The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches

Abstract

The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches

Transposition ofHOPPLAin siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility inBrachypodium distachyon

“…B. distachyon naturally occurs around the Mediterranean rim ( Fig 1A ) and groups into three main genetic lineages (A, B and C) that further split into five genetic clades (Stritt et al ., 2022; Minadakis et al ., 2023): an early diverged C clade and four clades found in Spain and France (B_West), Italy (A_Italia), the Balkans and coastal Turkey (A_East) and inland Turkey and Lesser Caucasus (B_East). We first aligned genomic reads of 320 accessions to the LTR-RT consensus sequences of B. distachyon obtained from the TRansposable Elements Platform (TREP).…”

“…The transcriptional activity of LTR-RTs can be triggered by specific environmental stresses (Grandbastien, 2015; Negi et al ., 2016). Given that B. distachyon occurs in a wide range of different habitats in the Mediterranean area (Minadakis et al ., 2023), this characteristic feature of LTR-RTs provides a potential explanation for the pCN variation we observed across natural accessions (Quadrana et al ., 2016; Baduel et al ., 2021). Yet, for the large majority of LTR-RT families, pCNs correlate only moderately with environmental factors.…”

“…Indeed, many LTR-RT families, and especially the old RLG elements, do not show signs of increased activity in the recent past in B. distachyon (Stritt et al, 2020). Considering that their copy number expansions took place in a climate that has drastically changed following the last glacial maximum (Minadakis et al ., 2023), a limited link between their activity and the current environmental conditions is actually expected for most families. In contrast, the lack of correlation between current bioclimatic variables and copy number variation for families with ongoing activity (RLC_BdisC022, RLC_BdisC024, RLC_BdisC030, RLC_BdisC209 and RLG_BdisC004; Stritt et al, 2020), suggests a more complex mechanism than their pure dependence on specific stresses in certain environments.…”

“…We used publicly available genomic reads of 320 sequenced natural accessions of B. distachyon (Gordon et al ., 2017, 2020; Skalska et al ., 2020; Stritt et al ., 2022; Minadakis et al ., 2023) to assess the natural variation of copy numbers of LTR-RTs. Because sequencing depth differed substantially between accessions (Minadakis et al ., 2023), we first downsampled all fastq files to the read number of the sample with the lowest number of reads (4.230.721 reads) using the reformat.sh function of BBtools (v 38.75, BBMap Bushnell B., http://sourceforge.net/projects/bbmap/). Downsampled reads were aligned to the TREP consensus sequences of LTR-RTs and the reference assembly of Bd21 (v 3.0) using BWA-MEM (v 0.7.17-r1188) (Li & Durbin, 2009) with the -M and the -a options set, hence outputting all alignments found.…”

“…While the activity of LTR-RTs has been extensively studied in the model A. thaliana (Baduel et al ., 2021), the interplay between genetic and environmental factors in other wild plant species remains poorly investigated. To clarify these questions, we exploit here the Brachypodium distachyon diversity panel (Minadakis et al ., 2023) and explore LTR-RT activity in a wild monocot . B. distachyon is a Mediterranean grass with a compact diploid genome of ∼272 Mb (International Brachypodium Initiative, 2010; Hasterok et al ., 2022) harboring 40 LTR-RT families (Stritt et al ., 2020) that constitute about 30 % of the genome (International Brachypodium Initiative, 2010).…”