as the presence of B chromosomes. For T. porosus this is the first report of a supernumerary. The sympatric species of T. galeatus and T. porosus from Amazon River had 1-3 B chromosomes and T. galeatus from Paraguay River had 1-2 B chromosomes, all of them showed intra- and interindividual numerical variation. Two females of T. porosus exhibited a new variant B chromosome (B2), previously not seen in Auchenipteridae, which might have originated from B1 chromosomes. All B chromosomes were entirely heterochromatic. In contrast to all complement A and B2 chromosomes, in which the telomeric sequences were found in the telomeric regions, B1 chromosomes of all populations were totally marked by (TTAGGG)n probes. (GATA)n sequence sites were found through all complement A chromosomes, but B1 and B2 chromosomes exhibited only a clustered block in one of the chromosome arms. The most frequent B chromosomes (B1) in all populations/species, including those previously studied in Auchenipteridae catfishes, share the following characteristics: totally heterochromatic, small, metacentric, with accumulation of repetitive (TTAGGG)n sequences, and a low number of (GATA)n copies, which might suggest a common ancient origin in Trachelyopterus species/populations.
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Affiliation(s)
- Denise Felicetti
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
| | - Chrystian A G Haerter
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
| | - Lucas Baumgärtner
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
| | - Leonardo M Paiz
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
| | - Fábio H Takagui
- Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Vladimir P Margarido
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
| | - Daniel R Blanco
- Universidade Tecnológica Federal do Paraná, Santa Helena, Brazil
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
| | - Maelin da Silva
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Roberto L Lui
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil,
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28
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Martins C, Jehangir M. A genomic glimpse of B chromosomes in cichlids. Genes Genomics 2021; 43:199-208. [PMID: 33547625 DOI: 10.1007/s13258-021-01049-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 01/25/2023]
Abstract
BACKGROUND B chromosomes (Bs) are extra karyotype elements in addition to A chromosomes and are found in all major eukaryotic taxa. Among hundreds of investigated species, cichlid fishes have emerged as an interesting group of model and have contributed to unravel the complex biology of B chromosome. OBJECTIVE We review the current state of knowledge on B chromosome investigation in cichlid fish and discuss the recent genomic advances over gene and sequences hunting on Bs and their impact on the current concept of B chromosomes. RESULTS The Bs of cichlids have been under the subject of classical cytogenetics and high scale DNA, RNA and epigenetics analysis and a list of B chromosome genes and functional sequences has been generated. B chromosomes of cichlids are restricted to females in some species and are enriched with genes, relics of genes, transposable elements and sequences transcribing for many significant biological functions. Diverse potentially functional sequences have been described in the B chromosome of cichlids and could influence important biological characteristics as well seems to affect transcription and epigenetic modifications of the whole genome. CONCLUSION One of the most enigmatic characteristics of Bs in cichlids is their genic content related to cell cycle and chromosome structure, and their influence over sex rates. The relationship of Bs with cell cycle and sex determination looks like to be connected with the drive of the Bs during cell divisions.
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Affiliation(s)
- Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
| | - Maryam Jehangir
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
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29
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Iannucci A, Makunin AI, Lisachov AP, Ciofi C, Stanyon R, Svartman M, Trifonov VA. Bridging the Gap between Vertebrate Cytogenetics and Genomics with Single-Chromosome Sequencing (ChromSeq). Genes (Basel) 2021; 12:124. [PMID: 33478118 PMCID: PMC7835784 DOI: 10.3390/genes12010124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/10/2021] [Accepted: 01/15/2021] [Indexed: 01/23/2023] Open
Abstract
The study of vertebrate genome evolution is currently facing a revolution, brought about by next generation sequencing technologies that allow researchers to produce nearly complete and error-free genome assemblies. Novel approaches however do not always provide a direct link with information on vertebrate genome evolution gained from cytogenetic approaches. It is useful to preserve and link cytogenetic data with novel genomic discoveries. Sequencing of DNA from single isolated chromosomes (ChromSeq) is an elegant approach to determine the chromosome content and assign genome assemblies to chromosomes, thus bridging the gap between cytogenetics and genomics. The aim of this paper is to describe how ChromSeq can support the study of vertebrate genome evolution and how it can help link cytogenetic and genomic data. We show key examples of ChromSeq application in the refinement of vertebrate genome assemblies and in the study of vertebrate chromosome and karyotype evolution. We also provide a general overview of the approach and a concrete example of genome refinement using this method in the species Anolis carolinensis.
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Affiliation(s)
- Alessio Iannucci
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy; (C.C.); (R.S.)
| | - Alexey I. Makunin
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK;
- Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia;
| | - Artem P. Lisachov
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, 625003 Tyumen, Russia;
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Claudio Ciofi
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy; (C.C.); (R.S.)
| | - Roscoe Stanyon
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy; (C.C.); (R.S.)
