Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F25%3A00646300" target="_blank" >RIV/60077344:_____/25:00646300 - isvavai.cz</a>
Result on the web
<a href="https://acsess.onlinelibrary.wiley.com/doi/pdf/10.1002/tpg2.20551?getft_integrator=clarivate&utm_source=clarivate" target="_blank" >https://acsess.onlinelibrary.wiley.com/doi/pdf/10.1002/tpg2.20551?getft_integrator=clarivate&utm_source=clarivate</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1002/tpg2.20551" target="_blank" >10.1002/tpg2.20551</a>
Alternative languages
Result language
angličtina
Original language name
Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis
Original language description
Repetitive DNA contributes significantly to plant genome size, adaptation, and evolution. However, little is understood about the transcription of repeats. This is addressed here in the plant green foxtail millet (Setaria viridis). First, we used RepeatExplorer2 to calculate the genome proportion (GP) of all repeat types and compared the GP of long terminal repeat (LTR) retroelements against annotated complete and incomplete LTR retroelements (Ty1/copia and Ty3/gypsy) identified by DANTE in a whole genome assembly. We show that DANTE-identified LTR retroelements can comprise similar to 0.75% of the inflorescence poly-A transcriptome and similar to 0.24% of the stem ribo-depleted transcriptome. In the RNA libraries from inflorescence tissue, both LTR retroelements and DNA transposons identified by RepeatExplorer2 were highly abundant, where they may be taking advantage of the reduced epigenetic silencing in the germ line to amplify. Typically, there was a higher representation of DANTE-identified LTR retroelements in the transcriptome than RepeatExplorer2-identified LTR retroelements, potentially reflecting the transcription of elements that have insufficient genomic copy numbers to be detected by RepeatExplorer2. In contrast, for ribo-depleted libraries of stem tissues, the reverse was observed, with a higher transcriptome representation of RepeatExplorer2-identified LTR retroelements. For RepeatExplorer2-identified repeats, we show that the GP of most Ty1/copia and Ty3/gypsy families were positively correlated with their transcript proportion. In addition, guanine- and cytosine-rich repeats with high sequence similarity were also the most abundant in the transcriptome, and these likely represent young elements that are most capable of amplification due to their ability to evade epigenetic silencing.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10603 - Genetics and heredity (medical genetics to be 3)
Result continuities
Project
<a href="/en/project/LM2018131" target="_blank" >LM2018131: Czech National Infrastructure for Biological Data</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Plant Genome
ISSN
1940-3372
e-ISSN
1940-3372
Volume of the periodical
18
Issue of the periodical within the volume
1
Country of publishing house
US - UNITED STATES
Number of pages
20
Pages from-to
e20551
UT code for WoS article
001396307400001
EID of the result in the Scopus database
2-s2.0-85214682700