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Volarić M, Despot-Slade E, Veseljak D, Pavlek M, Vojvoda Zeljko T, Mravinac B, Meštrović N. The Genome Organization of 5S rRNA Genes in the Model Organism Tribolium castaneum and Its Sibling Species Tribolium freemani. Genes (Basel) 2024; 15:776. [PMID: 38927712 PMCID: PMC11202950 DOI: 10.3390/genes15060776] [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: 04/11/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
5S ribosomal DNAs (rDNAs) are arranged in tandem and are often under-represented in genome assemblies. In the present study, we performed a global and in-depth analysis of the 5S rDNAs in the model insect Tribolium castaneum and its closely related species Tribolium freemani. To accomplish this goal, we used our recently published genome assemblies based on Nanopore and PacBio long-read sequencing. Although these closely related species share the 5S rRNA gene sequence with high homology, they show a different organization of the 5S rDNA locus. Analysis of 5S rDNA arrays in T. castaneum revealed a typical tandemly repeated organization characterized by repeat units consisting of the 121 bp long 5S rRNA gene and the 71 bp long nontranscribed spacer (NTS). In contrast, T. freemani showed a much more complex organization of 5S rDNA arrays characterized by two patterns. The first is based on the association of 5S rRNA gene with arrays of a satellite DNA, representing the NTS sequence of the 5S rDNA genes in T. freemani. The second, more complex type is characterized by a somewhat less frequent occurrence of the 5S rRNA gene and its association with longer satellite DNA arrays that are regularly interrupted by Jockey-like retrotransposons. This organization, in which the ribosomal gene is associated with two completely different repetitive elements such as satellite DNAs and retrotransposons, suggests that the 5S rRNA gene, regardless of its crucial function in the genome, could be a subject of extremely dynamic genomic rearrangements.
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Affiliation(s)
| | | | | | | | | | | | - Nevenka Meštrović
- Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.V.); (E.D.-S.); (D.V.); (M.P.); (T.V.Z.); (B.M.)
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2
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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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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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Garrido-Ramos MA. The Genomics of Plant Satellite DNA. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:103-143. [PMID: 34386874 DOI: 10.1007/978-3-030-74889-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The twenty-first century began with a certain indifference to the research of satellite DNA (satDNA). Neither genome sequencing projects were able to accurately encompass the study of satDNA nor classic methodologies were able to go further in undertaking a better comprehensive study of the whole set of satDNA sequences of a genome. Nonetheless, knowledge of satDNA has progressively advanced during this century with the advent of new analytical techniques. The enormous advantages that genome-wide approaches have brought to its analysis have now stimulated a renewed interest in the study of satDNA. At this point, we can look back and try to assess more accurately many of the key questions that were left unsolved in the past about this enigmatic and important component of the genome. I review here the understanding gathered on plant satDNAs over the last few decades with an eye on the near future.