| | - Marta Svartman
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, 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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31
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B Chromosomes and Cytogenetic Characteristics of the Common Nase Chondrostoma nasus (Linnaeus, 1758). Genes (Basel) 2020; 11:genes11111317. [PMID: 33172121 PMCID: PMC7694786 DOI: 10.3390/genes11111317] [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: 10/07/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/21/2022] Open
Abstract
Supernumerary B chromosomes (Bs) are very promising structures, among others, in that they are an additional genomic compartment for evolution. In this study, we tested the presence and frequency of B chromosomes and performed the first cytogenetic examination of the common nase (Chondrostoma nasus). We investigated the individuals from two populations in the Vistula River basin, in Poland, according to the chromosomal distribution of the C-bands and silver nucleolar organizer regions (Ag-NORs), using sequential staining with AgNO3 and chromomycin A3 (CMA3). Furthermore, we analyzed the chromosomal localization of two rDNA families (45S and 5S rDNA) using fluorescence in situ hybridization (FISH) with rDNA probes. Chondrostoma nasus individuals showed a standard (A) chromosome set consisting of 2n = 50: 12 metacentric, 32 submetacentric, and 6 acrocentric chromosomes (NF = 94). Fourteen out of the 20 analyzed individuals showed 1–2 mitotically unstable submetacentric B chromosomes of different sizes. Six of them, in 14.1% of the analyzed metaphase plates, had a single, medium-sized submetacentric B (Bsm) chromosome (2n = 51) with a heterochromatic block located in its pericentromeric region. The other seven individuals possessed a Bsm (2n = 51) in 19.4% of the analyzed metaphase plates, and a second Bsm chromosome (2n = 52), the smallest in the set, in 15.5% of metaphase plates, whereas one female was characterized by both Bsm chromosomes (2n = 52) in 14.3% of the analyzed metaphase plates. AgNORs, GC-rich DNA sites, and 28S rDNA hybridization sites were observed in the short arms of two submetacentric chromosome pairs of A set. The constitutive heterochromatin was visible as C bands in the centromeric regions of almost all Chondrostoma nasus chromosomes and in the pericentromeric region of several chromosome pairs. Two 5S rDNA hybridization sites in the pericentromeric position of the largest acrocentric chromosome pair were observed, whereas two other such sites in co-localization on a smaller pair of NOR chromosomes indicate a species-specific character. The results herein broaden our knowledge in the field of B chromosome distribution and molecular cytogenetics of Chondrostoma nasus: a freshwater species from the Leuciscidae family.
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Ahmad SF, Jehangir M, Cardoso AL, Wolf IR, Margarido VP, Cabral-de-Mello DC, O'Neill R, Valente GT, Martins C. B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes. BMC Genomics 2020; 21:656. [PMID: 32967626 PMCID: PMC7509943 DOI: 10.1186/s12864-020-07072-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/14/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND One of the biggest challenges in chromosome biology is to understand the occurrence and complex genetics of the extra, non-essential karyotype elements, commonly known as supernumerary or B chromosomes (Bs). The non-Mendelian inheritance and non-pairing abilities of B chromosomes make them an interesting model for genomics studies, thus bringing to bear different questions about their genetic composition, evolutionary survival, maintenance and functional role inside the cell. This study uncovers these phenomena in multiple species that we considered as representative organisms of both vertebrate and invertebrate models for B chromosome analysis. RESULTS We sequenced the genomes of three animal species including two fishes Astyanax mexicanus and Astyanax correntinus, and a grasshopper Abracris flavolineata, each with and without Bs, and identified their B-localized genes and repeat contents. We detected unique sequences occurring exclusively on Bs and discovered various evolutionary patterns of genomic rearrangements associated to Bs. In situ hybridization and quantitative polymerase chain reactions further validated our genomic approach confirming detection of sequences on Bs. The functional annotation of B sequences showed that the B chromosome comprises regions of gene fragments, novel genes, and intact genes, which encode a diverse set of functions related to important biological processes such as metabolism, morphogenesis, reproduction, transposition, recombination, cell cycle and chromosomes functions which might be important for their evolutionary success. CONCLUSIONS This study reveals the genomic structure, composition and function of Bs, which provide new insights for theories of B chromosome evolution. The selfish behavior of Bs seems to be favored by gained genes/sequences.
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Affiliation(s)
- Syed F Ahmad
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Maryam Jehangir
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Adauto L Cardoso
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Ivan R Wolf
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Vladimir P Margarido
- Western Paraná State University (UNIOESTE), Center for Biology Science and Health, Cascavel, PR, Brazil
| | - Diogo C Cabral-de-Mello
- Department of General and Applied Biology, Institute of Biosciences, Sao Paulo State University (UNESP), Rio Claro, SP, Brazil
| | - Rachel O'Neill
- Department of Molecular and Cell Biology, University of Connecticut (UCONN), Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut (UCONN), Storrs, CT, USA
| | - Guilherme T Valente
- Bioprocess and Biotechnology Department, Agronomical Science Faculty, Sao Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
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Structure and Sequence of the Sex Determining Locus in Two Wild Populations of Nile Tilapia. Genes (Basel) 2020; 11:genes11091017. [PMID: 32872430 PMCID: PMC7563666 DOI: 10.3390/genes11091017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/15/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
In domesticated strains of the Nile tilapia, phenotypic sex has been linked to genetic variants on linkage groups 1, 20 and 23. This diversity of sex-loci might reflect a naturally polymorphic sex determination system in Nile tilapia, or it might be an artefact arising from the process of domestication. Here, we searched for sex-determiners in wild populations from Kpandu, Lake Volta (Ghana-West Africa), and from Lake Koka (Ethiopia-East Africa) that have not been subjected to any genetic manipulation. We analysed lab-reared families using double-digest Restriction Associated DNA sequencing (ddRAD) and analysed wild-caught males and females with pooled whole-genome sequencing (WGS). Strong sex-linked signals were found on LG23 in both populations, and sex-linked signals with LG3 were observed in Kpandu samples. WGS uncovered blocks of high sequence coverage, suggesting the presence of B chromosomes. We confirmed the existence of a tandem amh duplication in LG23 in both populations and determined its breakpoints between the oaz1 and dot1l genes. We found two common deletions of ~5 kb in males and confirmed the presence of both amhY and amh∆Y genes. Males from Lake Koka lack both the previously reported 234 bp deletion and the 5 bp frameshift-insertion that creates a premature stop codon in amh∆Y.
