Wos Guillaume, Choudhury Rimjhim Roy, Kolář Filip, Parisod Christian
Department of Botany, Charles University, 128 01, Prague, Czech Republic.
Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland.
Mob DNA. 2021 Feb 27;12(1):7. doi: 10.1186/s13100-021-00236-0.
Plant genomes can respond rapidly to environmental changes and transposable elements (TEs) arise as important drivers contributing to genome dynamics. Although some elements were reported to be induced by various abiotic or biotic factors, there is a lack of general understanding on how environment influences the activity and diversity of TEs. Here, we combined common garden experiment with short-read sequencing to investigate genomic abundance and expression of 2245 consensus TE sequences (containing retrotransposons and DNA transposons) in an alpine environment in Arabidopsis arenosa. To disentangle general trends from local differentiation, we leveraged four foothill-alpine population pairs from different mountain regions. Seeds of each of the eight populations were raised under four treatments that differed in temperature and irradiance, two factors varying with elevation. RNA-seq analysis was performed on leaves of young plants to test for the effect of elevation and subsequently of temperature and irradiance on expression of TE sequences.
Genomic abundance of the 2245 consensus TE sequences varied greatly between the mountain regions in line with neutral divergence among the regions, representing distinct genetic lineages of A. arenosa. Accounting for intraspecific variation in abundance, we found consistent transcriptomic response for some TE sequences across the different pairs of foothill-alpine populations suggesting parallelism in TE expression. In particular expression of retrotransposon LTR Copia (e.g. Ivana and Ale clades) and LTR Gypsy (e.g. Athila and CRM clades) but also non-LTR LINE or DNA transposon TIR MuDR consistently varied with elevation of origin. TE sequences responding specifically to temperature and irradiance belonged to the same classes as well as additional TE clades containing potentially stress-responsive elements (e.g. LTR Copia Sire and Tar, LTR Gypsy Reina).
Our study demonstrated that the A. arenosa genome harbours a considerable diversity of TE sequences whose abundance and expression response varies across its native range. Some TE clades may contain transcriptionally active elements responding to a natural environmental gradient. This may further contribute to genetic variation between populations and may ultimately provide new regulatory mechanisms to face environmental challenges.
植物基因组能够对环境变化迅速做出反应，转座元件（TEs）成为推动基因组动态变化的重要因素。尽管有报道称某些元件会受到各种非生物或生物因素的诱导，但对于环境如何影响TEs的活性和多样性，人们仍缺乏全面的了解。在此，我们将常见园实验与短读测序相结合，以研究拟南芥在高山环境中2245个共有TE序列（包括反转录转座子和DNA转座子）的基因组丰度和表达情况。为了区分一般趋势与局部分化，我们利用了来自不同山区的四对山麓 - 高山种群。八个种群中的每个种群的种子在四种温度和光照条件不同的处理下培育，这两个因素随海拔高度而变化。对幼苗的叶片进行RNA测序分析，以测试海拔高度以及随后的温度和光照对TE序列表达的影响。
2245个共有TE序列的基因组丰度在不同山区之间差异很大，这与各区域之间的中性分歧一致，代表了拟南芥不同的遗传谱系。考虑到丰度的种内变异，我们发现一些TE序列在不同的山麓 - 高山种群对之间具有一致的转录组反应，表明TE表达存在平行性。特别是反转录转座子LTR Copia（如Ivana和Ale分支）和LTR Gypsy（如Athila和CRM分支）的表达，以及非LTR LINE或DNA转座子TIR MuDR的表达，始终随起源海拔高度而变化。对温度和光照有特异性反应的TE序列属于相同的类别，以及其他包含潜在应激反应元件的TE分支（如LTR Copia Sire和Tar，LTR Gypsy Reina）。
我们的研究表明，拟南芥基因组包含大量多样的TE序列，其丰度和表达反应在其原生范围内各不相同。一些TE分支可能包含对自然环境梯度有反应的转录活性元件。这可能进一步导致种群之间的遗传变异，并最终可能提供应对环境挑战的新调控机制。