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Bueno GDP, Gatto KP, Gazolla CB, Leivas PT, Struett MM, Moura M, Bruschi DP. Cytogenetic characterization and mapping of the repetitive DNAs in Cycloramphus bolitoglossus (Werner, 1897): More clues for the chromosome evolution in the genus Cycloramphus (Anura, Cycloramphidae). PLoS One 2021; 16:e0245128. [PMID: 33439901 PMCID: PMC7806164 DOI: 10.1371/journal.pone.0245128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/22/2020] [Indexed: 01/13/2023] Open
Abstract
Cycloramphus bolitoglossus (Werner, 1897) is a rare species with a low population density in the Serra do Mar region of Paraná and Santa Catarina, in southern Brazil. Currently, it has been assigned to the Near Threatened (NT) category in the Brazilian List of Endangered Animal Species. Here, we described the karyotype of this species for the first time and investigated the patterns of some repetitive DNA classes in the chromosomes using molecular cytogenetic approaches. We isolated, sequenced and mapped the 5S rDNA and the satellite DNA PcP190 of C. bolitoglossus, as well as mapped the telomeric sequences and seven microsatellites motifies [(GA)15, (CA)15, (GACA)4, (GATA)8, (CAG)10, (CGC)10, and (GAA)]10. Cycloramphus bolitoglossus has 2n = 26 chromosomes and a fundamental number (FN) equal to 52, with a highly conserved karyotype compared to other genus members. Comparative cytogenetic under the phylogenetic context of genus allowed evolutionary interpretations of the morphological changes in the homologs of pairs 1, 3, and 6 along with the evolutionary history of Cycloramphus. Two subtypes of 5S rDNA type II were isolated in C. bolitoglossus genome, and several comparative analysis suggests mixed effects of concerted and birth-and-death evolution acting in this repetitive DNA. The 5S rDNA II subtype "a" and "b" was mapped on chromosome 1. However, their different position along chromosome 1 provide an excellent chromosome marker for future studies. PcP190 satellite DNA, already reported for species of the families Hylidae, Hylodidae, Leptodactylidae, and Odontophrynidae, is scattered throughout the C. bolitoglossus genome, and even non-heterochromatic regions showed hybridization signals using the PcP190 probe. Molecular analysis suggests that PcP190 satellite DNA exhibit a high-level of homogenization of this sequence in the genome of C. bolitoglossus. The PcP190 satDNA from C. bolitoglossus represents a novel sequence group, compared to other anurans, based on its hypervariable region. Overall, the present data on repetitive DNA sequences showed pseudogenization evidence and corroborated the hypothesis of the emergence of satDNA from rDNA 5S clusters. These two arguments that reinforced the importance of the birth-and-death evolutionary model to explain 5S rDNA patterns found in anuran genomes.
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Affiliation(s)
- Gislayne de Paula Bueno
- Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Kaleb Pretto Gatto
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, (UNESP), Rio Claro, São Paulo, Brazil
| | - Camilla Borges Gazolla
- Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Peterson T. Leivas
- Curso de Ciências Biológicas, Universidade Positivo (UP), Curitiba, Paraná, Brazil
| | - Michelle M. Struett
- Departamento de Zoologia, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Maurício Moura
- Departamento de Zoologia, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Daniel Pacheco Bruschi
- Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, 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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Gržan T, Despot-Slade E, Meštrović N, Plohl M, Mravinac B. CenH3 distribution reveals extended centromeres in the model beetle Tribolium castaneum. PLoS Genet 2020; 16:e1009115. [PMID: 33125365 PMCID: PMC7598501 DOI: 10.1371/journal.pgen.1009115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/14/2020] [Indexed: 11/18/2022] Open
Abstract
Centromeres are chromosomal domains essential for kinetochore assembly and correct chromosome segregation. Inconsistent in their underlying DNA sequences, centromeres are defined epigenetically by the presence of the centromere-specific histone H3 variant CenH3. Most of the analyzed eukaryotes have monocentric chromosomes in which CenH3 proteins deposit into a single, primary constriction visible at metaphase chromosomes. Contrary to monocentrics, evolutionary sporadic holocentric chromosomes lack a primary constriction and have kinetochore activity distributed along the entire chromosome length. In this work, we identified cCENH3 protein, the centromeric H3 histone of the coleopteran model beetle Tribolium castaneum. By ChIP-seq analysis we disclosed that cCENH3 chromatin assembles upon a repertoire of repetitive DNAs. cCENH3 in situ mapping revealed unusually elongated T. castaneum centromeres that comprise approximately 40% of the chromosome length. Being the longest insect regional centromeres evidenced so far, T. castaneum centromeres are characterized by metapolycentric structure composed of several individual cCENH3-containing domains. We suggest that the model beetle T. castaneum with its metapolycentromeres could represent an excellent model for further studies of non-canonical centromeres in insects.