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Malimpensa GDC, Traldi JB, Martinez JDF, Deon G, Azambuja M, Nogaroto V, Vicari MR, Moreira-Filho O. Chromosomal Diversification in Two Species of Pimelodus (Siluriformes: Pimelodidae): Comparative Cytogenetic Mapping of Multigene Families. Zebrafish 2020; 17:278-286. [DOI: 10.1089/zeb.2020.1892] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
| | | | | | - Geize Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Matheus Azambuja
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Marcelo Ricardo Vicari
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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35
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Melo AS, Cruz GAS, Félix AP, Rocha MF, Loreto V, Moura RC. Wide dispersion of B chromosomes in Rhammatocerus brasiliensis (Orthoptera, Acrididae). Genet Mol Biol 2020; 43:e20190077. [PMID: 32542305 PMCID: PMC7295183 DOI: 10.1590/1678-4685-gmb-2019-0077] [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: 03/13/2019] [Accepted: 07/16/2019] [Indexed: 01/01/2023] Open
Abstract
The grasshopper Rhammatocerus brasiliensis shows polymorphism of B chromosomes, but the magnitude of B-chromosome occurrence and the factors that may contribute to their dispersion in the species remain unknown thus far. The present study analyzed the occurrence and dispersion of B chromosomes in R. brasiliensis individuals from 21 populations widely distributed in the Brazilian Northeast. The genetic connectivity between 10 populations was verified through analysis of ISSR markers from 200 individuals. Of the 21 populations, 19 presented individuals with one B chromosome, three with two, and one with three B chromosomes. The B chromosome is of medium size and constitutive heterochromatin (CH) located in the pericentromeric region. A variant B chromosome was observed in three populations, similar in size to that of chromosome X, gap and CH, and located in the terminal region. B chromosome frequencies in different populations varied from 0% to 18,8%, mean 8,5%. The wide distribution of the B chromosome is likely a consequence of the positive gene flow among the analyzed populations. B-chromosome occurrence in populations of R. brasiliensis possibly follows the population genetic structure of the species and, owing to the existence of a variant, its origin may not be recent.
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Affiliation(s)
- Adriana S Melo
- Universidade de Pernambuco (UPE), Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
| | - Geyner A S Cruz
- Universidade de Pernambuco (UPE), Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
- Universidade de Pernambuco (UPE), Laboratório de Biodiversidade e Genética Evolutiva, Campus Petrolina, Petrolina, PE, Brazil
| | - Aline P Félix
- Universidade de Pernambuco (UPE), Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
| | - Marília F Rocha
- Universidade de Pernambuco (UPE), Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
| | - Vilma Loreto
- Universidade Federal de Pernambuco (UFPE), Departamento de Genética, Laboratório de Genética Animal e Humana e Citogenética, Recife, PE, Brazil
| | - Rita C Moura
- Universidade de Pernambuco (UPE), Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, Recife, PE, Brazil
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Ruban A, Schmutzer T, Wu DD, Fuchs J, Boudichevskaia A, Rubtsova M, Pistrick K, Melzer M, Himmelbach A, Schubert V, Scholz U, Houben A. Supernumerary B chromosomes of Aegilops speltoides undergo precise elimination in roots early in embryo development. Nat Commun 2020; 11:2764. [PMID: 32488019 PMCID: PMC7265534 DOI: 10.1038/s41467-020-16594-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
Not necessarily all cells of an organism contain the same genome. Some eukaryotes exhibit dramatic differences between cells of different organs, resulting from programmed elimination of chromosomes or their fragments. Here, we present a detailed analysis of programmed B chromosome elimination in plants. Using goatgrass Aegilops speltoides as a model, we demonstrate that the elimination of B chromosomes is a strictly controlled and highly efficient root-specific process. At the onset of embryo differentiation B chromosomes undergo elimination in proto-root cells. Independent of centromere activity, B chromosomes demonstrate nondisjunction of chromatids and lagging in anaphase, leading to micronucleation. Chromatin structure and DNA replication differ between micronuclei and primary nuclei and degradation of micronucleated DNA is the final step of B chromosome elimination. This process might allow root tissues to survive the detrimental expression, or overexpression of B chromosome-located root-specific genes with paralogs located on standard chromosomes. B chromosomes are supernumerary chromosomes exhibiting dramatic differences between different organs in same species. Here, the authors show programmed B chromosome elimination in goatgrass starts at the onset of embryo differentiation by nondisjunction of chromatids, anaphase lagging, and ends with the degradation of micronucleated DNA.
