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Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species
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 chromo...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6409974/ https://www.ncbi.nlm.nih.gov/pubmed/30717300 http://dx.doi.org/10.3390/genes10020113 |
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author | Kroupin, Pavel Kuznetsova, Victoria Romanov, Dmitry Kocheshkova, Alina Karlov, Gennady Dang, Thi Xuan Khuat, Thi Mai L. Kirov, Ilya Alexandrov, Oleg Polkhovskiy, Alexander Razumova, Olga Divashuk, Mikhail |
author_facet | Kroupin, Pavel Kuznetsova, Victoria Romanov, Dmitry Kocheshkova, Alina Karlov, Gennady Dang, Thi Xuan Khuat, Thi Mai L. Kirov, Ilya Alexandrov, Oleg Polkhovskiy, Alexander Razumova, Olga Divashuk, Mikhail |
author_sort | Kroupin, Pavel |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6409974 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-64099742019-03-26 Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species Kroupin, Pavel Kuznetsova, Victoria Romanov, Dmitry Kocheshkova, Alina Karlov, Gennady Dang, Thi Xuan Khuat, Thi Mai L. Kirov, Ilya Alexandrov, Oleg Polkhovskiy, Alexander Razumova, Olga Divashuk, Mikhail Genes (Basel) Technical Note 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. MDPI 2019-02-01 /pmc/articles/PMC6409974/ /pubmed/30717300 http://dx.doi.org/10.3390/genes10020113 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Technical Note Kroupin, Pavel Kuznetsova, Victoria Romanov, Dmitry Kocheshkova, Alina Karlov, Gennady Dang, Thi Xuan Khuat, Thi Mai L. Kirov, Ilya Alexandrov, Oleg Polkhovskiy, Alexander Razumova, Olga Divashuk, Mikhail Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species |
title | Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species |
title_full | Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species |
title_fullStr | Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species |
title_full_unstemmed | Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species |
title_short | Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species |
title_sort | pipeline for the rapid development of cytogenetic markers using genomic data of related species |
topic | Technical Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6409974/ https://www.ncbi.nlm.nih.gov/pubmed/30717300 http://dx.doi.org/10.3390/genes10020113 |
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