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Affiliation(s)
- Tena Gržan
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Nevenka Meštrović
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- * E-mail: (MP); (BM)
| | - Brankica Mravinac
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- * E-mail: (MP); (BM)
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8
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Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nat Protoc 2020; 15:3745-3776. [PMID: 33097925 DOI: 10.1038/s41596-020-0400-y] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 08/21/2020] [Indexed: 11/08/2022]
Abstract
RepeatExplorer2 is a novel version of a computational pipeline that uses graph-based clustering of next-generation sequencing reads for characterization of repetitive DNA in eukaryotes. The clustering algorithm facilitates repeat identification in any genome by using relatively small quantities of short sequence reads, and additional tools within the pipeline perform automatic annotation and quantification of the identified repeats. The pipeline is integrated into the Galaxy platform, which provides a user-friendly web interface for script execution and documentation of the results. Compared to the original version of the pipeline, RepeatExplorer2 provides automated annotation of transposable elements, identification of tandem repeats and enhanced visualization of analysis results. Here, we present an overview of the RepeatExplorer2 workflow and provide procedures for its application to (i) de novo repeat identification in a single species, (ii) comparative repeat analysis in a set of species, (iii) development of satellite DNA probes for cytogenetic experiments and (iv) identification of centromeric repeats based on ChIP-seq data. Each procedure takes approximately 2 d to complete. RepeatExplorer2 is available at https://repeatexplorer-elixir.cerit-sc.cz .
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9
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Ebrahimzadegan R, Houben A, Mirzaghaderi G. Repetitive DNA landscape in essential A and supernumerary B chromosomes of Festuca pratensis Huds. Sci Rep 2019; 9:19989. [PMID: 31882680 PMCID: PMC6934454 DOI: 10.1038/s41598-019-56383-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/11/2019] [Indexed: 11/09/2022] Open
Abstract
Here, we characterized the basic properties of repetitive sequences in essential A and supernumerary B chromosomes of Festuca pratensis Huds. This was performed by comparative analysis of low-pass Illumina sequence reads of B chromosome lacking (-B) and B chromosome containing (+B) individuals of F. pratensis. 61% of the nuclear genome is composed of repetitive sequences. 43.1% of the genome are transposons of which DNA transposons and retrotransposons made up 2.3% and 40.8%, respectively. LTR retrotransposons are the most abundant mobile elements and contribute to 40.7% of the genome and divided into Ty3-gypsy and Ty1-copia super families with 32.97% and 7.78% of the genome, respectively. Eighteen different satellite repeats were identified making up 3.9% of the genome. Five satellite repeats were used as cytological markers for chromosome identification and genome analysis in the genus Festuca. Four satellite repeats were identified on B chromosomes among which Fp-Sat48 and Fp-Sat253 were specific to the B chromosome of F. pratensis.
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Affiliation(s)
- Rahman Ebrahimzadegan
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, 6617715175, Sanandaj, Iran
| | - Andreas Houben
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, 6617715175, Sanandaj, Iran.
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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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11
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Milani D, Bardella VB, Ferretti ABSM, Palacios-Gimenez OM, Melo ADS, Moura RC, Loreto V, Song H, Cabral-de-Mello DC. Satellite DNAs Unveil Clues about the Ancestry and Composition of B Chromosomes in Three Grasshopper Species. Genes (Basel) 2018; 9:genes9110523. [PMID: 30373193 PMCID: PMC6265867 DOI: 10.3390/genes9110523] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/12/2018] [Accepted: 10/21/2018] [Indexed: 11/16/2022] Open
Abstract
Supernumerary (B) chromosomes are dispensable genomic elements occurring frequently among grasshoppers. Most B chromosomes are enriched with repetitive DNAs, including satellite DNAs (satDNAs) that could be implicated in their evolution. Although studied in some species, the specific ancestry of B chromosomes is difficult to ascertain and it was determined in only a few examples. Here we used bioinformatics and cytogenetics to characterize the composition and putative ancestry of B chromosomes in three grasshopper species, Rhammatocerus brasiliensis, Schistocerca rubiginosa, and Xyleus discoideus angulatus. Using the RepeatExplorer pipeline we searched for the most abundant satDNAs in Illumina sequenced reads, and then we generated probes used in fluorescent in situ hybridization (FISH) to determine chromosomal position. We used this information to infer ancestry and the events that likely occurred at the origin of B chromosomes. We found twelve, nine, and eighteen satDNA families in the genomes of R. brasiliensis, S. rubiginosa, and X. d. angulatus, respectively. Some satDNAs revealed clustered organization on A and B chromosomes varying in number of sites and position along chromosomes. We did not find specific satDNA occurring in the B chromosome. The satDNAs shared among A and B chromosomes support the idea of putative intraspecific ancestry from small autosomes in the three species, i.e., pair S11 in R. brasiliensis, pair S9 in S. rubiginosa, and pair S10 in X. d. angulatus. The possibility of involvement of other chromosomal pairs in B chromosome origin is also hypothesized. Finally, we discussed particular aspects in composition, origin, and evolution of the B chromosome for each species.
