Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.)
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 cytogeneti...
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| Format: | Article |
| Language: | English |
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BMC
2017-05-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-017-3774-7 |
| _version_ | 1818155113419636736 |
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| author | Radka Symonová Konrad Ocalewicz Lech Kirtiklis Giovanni Battista Delmastro Šárka Pelikánová Sonia Garcia Aleš Kovařík |
| author_facet | Radka Symonová Konrad Ocalewicz Lech Kirtiklis Giovanni Battista Delmastro Šárka Pelikánová Sonia Garcia Aleš Kovařík |
| author_sort | Radka Symonová |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-11T14:37:14Z |
| format | Article |
| id | doaj.art-9cf162aa6b394b1088ccfeb7c43ed806 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-11T14:37:14Z |
| publishDate | 2017-05-01 |
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| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-9cf162aa6b394b1088ccfeb7c43ed8062022-12-22T01:02:06ZengBMCBMC Genomics1471-21642017-05-0118111610.1186/s12864-017-3774-7Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.)Radka Symonová0Konrad Ocalewicz1Lech Kirtiklis2Giovanni Battista Delmastro3Šárka Pelikánová4Sonia Garcia5Aleš Kovařík6Research Institute for Limnology, University of InnsbruckDepartment of Marine Biology and Ecology, Faculty of Oceanography and Geography, University of GdanskDepartment of Zoology, Faculty of Biology and Biotechnology, University of Warmia and MazuryMuseum of Natural HistoryLaboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of SciencesInstitut Botànic de Barcelona (IBB-CSIC-ICUB)Laboratory of Molecular Epigenetics, Institute of Biophysics, Czech Academy of ScienceAbstract 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.http://link.springer.com/article/10.1186/s12864-017-3774-7rDNAEvolutionChromosomeFishEsoxSingle cell PacBio sequencing |
| spellingShingle | Radka Symonová Konrad Ocalewicz Lech Kirtiklis Giovanni Battista Delmastro Šárka Pelikánová Sonia Garcia Aleš Kovařík Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.) BMC Genomics rDNA Evolution Chromosome Fish Esox Single cell PacBio sequencing |
| title | Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.) |
| title_full | Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.) |
| title_fullStr | Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.) |
| title_full_unstemmed | Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.) |
| title_short | Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.) |
| title_sort | higher order organisation of extremely amplified potentially functional and massively methylated 5s rdna in european pikes esox sp |
| topic | rDNA Evolution Chromosome Fish Esox Single cell PacBio sequencing |
| url | http://link.springer.com/article/10.1186/s12864-017-3774-7 |
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