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Affiliation(s)
- Alevtina Ruban
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany.,KWS SAAT SE & Co. KGaA, 37574, Einbeck, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany.,Martin Luther University Halle-Wittenberg, Institute for Agricultural and Nutritional Sciences, 06099, Halle (Saale), Germany
| | - Dan D Wu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany.,Triticeae Research Institute, Sichuan Agricultural University, 611130, Wenjiang, China
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany
| | - Anastassia Boudichevskaia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany.,KWS SAAT SE & Co. KGaA, 37574, Einbeck, Germany
| | - Myroslava Rubtsova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany.,SAATEN-UNION BIOTEC GmbH, 06466 Seeland, OT Gatersleben, Germany
| | - Klaus Pistrick
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, OT Gatersleben, Germany.
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37
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Demin SY, Berdieva MA, Podlipaeva YI, Goodkov AV. Karyotypic instability of endoprophase and mitotic cells of Amoeba sp. strain Cont from the "proteus-type" group (Amoebozoa, Euamoebida, Amoebidae). Eur J Protistol 2020; 74:125691. [PMID: 32200034 DOI: 10.1016/j.ejop.2020.125691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 02/21/2020] [Accepted: 03/03/2020] [Indexed: 01/01/2023]
Abstract
We performed karyotyping of Amoeba sp. strain Cont. Based on the results of a cytological analysis, we concluded that the chromosome number of Amoeba sp. strain Cont in mitosis was unstable. In all cases they appeared to be hypergaploid (the basic chromosome number is 30), with monosomy of all chromosomes except four shortest ones. The presence of "extrachromosomes" in the nucleus could prolong until the beginning of the anaphase. It was only then that they were ejected from the nucleus and the euploidy (haploidy) was restored. The stage of endoprophase nucleus was revealed in the cell cycle of Amoeba sp. strain Cont. This stage has not yet been found in other amoebae from the "proteus-type" group that had been previously studied (A. proteus strain B and A. borokensis). The maximum number of endoreplication rounds in the strain Cont amoebae nuclear cycle was 4 or 5. The regular extrusion of chromosomes from the nucleus into the cytoplasm occurred in each of the endoreplication rounds. Comparative cytological analysis of A. proteus strain B, A. borokensis and Amoeba sp. strain Cont karyotypes indicated that strain Cont, though rather close to the former two amoebae, is actually a distinct species.
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Affiliation(s)
- Sergei Yu Demin
- Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia
| | - Mariia A Berdieva
- Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia
| | - Yuliya I Podlipaeva
- Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia
| | - Andrew V Goodkov
- Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia.
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38
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Schemczssen-Graeff Z, Barbosa P, Castro JP, Silva MD, Almeida MCD, Moreira-Filho O, Artoni RF. Dynamics of Replication and Nuclear Localization of the B Chromosome in Kidney Tissue Cells in Astyanax scabripinnis (Teleostei: Characidae). Zebrafish 2020; 17:147-152. [PMID: 32159463 DOI: 10.1089/zeb.2019.1756] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
B chromosomes are extra genomic compounds found in different taxonomic groups, including plants and animals. Obtaining patterns of resolutive chromosomal bands is necessary to understand the nuclear organization, variability and nature of B chromosome chromatin and possible transcriptional regions. In this study, we analyzed 35 Astyanax scabripinnis specimens sampled from Fazenda Lavrinha, a stream in the Paraíba do Sul river basin, Brazil. Through the incorporation of the thymidine analog 5'-bromo-2'-deoxyuridine (5-BrdU) in vivo, it was possible to recognize the replicating regions of the B chromosome at the beginning of the S phase, differentially characterized in relationship to the regions of late replication. In this perspective, it is possible to suggest that the B chromosome of this species possesses a territory and the chromatin accessible for transcription, especially in the light (i.e., early replicating) bands (p1.1; p1.3; and p2.1 and q1.1, q1.3, q2.1, and q2.2). The late-replicating regions are corresponding to the blocks of constitutive heterochromatin. They show a preferential accumulation of satellite DNA As51. By the use of the fluorochrome chromomycin A3 (CMA3), it was possible to identify GC-rich chromosomal regions, corresponding to late-replicating parts of genome, confirming the revealed data by the replication banding and C-banding. In addition, the analysis by confocal microscopy in kidney cells indicates the location of a peripheral anchorage of this chromosome in the nuclear lamina, reinforcing the idea of downregulation of the associated regions.