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Affiliation(s)
- Diogo Milani
- Instituto de Biociências/IB, Departamento de Biologia, UNESP-Universidade Estadual Paulista, Rio Claro, São Paulo 01049-010, Brazil.
| | - Vanessa B Bardella
- Instituto de Biociências/IB, Departamento de Biologia, UNESP-Universidade Estadual Paulista, Rio Claro, São Paulo 01049-010, Brazil.
| | - Ana B S M Ferretti
- Instituto de Biociências/IB, Departamento de Biologia, UNESP-Universidade Estadual Paulista, Rio Claro, São Paulo 01049-010, Brazil.
| | - Octavio M Palacios-Gimenez
- Instituto de Biociências/IB, Departamento de Biologia, UNESP-Universidade Estadual Paulista, Rio Claro, São Paulo 01049-010, Brazil.
- Department of Evolutionary Biology, Evolutionary Biology Center, Uppsala University, 75236 Uppsala, Sweden.
| | - Adriana de S Melo
- Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, UPE-Universidade de Pernambuco, Recife 50100-130, Pernambuco, Brazil.
| | - Rita C Moura
- Instituto de Ciências Biológicas, Laboratório de Biodiversidade e Genética de Insetos, UPE-Universidade de Pernambuco, Recife 50100-130, Pernambuco, Brazil.
| | - Vilma Loreto
- Centro de Biociências/CB, Departamento de Genética, UFPE-Universidade Federal de Pernambuco, Recife 50670-901, Pernambuco, Brazil.
| | - Hojun Song
- Department of Entomology, Texas A&M University, 2475 TAMU, College Station, TX 77843-2475, USA.
| | - Diogo C Cabral-de-Mello
- Instituto de Biociências/IB, Departamento de Biologia, UNESP-Universidade Estadual Paulista, Rio Claro, São Paulo 01049-010, Brazil.
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12
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Marques A, Klemme S, Houben A. Evolution of Plant B Chromosome Enriched Sequences. Genes (Basel) 2018; 9:genes9100515. [PMID: 30360448 PMCID: PMC6210368 DOI: 10.3390/genes9100515] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/13/2018] [Accepted: 10/18/2018] [Indexed: 01/10/2023] Open
Abstract
B chromosomes are supernumerary chromosomes found in addition to the normal standard chromosomes (A chromosomes). B chromosomes are well known to accumulate several distinct types of repeated DNA elements. Although the evolution of B chromosomes has been the subject of numerous studies, the mechanisms of accumulation and evolution of repetitive sequences are not fully understood. Recently, new genomic approaches have shed light on the origin and accumulation of different classes of repetitive sequences in the process of B chromosome formation and evolution. Here we discuss the impact of repetitive sequences accumulation on the evolution of plant B chromosomes.
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Affiliation(s)
- André Marques
- Laboratory of Genetic Resources, Federal University of Alagoas, Av. Manoel Severino Barbosa, 57309-005 Arapiraca-AL, Brazil.
| | - Sonja Klemme
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, CZ-37005 České Budějovice, Czech Republic.
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany.
