Transposable Elements: Distribution, Polymorphism, and Climate Adaptation in Populus.

Yiyang Zhao,Jianbo Xie,Deqiang Zhang,Sisi Chen,Yousry A El-Kassaby,Jiadong Wu,Xian Li,Sijia Liu,Xiang Zhang,Weijie Xu

doi:10.3389/fpls.2022.814718

Abstract

Transposable elements (TEs) are a class of mobile genetic elements that make effects on shaping rapid phenotypic traits of adaptive significance. TE insertions are usually related to transcription changes of nearby genes, and thus may be subjected to purifying selection. Based on the available genome resources of Populus, we found that the composition of Helitron DNA family were highly variable and could directly influence the transcription of nearby gene expression, which are involving in stress-responsive, programmed cell death, and apoptosis pathway. Next, we indicated TEs are highly enriched in Populus trichocarpa compared with three other congeneric poplar species, especially located at untranslated regions (3′UTRs and 5′UTRs) and Helitron transposons, particularly 24-nt siRNA-targeted, are significantly associated with reduced gene expression. Additionally, we scanned a representative resequenced Populus tomentosa population, and identified 9,680 polymorphic TEs loci. More importantly, we identified a Helitron transposon located at the 3′UTR, which could reduce WRKY18 expression level. Our results highlight the importance of TE insertion events, which could regulate gene expression and drive adaptive phenotypic variation in Populus.

Highlights

Transposable elements (TEs), which are known as a source of genetic variation (McClintock, 1984), and its composition is extremely different in diverse species (Le Rouzic et al, 2007; Barron et al, 2014; Le et al, 2015; Li et al, 2018)
A large number of studies have shown that TEs can directly affect the regulation of nearby gene expression in a variety of ways, including transcriptional level and post transcriptional level (Kobayashi et al, 2004; Studer et al, 2011; Chuong et al, 2017)
Gene expression increased with increasing distance from the nearest TE (Figure 2A), and the Helitron inserted into 3 untranslated regions (UTRs) significantly repressed nearby gene expression (Figure 5D)

Summary

Introduction

Transposable elements (TEs), which are known as a source of genetic variation (McClintock, 1984), and its composition is extremely different in diverse species (Le Rouzic et al, 2007; Barron et al, 2014; Le et al, 2015; Li et al, 2018). TEs are mobile genetic sequences, with known two major categories: Class I retrotransposons and Class II DNA transposons (Wicker et al, 2007). Different transposons often form the major branches in diverse species. TEs play an important role in the formation of genomic structure and phenotypic variation in different organisms

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