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Affiliation(s)
- Zelinda Schemczssen-Graeff
- Programa de Pós-Graduação em Biologia Evolutiva, Laboratório de Genética Evolutiva, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Patrícia Barbosa
- Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular, Laboratório de Citogenética de Peixes, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Jonathan Pena Castro
- Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular, Laboratório de Citogenética de Peixes, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Maelin da Silva
- Programa de Pós-Graduação em Biologia Evolutiva, Laboratório de Genética Evolutiva, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Mara Cristina de Almeida
- Programa de Pós-Graduação em Biologia Evolutiva, Laboratório de Genética Evolutiva, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Orlando Moreira-Filho
- Programa de Pós-Graduação em Biologia Evolutiva, Laboratório de Genética Evolutiva, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil.,Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular, Laboratório de Citogenética de Peixes, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Roberto Ferreira Artoni
- Programa de Pós-Graduação em Biologia Evolutiva, Laboratório de Genética Evolutiva, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil.,Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular, Laboratório de Citogenética de Peixes, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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39
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Zadesenets KS, Jetybayev IY, Schärer L, Rubtsov NB. Genome and Karyotype Reorganization after Whole Genome Duplication in Free-Living Flatworms of the Genus Macrostomum. Int J Mol Sci 2020; 21:E680. [PMID: 31968653 PMCID: PMC7013459 DOI: 10.3390/ijms21020680] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/09/2020] [Indexed: 01/31/2023] Open
Abstract
The genus Macrostomum represents a diverse group of rhabditophoran flatworms with >200 species occurring around the world. Earlier we uncovered karyotype instability linked to hidden polyploidy in both M. lignano (2n = 8) and its sibling species M. janickei (2n = 10), prompting interest in the karyotype organization of close relatives. In this study, we investigated chromosome organization in two recently described and closely related Macrostomum species, M. mirumnovem and M. cliftonensis, and explored karyotype instability in laboratory lines and cultures of M. lignano (DV1/10, 2n = 10) and M. janickei in more detail. We revealed that three of the four studied species are characterized by karyotype instability, while M. cliftonensis showed a stable 2n = 6 karyotype. Next, we performed comparative cytogenetics of these species using fluorescent in situ hybridization (FISH) with a set of DNA probes (including microdissected DNA probes generated from M. lignano chromosomes, rDNA, and telomeric DNA). To explore the chromosome organization of the unusual 2n = 9 karyotype discovered in M. mirumnovem, we then generated chromosome-specific DNA probes for all chromosomes of this species. Similar to M. lignano and M. janickei, our findings suggest that M. mirumnovem arose via whole genome duplication (WGD) followed by considerable chromosome reshuffling. We discuss possible evolutionary scenarios for the emergence and reorganization of the karyotypes of these Macrostomum species and consider their suitability as promising animal models for studying the mechanisms and regularities of karyotype and genome evolution after a recent WGD.
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Affiliation(s)
- Kira S. Zadesenets
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Lavrentiev ave. 10, 630090 Novosibirsk, Russia;
| | - Ilyas Y. Jetybayev
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Lavrentiev ave. 10, 630090 Novosibirsk, Russia;
| | - Lukas Schärer
- Evolutionary Biology, Zoological Institute, University of Basel, CH-4051 Basel, Switzerland;
| | - Nikolay B. Rubtsov
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Lavrentiev ave. 10, 630090 Novosibirsk, Russia;
- Department of Cytology and Genetics, Novosibirsk State University, Pirogova str. 2, 630090 Novosibirsk, Russia
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40
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Kratochwil CF, Liang Y, Urban S, Torres-Dowdall J, Meyer A. Evolutionary Dynamics of Structural Variation at a Key Locus for Color Pattern Diversification in Cichlid Fishes. Genome Biol Evol 2019; 11:3452-3465. [PMID: 31821504 PMCID: PMC6916709 DOI: 10.1093/gbe/evz261] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2019] [Indexed: 02/07/2023] Open
Abstract
Color patterns in African cichlid fishes vary spectacularly. Although phylogenetic analysis showed already 30 years ago that many color patterns evolved repeatedly in these adaptive radiations, only recently have we begun to understand the genomic basis of color variation. Horizontal stripe patterns evolved and were lost several times independently across the adaptive radiations of Lake Victoria, Malawi, and Tanganyika and regulatory evolution of agouti-related peptide 2 (agrp2/asip2b) has been linked to this phenotypically labile trait. Here, we asked whether the agrp2 locus exhibits particular characteristics that facilitate divergence in color patterns. Based on comparative genomic analyses, we discovered several recent duplications, insertions, and deletions. Interestingly, one of these events resulted in a tandem duplication of the last exon of agrp2. The duplication likely precedes the East African radiations that started 8-12 Ma, is not fixed within any of the radiations, and is found to vary even within some species. Moreover, we also observed variation in copy number (two to five copies) and secondary loss of the duplication, illustrating a surprising dynamic at this locus that possibly promoted functional divergence of agrp2. Our work suggests that such instances of exon duplications are a neglected mechanism potentially involved in the repeated evolution and diversification that deserves more attention.
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Affiliation(s)
- Claudius F Kratochwil
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Radolfzell, Germany
- Zukunftskolleg, University of Konstanz, Germany
| | - Yipeng Liang
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
| | - Sabine Urban
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Radolfzell, Germany
| | - Julián Torres-Dowdall
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- Zukunftskolleg, University of Konstanz, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Radolfzell, Germany
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41
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Novel B-chromosome-specific transcriptionally active sequences are present throughout the maize B chromosome. Mol Genet Genomics 2019; 295:313-325. [PMID: 31729549 DOI: 10.1007/s00438-019-01623-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
Supernumerary B chromosomes are dispensable parts of the nuclear genome and occur in all eukaryotic groups. They differ from the normal A chromosomes in morphology, genetic behavior, and inheritance. Because they are nonessential for individual development, B chromosomes are considered to be genetically inert and to lack functional genes. However, the maize B chromosome carries control elements that direct its behavior and affects A chromosomes during cell division. Therefore, the maize B chromosome might contain genic regions that differ from the genic regions of A chromosomes. Yet, only a few B-specific transcript sequences have been isolated. To identify more B-specific transcriptionally active sequences, we constructed de novo transcriptome assemblies for maize B73 inbred lines with 0B (+0B) and 2B (+2B). Comparative analysis of the B73 + 0B and B73 + 2B assemblies revealed that unigenes annotated to 201 gene ontology terms were differentially expressed. Using RT-PCR analysis of novel transcript sequences specific to B73 + 2B, we identified 32 novel B-related transcript sequences, and most sequences showed consistent B-specific transcription in different inbred lines. Moreover, 20 of those novel B-related transcript sequences were further confirmed to be located only on the B chromosome by genomic PCR analysis. A total of 19 novel B-specific transcript sequences were mapped to various positions along the B chromosome using B-10L translocations. Taken together, our results suggest that the maize B chromosome indeed affects the expression of A-located genes and that a substantial amount of novel B-specific transcriptionally active sequences are present throughout the maize B chromosome. Therefore, the maize B chromosome seems not to be genetically inert.