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Yang X, Zhao H, Zhang T, Zeng Z, Zhang P, Zhu B, Han Y, Braz GT, Casler MD, Schmutz J, Jiang J. Amplification and adaptation of centromeric repeats in polyploid switchgrass species. THE NEW PHYTOLOGIST 2018; 218:1645-1657. [PMID: 29577299 DOI: 10.1111/nph.15098] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/09/2018] [Indexed: 05/24/2023]
Abstract
Centromeres in most higher eukaryotes are composed of long arrays of satellite repeats from a single satellite repeat family. Why centromeres are dominated by a single satellite repeat and how the satellite repeats originate and evolve are among the most intriguing and long-standing questions in centromere biology. We identified eight satellite repeats in the centromeres of tetraploid switchgrass (Panicum virgatum). Seven repeats showed characteristics associated with classical centromeric repeats with monomeric lengths ranging from 166 to 187 bp. Interestingly, these repeats share an 80-bp DNA motif. We demonstrate that this 80-bp motif may dictate translational and rotational phasing of the centromeric repeats with the cenH3 nucleosomes. The sequence of the last centromeric repeat, Pv156, is identical to the 5S ribosomal RNA genes. We demonstrate that a 5S ribosomal RNA gene array was recruited to be the functional centromere for one of the switchgrass chromosomes. Our findings reveal that certain types of satellite repeats, which are associated with unique sequence features and are composed of monomers in mono-nucleosomal length, are favorable for centromeres. Centromeric repeats may undergo dynamic amplification and adaptation before the centromeres in the same species become dominated by the best adapted satellite repeat.
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Affiliation(s)
- Xueming Yang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Hainan Zhao
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Zixian Zeng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Pingdong Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- College of Bioscience and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Bo Zhu
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yonghua Han
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Guilherme T Braz
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Departmento de Biologia, Universidade Federal de Lavras, Lavras, MG, 37200, Brazil
| | - Michael D Casler
- Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI, 53706, USA
| | - Jeremy Schmutz
- Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
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14
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Ruban A, Schmutzer T, Scholz U, Houben A. How Next-Generation Sequencing Has Aided Our Understanding of the Sequence Composition and Origin of B Chromosomes. Genes (Basel) 2017; 8:E294. [PMID: 29068386 PMCID: PMC5704207 DOI: 10.3390/genes8110294] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/18/2017] [Accepted: 10/24/2017] [Indexed: 12/21/2022] Open
Abstract
Accessory, supernumerary, or-most simply-B chromosomes, are found in many eukaryotic karyotypes. These small chromosomes do not follow the usual pattern of segregation, but rather are transmitted in a higher than expected frequency. As increasingly being demonstrated by next-generation sequencing (NGS), their structure comprises fragments of standard (A) chromosomes, although in some plant species, their sequence also includes contributions from organellar genomes. Transcriptomic analyses of various animal and plant species have revealed that, contrary to what used to be the common belief, some of the B chromosome DNA is protein-encoding. This review summarizes the progress in understanding B chromosome biology enabled by the application of next-generation sequencing technology and state-of-the-art bioinformatics. In particular, a contrast is drawn between a direct sequencing approach and a strategy based on a comparative genomics as alternative routes that can be taken towards the identification of B chromosome sequences.
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Affiliation(s)
- Alevtina Ruban
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Seeland, Germany.
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Seeland, Germany.
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Seeland, Germany.
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Seeland, Germany.
