Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F20%3A00114759" target="_blank" >RIV/00216224:14740/20:00114759 - isvavai.cz</a>

Result on the web

<a href="https://genome.cshlp.org/content/30/11/1583" target="_blank" >https://genome.cshlp.org/content/30/11/1583</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1101/gr.261586.120" target="_blank" >10.1101/gr.261586.120</a>

Result language

angličtina

Original language name

Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response

Original language description

Rapid plant genome evolution is crucial to adapt to environmental changes. Chromosomal rearrangements and gene copy number variation (CNV) are two important tools for genome evolution and sources for the creation of new genes. However, their emergence takes many generations. In this study, we show that in Arabidopsis thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the genome structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. Our data suggest that these TDDOs appeared within a few generations, leading to the duplication of hundreds of genes. By subsequently focusing on a line only containing 20% of rRNA gene copies (20rDNA line), we investigated the impact of TDDOs on 3D genome organization, gene expression, and cytosine methylation. We found that duplicated genes often accumulate more transcripts. Among them, several are involved in plant-pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and discuss their potential implications for the evolution of plant genomes.

Czech name

—

Czech description

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Type

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

CEP classification

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OECD FORD branch

10608 - Biochemistry and molecular biology

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2020

Confidentiality

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

Name of the periodical

Genome research

ISSN

1088-9051

e-ISSN

—

Volume of the periodical

30

Issue of the periodical within the volume

11

Country of publishing house

US - UNITED STATES

Number of pages

10

Pages from-to

1583-1592

UT code for WoS article

000586893200004

EID of the result in the Scopus database

2-s2.0-85095461441