Transposable element dynamics in a wild population collection of the Brassicaceae Thlaspi arvense.
Year: 2022
Type: preprint
Abstract: This repository contains data related to this study. The raw genomic data used in this study proceeds from 3 different studies: Nunn et al. Plant Biotechnol J. (2021) Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates. DOI: https://doi.org/10.1111/pbi.13775 Y. Geng et al. BMC Biol. (2021) Genomic Analysis of Field Pennycress (Thlaspi Arvense) Provides Insights into Mechanisms of Adaptation to High Elevation. DOI: https://doi.org/10.1186/s12915-021-01079-0 D. Galanti et al. PLoS Genet. (2022) Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense. DOI: 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/).
Authors: Contreras-Garrido, Adrián, Galanti, Dario, Bossdorf, Oliver, Weigel, Detlef, Movili, Andrea, Becker, Claude
Language: English
Subfield: Plant Science
Domain: Life Sciences
Open Access status: green
Funder: European Commission
OpenAlex ID: W6912700563