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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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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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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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4
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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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5
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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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6
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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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7
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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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8
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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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9
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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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10
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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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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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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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