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)

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F21%3A00555388" target="_blank" >RIV/68081707:_____/21:00555388 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14310/21:00123187

Result on the web

<a href="https://www.frontiersin.org/articles/10.3389/fpls.2021.738119/full" target="_blank" >https://www.frontiersin.org/articles/10.3389/fpls.2021.738119/full</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3389/fpls.2021.738119" target="_blank" >10.3389/fpls.2021.738119</a>

Result language

angličtina

Original language name

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)

Original language 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.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10611 - Plant sciences, botany

Project

<a href="/en/project/GC20-14133J" target="_blank" >GC20-14133J: When sex may or may not happen – The impact of asymmetrical meiosis on the evolutionary fate of genes in polyploid roses</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2021

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Frontiers in Plant Science

ISSN

1664-462X

e-ISSN

1664-462X

Volume of the periodical

12

Issue of the periodical within the volume

DEC 7 2021

Country of publishing house

CH - SWITZERLAND

Number of pages

19

Pages from-to

738119

UT code for WoS article

000742948200001

EID of the result in the Scopus database

2-s2.0-85121580612