Repetitive DNA sequences in plant genomes

Shcherban, A. B.

doi:10.1134/s2079059715030168

Cited by 16 publications

(12 citation statements)

References 87 publications

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“…Similarly, other C. annuum accessions from the Capsicum germplasm bank in Mexico showed high TCL polymorphisms, demonstrating the high inter-and intraspecific chromosome diversity found in Capsicum (Teodoro-Pardo et al 2007). The observed differences in chromosome sizes of the different accessions could be related to unequal degrees of chromosome contraction during cell division (Moscone 1990), differences in pretreatment and chromosome condensation (Pozzobon et al 2006), and/ or to different classes of repetitive DNA sequences as evolutionary components of pepper genome structures based on constitutive heterochromatin expansions (Shcherban 2015, Scaldaferro et al 2016).…”

Section: Resultsmentioning

confidence: 99%

Heterochromatin distribution and histone modification patterns of H4K5 acetylation and H3S10 phosphorylation in Capsicum L.

Martins

Perón

Lopes

et al. 2018

Crop Breed. Appl. Biotechnol.

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Section: Resultsmentioning

confidence: 99%

Heterochromatin distribution and histone modification patterns of H4K5 acetylation and H3S10 phosphorylation in Capsicum L.

Martins

Perón

Lopes

et al. 2018

Crop Breed. Appl. Biotechnol.

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“…Slight preferences in primer annealing in the initial low temperature PCR might produce asymmetries during amplification (Christian et al, 1999). Therefore, a high amount of non-chromosome-specific repetitive sequences, which are common in plant genomes (Shcherban, 2015), would favor the generation of asymmetric and poorly representative probes. In addition, the presence of contaminant DNA from other chromosomes due to insufficiently spread metaphases might also contribute to the generation of unspecific sequences in the probe pool (Christian et al, 1999;Guan, 2003).…”

Section: Discussionmentioning

confidence: 99%

Plant Chromosome-Specific Probes by Microdissection of a Single Chromosome: Is That a Reality?

et al. 2020

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Painting plant chromosomes through chromosomal in situ suppression (CISS) hybridization has long been considered impracticable. Seeking to build specific and complex probes from a single microdissected chromosome, we employed human chromosomes as models to standardize all the necessary steps for application in plants. Human metaphases were used to define the adequate conditions for microdissection, chromosome DNA amplification and labeling through degenerate oligonucleotideprimed PCR, and in situ hybridization stringency. Subsequently, these methodologies were applied in the plant species Zea mays (chromosome 1) and Capsicum annuum (chromosome 7 or 8). The high quality of human and plant cytogenetic preparations and the meticulous standardization of each step, especially the most critical onesmicrodissection and first round of DNA amplification -were crucial to eliminate the signs of non-specific hybridization and for direct application in plants. By overcoming these challenges, we obtained chromosome-specific probes, which allowed to achieve a clear and uniform painting of the entire target chromosomes with little or no background, evidencing their complexity and specificity. Despite the high amount of ubiquitous repetitive sequences in plant genomes, the main drawback for chromosome painting, we successfully employed our methodology on two plant species. Both have more than 80% repetitive sequences, which is compared to the human genome (66-69%). This is the first time that plant chromosome-specific probes were successfully obtained from a single A mitotic or meiotic microdissected chromosome. Thereby, we assume that chromosome painting through microdissection and CISS hybridization can now be considered a reality in the field of plant cytogenetics.

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“…Repeated DNA occupies a large chromosome region and can be easily detected using FISH. The cytogenetic markers based on TRs are widely used for comparative cytogenetics to study chromosome collinearity and to identify chromosomal rearrangements in evolutionary and breeding studies [ 5 , 6 ]. Although in some cases, BAC clones can be efficient as probes as well, their preparation is rather complex.…”

Section: Discussionmentioning

confidence: 99%

“…That makes it possible to use the same satDNA family as a tool to compare different closely related species and their hybrids. Different satDNA families are fast evolving, and due to their high evolutionary rate, they are species- or genus-specific [4,5,6]. Therefore, identifying satDNA in phylogenetically distant species is not possible; inversely, once found in one genome, a given repeat may be found in a closely related genome.…”

Section: Introductionmentioning

confidence: 99%

“…Since high-copy-number satDNAs form long arrays in the chromosome locus, they are well-detected using a FISH assay when a labeled monomer or its fragment is used as a probe. The isolated satDNA is used to develop molecular cytogenetic markers, which have been widely and successfully applied in comparative cytogenetic evolutionary and breeding studies [4,5,6]. Therefore, a rapid and high-throughput assay for the de novo identification of satDNAs and verification of their feasibility as FISH markers is necessary to saturate FISH maps for fine cytogenetic studies.…”

Section: Introductionmentioning

confidence: 99%

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Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species

Kroupin

Kuznetsova

Romanov

et al. 2019

Genes

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Repetitive DNA including tandem repeats (TRs) is a significant part of most eukaryotic genomes. TRs include rapidly evolving satellite DNA (satDNA) that can be shared by closely related species, their abundance may be associated with evolutionary divergence, and they have been widely used for chromosome karyotyping using fluorescence in situ hybridization (FISH). The recent progress in the development of whole-genome sequencing and bioinformatics tools enables rapid and cost-effective searches for TRs including satDNA that can be converted into molecular cytogenetic markers. In the case of closely related taxa, the genome sequence of one species (donor) can be used as a base for the development of chromosome markers for related species or genomes (target). Here, we present a pipeline for rapid and high-throughput screening for new satDNA TRs in whole-genome sequencing of the donor genome and the development of chromosome markers based on them that can be applied in the target genome. One of the main peculiarities of the developed pipeline is that preliminary estimation of TR abundance using qPCR and ranking found TRs according to their copy number in the target genome; it facilitates the selection of the most prospective (most abundant) TRs that can be converted into cytogenetic markers. Another feature of our pipeline is the probe preparation for FISH using PCR with primers designed on the aligned TR unit sequences and the genomic DNA of a target species as a template that enables amplification of a whole pool of monomers inherent in the chromosomes of the target species. We demonstrate the efficiency of the developed pipeline by the example of FISH probes developed for A, B, and R subgenome chromosomes of hexaploid triticale (BBAARR) based on a bioinformatics analysis of the D genome of Aegilops tauschii (DD) whole-genome sequence. Our pipeline can be used to develop chromosome markers in closely related species for comparative cytogenetics in evolutionary and breeding studies.

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Repetitive DNA sequences in plant genomes

Cited by 16 publications

References 87 publications

Heterochromatin distribution and histone modification patterns of H4K5 acetylation and H3S10 phosphorylation in Capsicum L.

Heterochromatin distribution and histone modification patterns of H4K5 acetylation and H3S10 phosphorylation in Capsicum L.

Plant Chromosome-Specific Probes by Microdissection of a Single Chromosome: Is That a Reality?

Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species

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