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Milani D, Ramos É, Loreto V, Martí DA, Cardoso AL, de Moraes KCM, Martins C, Cabral-de-Mello DC. The satellite DNA AflaSAT-1 in the A and B chromosomes of the grasshopper Abracris flavolineata. BMC Genet 2017; 18:81. [PMID: 28851268 PMCID: PMC5575873 DOI: 10.1186/s12863-017-0548-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/22/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Satellite DNAs (satDNAs) are organized in repetitions directly contiguous to one another, forming long arrays and composing a large portion of eukaryote genomes. These sequences evolve according to the concerted evolution model, and homogenization of repeats is observed at the intragenomic level. Satellite DNAs are the primary component of heterochromatin, located primarily in centromeres and telomeres. Moreover, satDNA enrichment in specific chromosomes has been observed, such as in B chromosomes, that can provide clues about composition, origin and evolution of this chromosome. In this study, we isolated and characterized a satDNA in A and B chromosomes of Abracris flavolineata by integrating cytogenetic, molecular and genomics approaches at intra- and inter-population levels, with the aim to understand the evolution of satDNA and composition of B chromosomes. RESULTS AflaSAT-1 satDNA was shared with other species and in A. flavolineata, was associated with another satDNA, AflaSAT-2. Chromosomal mapping revealed centromeric blocks variable in size in almost all chromosomes (except pair 11) of A complement for both satDNAs, whereas for B chromosome, only a small centromeric signal occurred. In distinct populations, variable number of AflaSAT-1 chromosomal sites correlated with variability in copy number. Instead of such variability, low sequence diversity was observed in A complement, but monomers from B chromosome were more variable, presenting also exclusive mutations. AflaSAT-1 was transcribed in five tissues of adults in distinct life cycle phases. CONCLUSIONS The sharing of AflaSAT-1 with other species is consistent with the library hypothesis and indicates common origin in a common ancestor; however, AflaSAT-1 was highly amplified in the genome of A. flavolineata. At the population level, homogenization of repeats in distinct populations was documented, but dynamic expansion or elimination of repeats was also observed. Concerning the B chromosome, our data provided new information on the composition in A. flavolineata. Together with previous results, the sequences of heterochromatic nature were not likely highly amplified in the entire B chromosome. Finally, the constitutive transcriptional activity suggests a possible unknown functional role, which should be further investigated.
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Affiliation(s)
- Diogo Milani
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo CEP 13506-900 Brazil
| | - Érica Ramos
- Departamento de Morfologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Botucatu, São Paulo Brazil
| | - Vilma Loreto
- Departamento de Genética, UFPE - Univ Federal de Pernambuco, Centro de Biociências/CB, Recife, Pernambuco Brazil
| | | | - Adauto Lima Cardoso
- Departamento de Morfologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Botucatu, São Paulo Brazil
| | | | - Cesar Martins
- Departamento de Morfologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Botucatu, São Paulo Brazil
| | - Diogo Cavalcanti Cabral-de-Mello
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo CEP 13506-900 Brazil
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Vanzela ALL, de Paula AA, Quintas CC, Fernandes T, Baldissera JNDC, de Souza TB. Cestrum strigilatum (Ruiz & Pavón, 1799) B chromosome shares repetitive DNA sequences with A chromosomes of different Cestrum (Linnaeus, 1753) species. COMPARATIVE CYTOGENETICS 2017; 11:511-524. [PMID: 29118929 PMCID: PMC5672077 DOI: 10.3897/compcytogen.v11i3.13418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
Species of Cestrum (Linnaeus, 1753) have shown large diversity in the accumulation and distribution of repetitive DNA families, and B chromosomes have been described in seven species. Some types of repetitive DNA were identified in A and B chromosomes in species of this plant group, such as AT-rich SSR, 35S and 5S rDNA, C-Giemsa and C-CMA/DAPI bands and retrotransposons. To increase our understanding of the relationships of A and B chromosomes, the B of C. strigilatum Ruiz & Pavón, 1799 was microdissected, amplified and hybridized in situ against chromosomes of this species, and in six other species of this genus. FISH signals were observed in whole the B of C. strigilatum, including stretches of A chromosomes, as well as in some A chromosomes of all tested species. A strong FISH signal was seen adjacent to the 5S rDNA in the proximal region of pair 8 of all species and, due to this, we have searched for 5S rDNA fragments in the microdissected B chromosome. PCR and sequencing data evidenced 5S rDNA deletion along evolutionary pathways of the B of C. strigilatum. Although A and B chromosomes displayed redundancy in the repetitive DNA families in different species, the B of C. strigilatum seemed to differ from those Bs of other Cestrum species by the loss of rDNA fractions. A possible origin of Bs in Cestrum was discussed.