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42
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Serrano-Freitas ÉA, Silva DMZA, Ruiz-Ruano FJ, Utsunomia R, Araya-Jaime C, Oliveira C, Camacho JPM, Foresti F. Satellite DNA content of B chromosomes in the characid fish Characidium gomesi supports their origin from sex chromosomes. Mol Genet Genomics 2019; 295:195-207. [PMID: 31624915 DOI: 10.1007/s00438-019-01615-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 10/01/2019] [Indexed: 12/28/2022]
Abstract
The origin of supernumerary (B) chromosomes is clearly conditioned by their ancestry from the standard (A) chromosomes. Sequence similarity between A and B chromosomes is thus crucial to determine B chromosome origin. For this purpose, we compare here the DNA sequences from A and B chromosomes in the characid fish Characidium gomesi using two main approaches. First, we found 59 satellite DNA (satDNA) families constituting the satellitome of this species and performed FISH analysis for 18 of them. This showed the presence of six satDNAs on the B chromosome: one shared with sex chromosomes and autosomes, two shared with sex chromosomes, one shared with autosomes and two being B-specific. This indicated that B chromosomes most likely arose from the sex chromosomes. Our second approach consisted of the analysis of five repetitive DNA families: 18S and 5S ribosomal DNA (rDNA), the H3 histone gene, U2 snDNA and the most abundant satDNA (CgoSat01-184) on DNA obtained from microdissected B chromosomes and from B-lacking genomes. PCR and sequence analysis of these repetitive sequences was successful for three of them (5S rDNA, H3 histone gene and CgoSat01-184), and sequence comparison revealed that DNA sequences obtained from the B chromosomes displayed higher identity with C. gomesi genomic DNA than with those obtained from other Characidium species. Taken together, our results support the intraspecific origin of B chromosomes in C. gomesi and point to sex chromosomes as B chromosome ancestors, which raises interesting prospects for future joint research on the genetic content of sex and B chromosomes in this species.
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Affiliation(s)
- Érica A Serrano-Freitas
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil.,Centro de Ciências Biológicas e da Saúde, Fundação Educacional de Penápolis, Funepe, Penápolis, SP, 16303-180, Brazil
| | - Duílio M Z A Silva
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil.
| | - Francisco J Ruiz-Ruano
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.,Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236, Uppsala, Sweden
| | - Ricardo Utsunomia
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
| | - Cristian Araya-Jaime
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, 1720256, La Serena, Chile.,Laboratorio de Genética y Citogenética Vegetal, Departamento de Biología, Universidad de La Serena, 1720256, La Serena, Chile
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | | | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
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43
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Park D, Kim JH, Kim NS. De novo transcriptome sequencing and gene expression profiling with/without B-chromosome plants of Lilium amabile. Genomics Inform 2019; 17:e27. [PMID: 31610623 PMCID: PMC6808634 DOI: 10.5808/gi.2019.17.3.e27] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 03/23/2019] [Indexed: 11/20/2022] Open
Abstract
Supernumerary B chromosomes were found in Lilium amabile (2n = 2x = 24), an endemic Korean lily that grows in the wild throughout the Korean Peninsula. The extra B chromosomes do not affect the host-plant morphology; therefore, whole transcriptome analysis was performed in 0B and 1B plants to identify differentially expressed genes. A total of 154,810 transcripts were obtained from over 10 Gbp data by de novo assembly. By mapping the raw reads to the de novo transcripts, we identified 7,852 differentially expressed genes (log2FC > |10|), in which 4,059 and 3,794 were up-and down-regulated, respectively, in 1B plants compared to 0B plants. Functional enrichment analysis revealed that various differentially expressed genes were involved in cellular processes including the cell cycle, chromosome breakage and repair, and microtubule formation; all of which may be related to the occurrence and maintenance of B chromosomes. Our data provide insight into transcriptomic changes and evolution of plant B chromosomes and deliver an informative database for future study of B chromosome transcriptomes in the Korean lily.
