Transposable element dynamics in a wild population collection of the Brassicaceae Thlaspi arvense.

This repository contains molecular phenotype data of transposable element (TE) activity within individuals of the species Thlaspi arvense. The raw genomic data used in this study proceeds from 2 different studies:

• Y. Geng et al. (2021). Genomic Analysis of Field Pennycress (Thlaspi Arvense) Provides Insights into Mechanisms of Adaptation to High Elevation (https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01079-0).
• D. Galanti et al. (2022). Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense (https://doi.org/10.1101/2022.03.16.484610).

Transposon insertion polymorphisms (TIPS) were detected using SPLITREADER (https://github.com/LeanQ/SPLITREADER) and the initial calls were curated following the steps described in P. Baduel et al. (2021). Efficient Detection of Transposable Element Insertion Polymorphisms Between Genomes Using Short-Read Sequencing Data. J. Cho. Plant Transposable Elements: Methods and Protocols. Springer US.  (https://link.springer.com/book/10.1007/978-1-0716-1134-0).  We also screen the samples searching for transposon absence polymorphisms (TAPS) using a custom pipeline deposited at https://github.com/weigelworld/popTAP.

All TE polymorphisms were detected using as reference genome published by A. Nunn et al. (2021).  Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates. (https://pubmed.ncbi.nlm.nih.gov/34990041/).

Both datasets and their corresponding metadata are included in this repository.