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Affiliation(s)
- André Luís Laforga Vanzela
- Laboratory of Cytogenetics and Plant Diversity, Center for Biological Sciences, State University of Londrina, Londrina, 86051-980, Paraná, Brazil
| | - Adriano Alves de Paula
- Laboratory of Cytogenetics and Plant Diversity, Center for Biological Sciences, State University of Londrina, Londrina, 86051-980, Paraná, Brazil
| | - Carolina Cristina Quintas
- Laboratory of Cytogenetics and Plant Diversity, Center for Biological Sciences, State University of Londrina, Londrina, 86051-980, Paraná, Brazil
| | - Thiago Fernandes
- Laboratory of Cytogenetics and Plant Diversity, Center for Biological Sciences, State University of Londrina, Londrina, 86051-980, Paraná, Brazil
| | - Joana Neres da Cruz Baldissera
- Laboratory of Cytogenetics and Plant Diversity, Center for Biological Sciences, State University of Londrina, Londrina, 86051-980, Paraná, Brazil
| | - Thaíssa Boldieri de Souza
- Laboratory of Cytogenetics and Plant Diversity, Center for Biological Sciences, State University of Londrina, Londrina, 86051-980, Paraná, Brazil
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17
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Dhar MK, Kour G, Kaul S. B chromosome in Plantago lagopus Linnaeus, 1753 shows preferential transmission and accumulation through unusual processes. COMPARATIVE CYTOGENETICS 2017; 11:375-392. [PMID: 28919970 PMCID: PMC5596978 DOI: 10.3897/compcytogen.11i2.11779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/13/2017] [Indexed: 06/07/2023]
Abstract
Plantago lagopus is a diploid (2n = 2x =12) weed belonging to family Plantaginaceae. We reported a novel B chromosome in this species composed of 5S and 45S ribosomal DNA and other repetitive elements. In the present work, presence of B chromosome(s) was confirmed through FISH on root tip and pollen mother cells. Several experiments were done to determine the transmission of B chromosome through male and female sex tracks. Progenies derived from the reciprocal crosses between plants with (1B) and without (0B) B chromosomes were studied. The frequency of B chromosome bearing plants was significantly higher than expected, in the progeny of 1B female × 0B male. Thus, the B chromosome seems to have preferential transmission through the female sex track, which may be due to meiotic drive. One of the most intriguing aspects of the present study was the recovery of plants having more chromosomes than the standard complement of 12 chromosomes. Such plants were isolated from the progenies of B chromosome carrying plants. The origin of these plants can be explained on the basis of a two step process; formation of unreduced gametes in 1B plants and fusion of unreduced gametes with the normal gametes or other unreduced gametes. Several molecular techniques were used which unequivocally confirmed similar genetic constitution of 1B (parent) and plants with higher number of chromosomes.
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Affiliation(s)
- Manoj K. Dhar
- School of Biotechnology, University of Jammu, Jammu-180006, INDIA
| | - Gurmeet Kour
- School of Biotechnology, University of Jammu, Jammu-180006, INDIA
| | - Sanjana Kaul
- School of Biotechnology, University of Jammu, Jammu-180006, INDIA
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18
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Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.). BMC Genomics 2017; 18:391. [PMID: 28521734 PMCID: PMC5437419 DOI: 10.1186/s12864-017-3774-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 05/09/2017] [Indexed: 12/16/2022] Open
Abstract
Background Pikes represent an important genus (Esox) harbouring a pre-duplication karyotype (2n = 2x = 50) of economically important salmonid pseudopolyploids. Here, we have characterized the 5S ribosomal RNA genes (rDNA) in Esox lucius and its closely related E. cisalpinus using cytogenetic, molecular and genomic approaches. Intragenomic homogeneity and copy number estimation was carried out using Illumina reads. The higher-order structure of rDNA arrays was investigated by the analysis of long PacBio reads. Position of loci on chromosomes was determined by FISH. DNA methylation was analysed by methylation-sensitive restriction enzymes. Results The 5S rDNA loci occupy exclusively (peri)centromeric regions on 30–38 acrocentric chromosomes in both E. lucius and E. cisalpinus. The large number