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Affiliation(s)
- Doori Park
- Department of Molecular Biosciences, Kangwon National University, Chuncheon 24341, Korea
| | - Jong-Hwa Kim
- Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea.,Oriental Bio-herb Research Institute, Kangwon National University, Chuncheon 24341, Korea
| | - Nam-Soo Kim
- Department of Molecular Biosciences, Kangwon National University, Chuncheon 24341, Korea.,Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Korea
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44
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Jehangir M, Ahmad SF, Cardoso AL, Ramos E, Valente GT, Martins C. De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes. Chromosoma 2019; 128:81-96. [PMID: 31115663 DOI: 10.1007/s00412-019-00707-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/27/2019] [Accepted: 05/07/2019] [Indexed: 12/15/2022]
Abstract
Supernumerary B chromosomes (Bs) are accessory elements to the regular chromosome set (As) and have been observed in a huge diversity of eukaryotic species. Although extensively investigated, the biological significance of Bs remains enigmatic. Here, we present de novo genome assemblies for the cichlid fish Astatotilapia latifasciata, a well-known model to study Bs. High coverage data with Illumina sequencing was obtained for males and females with 0B (B-), 1B, and 2B (B+) chromosomes to provide information regarding the diversity among these genomes. The draft assemblies comprised 771 Mb for the B- genome and 781 Mb for the B+ genome. Comparative analysis of the B+ and B- assemblies reveals syntenic discontinuity, duplicated blocks and several insertions, deletions, and inversions indicative of rearrangements in the B+ genome. Hundreds of transposable elements and 1546 protein coding sequences were annotated in the duplicated B+ regions. Our work contributes a list of thousands of genes harbored on the B chromosome, with functions in several biological processes, including the cell cycle.
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Affiliation(s)
- Maryam Jehangir
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Syed F Ahmad
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Adauto L Cardoso
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Erica Ramos
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Guilherme T Valente
- Bioprocess and Biotechnology Department, Agronomical Science Faculty, Sao Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil.
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45
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Cardoso AL, Fantinatti BEDA, Venturelli NB, Carmello BDO, de Oliveira RA, Martins C. Epigenetic DNA Modifications Are Correlated With B Chromosomes and Sex in the Cichlid Astatotilapia latifasciata. Front Genet 2019; 10:324. [PMID: 31031803 PMCID: PMC6474290 DOI: 10.3389/fgene.2019.00324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/22/2019] [Indexed: 12/11/2022] Open
Abstract
Supernumerary B chromosomes are dispensable elements found in several groups of eukaryotes, and their impacts in host organisms are not clear. The cichlid fish Astatotilapia latifasciata presents one or two large metacentric B chromosomes. These elements affect the transcription of several classes of RNAs. Here, we evaluated the epigenetic DNA modification status of B chromosomes using immunocytogenetics and assessed the impact of B chromosome presence on the global contents of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) and the molecular mechanisms underlying these variations. We found that the B chromosome of A. latifasciata has an active pattern of DNA epimarks, and its presence promotes the loss of 5mC in gonads of females with B chromosome (FB+) and promotes the loss of 5hmC in the muscle of males with the B element (MB+). Based on the transcriptional quantification of DNA modification genes (dnmt, tet, and tdg) and their candidate regulators (idh genes, microRNAs, and long non-coding RNAs) and on RNA-protein interaction prediction, we suggest the occurrence of passive demethylation in gonads of FB+ and 5hmC loss by Tet inhibition or by 5hmC oxidation in MB+ muscle. We suggest that these results can also explain the previously reported variations in the transcription levels of several classes of RNA depending on B chromosome presence. The DNA modifications detected here are also influenced by sex. Although the correlation between B chromosomes and sex has been previously reported, it remains unexplained. The B chromosome of A. latifasciata seems to be active and impacts cell physiology in a very complex way, including at the epigenetic level.
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Affiliation(s)
- Adauto Lima Cardoso
- Integrative Genomics Laboratory, Department of Morphology, Institute of Biosciences, São Paulo State University - Universidade Estadual Paulista, Botucatu, Brazil
| | - Bruno Evaristo de Almeida Fantinatti
- Integrative Genomics Laboratory, Department of Morphology, Institute of Biosciences, São Paulo State University - Universidade Estadual Paulista, Botucatu, Brazil
| | - Natália Bortholazzi Venturelli
- Integrative Genomics Laboratory, Department of Morphology, Institute of Biosciences, São Paulo State University - Universidade Estadual Paulista, Botucatu, Brazil
| | - Bianca de Oliveira Carmello
- Integrative Genomics Laboratory, Department of Morphology, Institute of Biosciences, São Paulo State University - Universidade Estadual Paulista, Botucatu, Brazil
| | - Rogério Antonio de Oliveira
- Department of Biostatistics, Institute of Biosciences, São Paulo State University - Universidade Estadual Paulista, Botucatu, Brazil
| | - Cesar Martins
- Integrative Genomics Laboratory, Department of Morphology, Institute of Biosciences, São Paulo State University - Universidade Estadual Paulista, Botucatu, Brazil
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46
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Karyotype and B chromosome variation in Lilium amabile Palibin. Genes Genomics 2019; 41:647-655. [DOI: 10.1007/s13258-019-00807-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 03/04/2019] [Indexed: 10/27/2022]
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47
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Dhar MK, Kour J, Kaul S. Origin, Behaviour, and Transmission of B Chromosome with Special Reference to Plantago lagopus. Genes (Basel) 2019; 10:E152. [PMID: 30781667 PMCID: PMC6410184 DOI: 10.3390/genes10020152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 11/30/2022] Open
Abstract
B chromosomes have been reported in many eukaryotic organisms. These chromosomes occur in addition to the standard complement of a species. Bs do not pair with any of the A chromosomes and they have generally been considered to be non-essential and genetically inert. However, due to tremendous advancements in the technologies, the molecular composition of B chromosomes has been determined. The sequencing data has revealed that B chromosomes have originated from A chromosomes and they are rich in repetitive elements. In our laboratory, a novel B chromosome was discovered in Plantago lagopus. Using molecular cytogenetic techniques, the B chromosome was found to be composed of ribosomal DNA sequences. However, further characterization of the chromosome using next generation sequencing (NGS) etc. revealed that the B chromosome is a mosaic of sequences derived from A chromosomes, 5S ribosomal DNA (rDNA), 45S rDNA, and various types of repetitive elements. The transmission of B chromosome through the female sex track did not follow the Mendelian principles. The chromosome was found to have drive due to which it was perpetuating in populations. The present paper attempts to summarize the information on nature, transmission, and origin of B chromosomes, particularly the current status of our knowledge in P. lagopus.
