Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis

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 LTR retroelements against annotated complete and incomplete LTR retroelements (Ty1/copia, 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 transcripto..., Datasets used in the analysis
The DNA sequences used to characterize genomic repeats with RepeatExplorer2 were downloaded from NCBI (See Table 1) and comprised paired-end Illumina NovaSeq 6000 sequence data with reads of 151 bp length from genomic DNA of Setaria viridis ‘A10’ (SRR10051273) (Mamidi et al., 2020).
For the RNA sequencing conducted here, Setaria viridis ‘A10’ seeds were washed with distilled water and sterilized by incubating in a solution of 20% sodium hypochlorite and 0.1% Tween 20. Seeds were germinated in petri dishes in MS medium for 5 days, followed by 7 days in plastic pots. After root system establishment, the seedlings were transferred to pots containing a mixture of substrate and sand (1:1) and grown in a plant chamber in the Federal University of Juiz de Fora (Brazil), under a photoperiod of 16/8h (light/dark), temperature 25°+/- 2°C for at least 20 days. RNA from c. 100 mg of leaf material was extracted with the RNeasy Plant Mini Kit, (74904 Qiagen).
Ribo-deplet..., , # Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis

[https://doi.org/10.5061/dryad.rjdfn2znh](https://doi.org/10.5061/dryad.rjdfn2znh)

Contributors:

Ana Luiza Franco: Federal University of Juiz de Fora, Institute of Biological Sciences, Brazil.

 Wenjia Gu: Queen Mary University of London, UK.

Petr Novák: Biology Centre, Czech Academy of Sciences, Czech Republic.

Ilia J. Leitch: Royal Botanic Gardens, Kew, UK.

Lyderson F. Viccini: Federal University of Juiz de Fora, Institute of Biological Sciences, Brazil.

Andrew R. Leitch: Queen Mary University of London, UK.

## Description of the data and file structure

#### Repeat Transcription Analysis Using RepeatExplorer2

##### Objective

This study explores the feasibility of analyzing repeat transcription using genome skimming data, enabling application across organisms regardless of genome assembly availability.

##### RepeatExplorer2

\- Builds a library of genomic repeats (e.g., LTR...