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Power and Weakness of Repetition – Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization (Rosa and Fragaria)

Plant genomes consist, to a considerable extent, of non-coding repetitive DNA. Several studies showed that phylogenetic signals can be extracted from such repeatome data by using among-species dissimilarities from the RepeatExplorer2 pipeline as distance measures. Here, we advanced this approach by...

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Autores principales: Herklotz, Veit, Kovařík, Aleš, Wissemann, Volker, Lunerová, Jana, Vozárová, Radka, Buschmann, Sebastian, Olbricht, Klaus, Groth, Marco, Ritz, Christiane M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8688825/
https://www.ncbi.nlm.nih.gov/pubmed/34950159
http://dx.doi.org/10.3389/fpls.2021.738119
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author Herklotz, Veit
Kovařík, Aleš
Wissemann, Volker
Lunerová, Jana
Vozárová, Radka
Buschmann, Sebastian
Olbricht, Klaus
Groth, Marco
Ritz, Christiane M.
author_facet Herklotz, Veit
Kovařík, Aleš
Wissemann, Volker
Lunerová, Jana
Vozárová, Radka
Buschmann, Sebastian
Olbricht, Klaus
Groth, Marco
Ritz, Christiane M.
author_sort Herklotz, Veit
collection PubMed
description Plant genomes consist, to a considerable extent, of non-coding repetitive DNA. Several studies showed that phylogenetic signals can be extracted from such repeatome data by using among-species dissimilarities from the RepeatExplorer2 pipeline as distance measures. Here, we advanced this approach by adjusting the read input for comparative clustering indirectly proportional to genome size and by summarizing all clusters into a main distance matrix subjected to Neighbor Joining algorithms and Principal Coordinate Analyses. Thus, our multivariate statistical method works as a “repeatomic fingerprint,” and we proved its power and limitations by exemplarily applying it to the family Rosaceae at intrafamilial and, in the genera Fragaria and Rosa, at the intrageneric level. Since both taxa are prone to hybridization events, we wanted to show whether repeatome data are suitable to unravel the origin of natural and synthetic hybrids. In addition, we compared the results based on complete repeatomes with those from ribosomal DNA clusters only, because they represent one of the most widely used barcoding markers. Our results demonstrated that repeatome data contained a clear phylogenetic signal supporting the current subfamilial classification within Rosaceae. Accordingly, the well-accepted major evolutionary lineages within Fragaria were distinguished, and hybrids showed intermediate positions between parental species in data sets retrieved from both complete repeatomes and rDNA clusters. Within the taxonomically more complicated and particularly frequently hybridizing genus Rosa, we detected rather weak phylogenetic signals but surprisingly found a geographic pattern at a population scale. In sum, our method revealed promising results at larger taxonomic scales as well as within taxa with manageable levels of reticulation, but success remained rather taxon specific. Since repeatomes can be technically easy and comparably inexpensively retrieved even from samples of rather poor DNA quality, our phylogenomic method serves as a valuable alternative when high-quality genomes are unavailable, for example, in the case of old museum specimens.
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spelling pubmed-86888252021-12-22 Power and Weakness of Repetition – Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization (Rosa and Fragaria) Herklotz, Veit Kovařík, Aleš Wissemann, Volker Lunerová, Jana Vozárová, Radka Buschmann, Sebastian Olbricht, Klaus Groth, Marco Ritz, Christiane M. Front Plant Sci Plant Science Plant genomes consist, to a considerable extent, of non-coding repetitive DNA. Several studies showed that phylogenetic signals can be extracted from such repeatome data by using among-species dissimilarities from the RepeatExplorer2 pipeline as distance measures. Here, we advanced this approach by adjusting the read input for comparative clustering indirectly proportional to genome size and by summarizing all clusters into a main distance matrix subjected to Neighbor Joining algorithms and Principal Coordinate Analyses. Thus, our multivariate statistical method works as a “repeatomic fingerprint,” and we proved its power and limitations by exemplarily applying it to the family Rosaceae at intrafamilial and, in the genera Fragaria and Rosa, at the intrageneric level. Since both taxa are prone to hybridization events, we wanted to show whether repeatome data are suitable to unravel the origin of natural and synthetic hybrids. In addition, we compared the results based on complete repeatomes with those from ribosomal DNA clusters only, because they represent one of the most widely used barcoding markers. Our results demonstrated that repeatome data contained a clear phylogenetic signal supporting the current subfamilial classification within Rosaceae. Accordingly, the well-accepted major evolutionary lineages within Fragaria were distinguished, and hybrids showed intermediate positions between parental species in data sets retrieved from both complete repeatomes and rDNA clusters. Within the taxonomically more complicated and particularly frequently hybridizing genus Rosa, we detected rather weak phylogenetic signals but surprisingly found a geographic pattern at a population scale. In sum, our method revealed promising results at larger taxonomic scales as well as within taxa with manageable levels of reticulation, but success remained rather taxon specific. Since repeatomes can be technically easy and comparably inexpensively retrieved even from samples of rather poor DNA quality, our phylogenomic method serves as a valuable alternative when high-quality genomes are unavailable, for example, in the case of old museum specimens. Frontiers Media S.A. 2021-12-07 /pmc/articles/PMC8688825/ /pubmed/34950159 http://dx.doi.org/10.3389/fpls.2021.738119 Text en Copyright © 2021 Herklotz, Kovařík, Wissemann, Lunerová, Vozárová, Buschmann, Olbricht, Groth and Ritz. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Herklotz, Veit
Kovařík, Aleš
Wissemann, Volker
Lunerová, Jana
Vozárová, Radka
Buschmann, Sebastian
Olbricht, Klaus
Groth, Marco
Ritz, Christiane M.
Power and Weakness of Repetition – Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization (Rosa and Fragaria)
title Power and Weakness of Repetition – Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization (Rosa and Fragaria)
title_full Power and Weakness of Repetition – Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization (Rosa and Fragaria)
title_fullStr Power and Weakness of Repetition – Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization (Rosa and Fragaria)
title_full_unstemmed Power and Weakness of Repetition – Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization (Rosa and Fragaria)
title_short Power and Weakness of Repetition – Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization (Rosa and Fragaria)
title_sort power and weakness of repetition – evaluating the phylogenetic signal from repeatomes in the family rosaceae with two case studies from genera prone to polyploidy and hybridization (rosa and fragaria)
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8688825/
https://www.ncbi.nlm.nih.gov/pubmed/34950159
http://dx.doi.org/10.3389/fpls.2021.738119
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