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Detection of tandem repeats in the Capsicum annuum genome

In this study, we modified the multiple alignment method based on the generation of random position weight matrices (RPWMs) and used it to search for tandem repeats (TRs) in the Capsicum annuum genome. The application of the modified (m)RPWM method, which considers the correlation of adjusting nucle...

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Autores principales: Rudenko, Valentina, Korotkov, Eugene
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10211496/
https://www.ncbi.nlm.nih.gov/pubmed/37186267
http://dx.doi.org/10.1093/dnares/dsad007
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author Rudenko, Valentina
Korotkov, Eugene
author_facet Rudenko, Valentina
Korotkov, Eugene
author_sort Rudenko, Valentina
collection PubMed
description In this study, we modified the multiple alignment method based on the generation of random position weight matrices (RPWMs) and used it to search for tandem repeats (TRs) in the Capsicum annuum genome. The application of the modified (m)RPWM method, which considers the correlation of adjusting nucleotides, resulted in the identification of 908,072 TR regions with repeat lengths from 2 to 200 bp in the C. annuum genome, where they occupied ~29%. The most common TRs were 2 and 3 bp long followed by those of 21, 4, and 15 bp. We performed clustering analysis of TRs with repeat lengths of 2 and 21 bp and created position-weight matrices (PWMs) for each group; these templates could be used to search for TRs of a given length in any nucleotide sequence. All detected TRs can be accessed through publicly available database (http://victoria.biengi.ac.ru/capsicum_tr/). Comparison of mRPWM with other TR search methods such as Tandem Repeat Finder, T-REKS, and XSTREAM indicated that mRPWM could detect significantly more TRs at similar false discovery rates, indicating its superior performance. The developed mRPWM method can be successfully applied to the identification of highly divergent TRs, which is important for functional analysis of genomes and evolutionary studies.
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spelling pubmed-102114962023-05-26 Detection of tandem repeats in the Capsicum annuum genome Rudenko, Valentina Korotkov, Eugene DNA Res Research Article In this study, we modified the multiple alignment method based on the generation of random position weight matrices (RPWMs) and used it to search for tandem repeats (TRs) in the Capsicum annuum genome. The application of the modified (m)RPWM method, which considers the correlation of adjusting nucleotides, resulted in the identification of 908,072 TR regions with repeat lengths from 2 to 200 bp in the C. annuum genome, where they occupied ~29%. The most common TRs were 2 and 3 bp long followed by those of 21, 4, and 15 bp. We performed clustering analysis of TRs with repeat lengths of 2 and 21 bp and created position-weight matrices (PWMs) for each group; these templates could be used to search for TRs of a given length in any nucleotide sequence. All detected TRs can be accessed through publicly available database (http://victoria.biengi.ac.ru/capsicum_tr/). Comparison of mRPWM with other TR search methods such as Tandem Repeat Finder, T-REKS, and XSTREAM indicated that mRPWM could detect significantly more TRs at similar false discovery rates, indicating its superior performance. The developed mRPWM method can be successfully applied to the identification of highly divergent TRs, which is important for functional analysis of genomes and evolutionary studies. Oxford University Press 2023-04-25 /pmc/articles/PMC10211496/ /pubmed/37186267 http://dx.doi.org/10.1093/dnares/dsad007 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Rudenko, Valentina
Korotkov, Eugene
Detection of tandem repeats in the Capsicum annuum genome
title Detection of tandem repeats in the Capsicum annuum genome
title_full Detection of tandem repeats in the Capsicum annuum genome
title_fullStr Detection of tandem repeats in the Capsicum annuum genome
title_full_unstemmed Detection of tandem repeats in the Capsicum annuum genome
title_short Detection of tandem repeats in the Capsicum annuum genome
title_sort detection of tandem repeats in the capsicum annuum genome
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10211496/
https://www.ncbi.nlm.nih.gov/pubmed/37186267
http://dx.doi.org/10.1093/dnares/dsad007
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