&lt;b&gt;&lt;i&gt;Plantago lagopus &lt;/i&gt;&lt;/b&gt;B Chromosome Is Enriched in 5S rDNA-Derived Satellite DNA

Kumke, Katrin; Macas, Jiří; Fuchs, Jörg; Altschmied, Lothar; Kour, Jasmeet; Dhar, Manoj K.; Houben, Andreas

doi:10.1159/000444873

Cited by 22 publications

(30 citation statements)

References 30 publications

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“…The predicted coding region within Pv156 showed 99–100% sequence identity with the coding sequence of 5S rRNA genes from other grass species, including rice ( O. sativa ), maize ( Zea mays ), and wheat ( Triticum aestivum ). A satellite repeat, PLsatB, identified in Plantago lagopus , was found to be derived from the 5S rDNA (Kumke et al ., ). However, the monomers (459–505 bp) of PLsatB contain only 82‐bp sequences derived from 5S rDNA.…”

Section: Resultsmentioning

confidence: 97%

Amplification and adaptation of centromeric repeats in polyploid switchgrass species

et al. 2018

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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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Section: Resultsmentioning

confidence: 97%

Amplification and adaptation of centromeric repeats in polyploid switchgrass species

et al. 2018

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“…In the fish H. malabaricus , 5S genes gave rise to an independent satellite with apparently centromeric function [76]. Similar conversion might have happened in other species [77, 78] as well. Thus, if 5S rDNA is supportive to the centromeric function and plays a role in the assembly of mitotic chromosomes then its “invasions” to centromeric positions might be favored in evolution.…”

Section: Discussionmentioning

confidence: 95%

Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.)

et al. 2017

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BackgroundPikes 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.ResultsThe 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.ConclusionsExtreme 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 materialThe 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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“…In the herb Plantago lagopus L. the B chromosome is the product of a spontaneous amplification process of 5S ribosomal DNA derived repeats (Dhar et al, 2002;Kumke et al, 2016). Interestingly, amplification of satellite DNA has been used for the formation of engineered mammalian chromosomes ('satellite-DNA-based-artificialchromosomes' [33]).…”

Section: Accumulation Of Satellite Dnamentioning

confidence: 99%

“…In Plantago lagopus, a weed of the Mediterranean region, a B-specific satellite PLsatB was identified originated from sequence amplification including 5S rDNA fragments [64]. The satellite repeat PLsatB makes up 3.3% of the 1B genotype but only 0.09% of the 0B genotype [18]. In situ hybridization with the B-repeat revealed an almost uniform labelling of the Bs at meiotic metaphase I, while extended mitotic prometaphase chromosomes showed a more clustered distribution of the hybridization signals.…”

Section: Plantago Lagopusmentioning

confidence: 99%

“…Identification of B chromosome-enriched sequences like satellite repeats, mobile elements or organelle-derived sequences by similarity-based clustering of next generation sequence reads was achieved using the RepeatExplorer software [16,17] for rye [1] and Plantago lagopus [18]. With the RepeatExplorer and RepeatMasker programs the satellite DNA composition of the migratory locust (E. plorans) B chromosomes were determined [19].…”

Section: Introductionmentioning

confidence: 99%

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Evolution of Plant B Chromosome Enriched Sequences

Marques

Klemme

Houben

2018

Preprint

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B chromosomes are supernumerary chromosomes which are found in addition to the normal standard chromosomes (A chromosomes). B chromosomes are well known to accumulate several types of repeats. Although the evolution of B chromosomes has been subject of numerous studies, the mechanisms of accumulation and evolution of repetitive sequences is 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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<b><i>Plantago lagopus </i></b>B Chromosome Is Enriched in 5S rDNA-Derived Satellite DNA

Cited by 22 publications

References 30 publications

Amplification and adaptation of centromeric repeats in polyploid switchgrass species

Amplification and adaptation of centromeric repeats in polyploid switchgrass species

Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.)

Evolution of Plant B Chromosome Enriched Sequences

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