of loci is accompanied by extreme amplification of genes (>20,000 copies), which is to the best of our knowledge one of the highest copy number of rRNA genes in animals ever reported. Conserved secondary structures of predicted 5S rRNAs indicate that most of the amplified genes are potentially functional. Only few SNPs were found in genic regions indicating their high homogeneity while intergenic spacers were more heterogeneous and several families were identified. Analysis of 10–30 kb-long molecules sequenced by the PacBio technology (containing about 40% of total 5S rDNA) revealed that the vast majority (96%) of genes are organised in large several kilobase-long blocks. Dispersed genes or short tandems were less common (4%). The adjacent 5S blocks were directly linked, separated by intervening DNA and even inverted. The 5S units differing in the intergenic spacers formed both homogeneous and heterogeneous (mixed) blocks indicating variable degree of homogenisation between the loci. Both E. lucius and E. cisalpinus 5S rDNA was heavily methylated at CG dinucleotides. Conclusions Extreme amplification of 5S rRNA genes in the Esox genome occurred in the absence of significant pseudogenisation suggesting its recent origin and/or intensive homogenisation processes. The dense methylation of units indicates that powerful epigenetic mechanisms have evolved in this group of fish to silence amplified genes. We discuss how the higher-order repeat structures impact on homogenisation of 5S rDNA in the genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3774-7) contains supplementary material, which is available to authorized users.
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Borisov YM, Kryshchuk IA, Gaiduchenko HS, Cherepanova EV, Zadyra SV, Levenkova ES, Lukashov DV, Orlov VN. Karyotypic differentiation of populations of the common shrew Sorex araneus L. (Mammalia) in Belarus. COMPARATIVE CYTOGENETICS 2017; 11:359-373. [PMID: 28919969 PMCID: PMC5596991 DOI: 10.3897/compcytogen.11i2.11142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/08/2017] [Indexed: 06/07/2023]
Abstract
The common shrews, Sorex araneus Linnaeus, 1758, inhabiting the territory of Belarus, are characterized by a significant variation in the frequency of Robertsonian (Rb) translocations. The frequency clines for translocations specific of three chromosome races: the West Dvina (gm, hk, ip, no, qr), Kiev (g/m, hi, k/o, n, p, q, r), and Białowieża (g/r, hn, ik, m/p, o, q) have already been studied in this territory. In this communication we report new data on polymorphic populations with Rb metacentrics specific of the Neroosa race (go, hi, kr, mn, p/q) in south-eastern Belarus, analyse the distribution of karyotypes in southern and central Belarus and draw particular attention to the fixation of the acrocentric variants of chromosomes in this area. The results show that certain Rb metacentrics specific of the Neroosa, West Dvina, Kiev, and Białowieża races (namely, go and pq; ip; ko; hn and ik, respectively) are absent in many polymorphic populations. Thus, the karyotypic differentiation of S. araneus in the studied area is determined by unequal spread of different Rb translocations and by fixation of acrocentric variants of specific chromosomes.
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Affiliation(s)
- Yury M. Borisov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskij Prosp. 33, 119071 Moscow, Russia
| | - Iryna A. Kryshchuk
- Scientific and Practical Center for Bioresources, National Academy of Sciences of Belarus, Akademicheskaya St. 27, 220072 Minsk, Republic of Belarus
| | - Helen S. Gaiduchenko
- Scientific and Practical Center for Bioresources, National Academy of Sciences of Belarus, Akademicheskaya St. 27, 220072 Minsk, Republic of Belarus
| | - Elena V. Cherepanova
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskij Prosp. 33, 119071 Moscow, Russia
| | - Svetlana V. Zadyra
- Shevchenko Kiev National University, Educational–Scientific Center Institute of Biology, Kiev, 03187 Ukraine
| | - Elena S. Levenkova
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskij Prosp. 33, 119071 Moscow, Russia
| | - Dmitriy V. Lukashov
- Shevchenko Kiev National University, Educational–Scientific Center Institute of Biology, Kiev, 03187 Ukraine
| | - Victor N. Orlov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskij Prosp. 33, 119071 Moscow, Russia
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