Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis.

Franco, Ana Luiza; Gu, Wenjia; Novák, Petr; Leitch, Ilia J.; Viccini, Lyderson F.; Leitch, Andrew R.

Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis.

Name

The_Plant_Genome_-_2025_-_Franco_-_Contrasting_distributions_and_expression_characteristics_of_transcribing_repeats_in.pdf

Description

visibility:open

Size

3.23 MB

Format

Adobe PDF

Checksum (CRC64NVME)

y4kuEV/p+co=

Resource type

Journal article

Creator (person)

Franco, Ana Luiza

ORCID

Gu, Wenjia

Novák, Petr

Leitch, Ilia J.

Viccini, Lyderson F.

Leitch, Andrew R.

Date published

January 9, 2025

Abstract

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 ( ). 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 ∼0.75% of the inflorescence poly‐A transcriptome and ∼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. Plant genomes are largely composed of repetitive DNA sequences. However, how these elements are expressed remains unclear, primarily due to the challenge of investigating repetitive sequences. Here, we used , an important crop model, to explore repeats present in different fractions of the transcriptome. Different types of RNA libraries were used to compare the proportion of each element in various tissues (leaf, stem, crown, and inflorescence). First, we explored bioinformatic tools that used raw reads to characterize genomic repeats, followed by the mapping of RNAseq reads. We observed different proportions of repeats depending on the type of RNA library, genomic features of repeats, and tissues analyzed. Among the library types, ribo‐depleted libraries had the highest proportion of transcribed repeats, especially libraries prepared from inflorescence tissues. Our study contributes to our understanding of the transcription dynamics of repetitive elements and highlights a novel strategy for exploring repeats in the transcriptome.

Project(s)

Priority 2: Trait Diversity and Function

Funder

Funder name	Awards
Queen Mary University of London, United Kingdom
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brazil	Ana Luiza Franco scholarship
Ministerstvo Školství, Mládeže a Tělovýchovy, Czechia	ELIXIR CZ Research Infrastructure Project, grant no. LM2018131