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Affiliation(s)
- Manoj K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu-180006, India.
| | - Jasmeet Kour
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu-180006, India.
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu-180006, India.
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48
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Ahmad SF, Martins C. The Modern View of B Chromosomes Under the Impact of High Scale Omics Analyses. Cells 2019; 8:E156. [PMID: 30781835 PMCID: PMC6406668 DOI: 10.3390/cells8020156] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/10/2019] [Accepted: 02/12/2019] [Indexed: 12/11/2022] Open
Abstract
Supernumerary B chromosomes (Bs) are extra karyotype units in addition to A chromosomes, and are found in some fungi and thousands of animals and plant species. Bs are uniquely characterized due to their non-Mendelian inheritance, and represent one of the best examples of genomic conflict. Over the last decades, their genetic composition, function and evolution have remained an unresolved query, although a few successful attempts have been made to address these phenomena. A classical concept based on cytogenetics and genetics is that Bs are selfish and abundant with DNA repeats and transposons, and in most cases, they do not carry any function. However, recently, the modern quantum development of high scale multi-omics techniques has shifted B research towards a new-born field that we call "B-omics". We review the recent literature and add novel perspectives to the B research, discussing the role of new technologies to understand the mechanistic perspectives of the molecular evolution and function of Bs. The modern view states that B chromosomes are enriched with genes for many significant biological functions, including but not limited to the interesting set of genes related to cell cycle and chromosome structure. Furthermore, the presence of B chromosomes could favor genomic rearrangements and influence the nuclear environment affecting the function of other chromatin regions. We hypothesize that B chromosomes might play a key function in driving their transmission and maintenance inside the cell, as well as offer an extra genomic compartment for evolution.
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Affiliation(s)
- Syed Farhan Ahmad
- Department of Morphology, Institute of Biosciences at Botucatu, Sao Paulo State University (UNESP), CEP 18618689, Botucatu, SP, Brazil.
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences at Botucatu, Sao Paulo State University (UNESP), CEP 18618689, Botucatu, SP, Brazil.
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49
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Dalla Benetta E, Akbari OS, Ferree PM. Sequence Expression of Supernumerary B Chromosomes: Function or Fluff? Genes (Basel) 2019; 10:E123. [PMID: 30744010 PMCID: PMC6409846 DOI: 10.3390/genes10020123] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 12/25/2022] Open
Abstract
B chromosomes are enigmatic heritable elements found in the genomes of numerous plant and animal species. Contrary to their broad distribution, most B chromosomes are non-essential. For this reason, they are regarded as genome parasites. In order to be stably transmitted through generations, many B chromosomes exhibit the ability to "drive", i.e., they transmit themselves at super-Mendelian frequencies to progeny through directed interactions with the cell division apparatus. To date, very little is understood mechanistically about how B chromosomes drive, although a likely scenario is that expression of B chromosome sequences plays a role. Here, we highlight a handful of previously identified B chromosome sequences, many of which are repetitive and non-coding in nature, that have been shown to be expressed at the transcriptional level. We speculate on how each type of expressed sequence could participate in B chromosome drive based on known functions of RNA in general chromatin- and chromosome-related processes. We also raise some challenges to functionally testing these possible roles, a goal that will be required to more fully understand whether and how B chromosomes interact with components of the cell for drive and transmission.
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Affiliation(s)
- Elena Dalla Benetta
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA.
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Patrick M Ferree
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA.
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50
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Gene expression changes elicited by a parasitic B chromosome in the grasshopper Eyprepocnemis plorans are consistent with its phenotypic effects. Chromosoma 2019; 128:53-67. [PMID: 30617552 DOI: 10.1007/s00412-018-00689-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 01/16/2023]
Abstract
Parasitism evokes adaptive physiological changes in the host, many of which take place through gene expression changes. This response can be more or less local, depending on the organ or tissue affected by the parasite, or else systemic when the parasite affects the entire host body. The most extreme of the latter cases is intragenomic parasitism, where the parasite is present in all host nuclei as any other genomic element. Here, we show the molecular crosstalk between a parasitic chromosome (also named B chromosome) and the host genome, manifested through gene expression changes. The transcriptome analysis of 0B and 1B females of the grasshopper Eyprepocnemis plorans, validated by a microarray experiment performed on four B-lacking and five B-carrying females, revealed changes in gene expression for 188 unigenes being consistent in both experiments. Once discarded B-derived transcripts, there were 46 differentially expressed genes (30 up- and 16 downregulated) related with the adaptation of the host genome to the presence of the parasitic chromosome. Interestingly, the functions of these genes could explain some of the most important effects of B chromosomes, such as nucleotypic effects derived from the additional DNA they represent, chemical defense and detoxification, protein modification and response to stress, ovary function, and regulation of gene expression. Collectively, these changes uncover an intimate host-parasite interaction between A and B chromosomes during crucial steps of gene expression and protein function.
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