Perumal Sampath, James Brian, Tang Lily, Kagale Sateesh, Robinson Stephen J, Yang Tae-Jin, Parkin Isobel A P
Agriculture and Agri-Food Canada, Saskatoon, SK, Canada.
National Research Council Canada, Saskatoon, SK, Canada.
Front Plant Sci. 2020 Jul 21;11:1104. doi: 10.3389/fpls.2020.01104. eCollection 2020.
Miniature inverted-repeat transposable elements (MITEs) are non-autonomous class II transposons which have been shown to influence genome evolution. L. (B-genome) is one of three diploids cultivated primarily as an oil crop, which harbors novel alleles important for breeding. Two new high copy hAT MITE families (BniHAT-1 and BniHAT-2) from the B-genome were characterized and their prevalence assessed in the genomes of the related diploids, L. (A) and L. (C). Both novel MITE families were present at high copy numbers in the B-genome with 434 and 331 copies of BniHAT-1 and BniHAT-2, respectively. Yet less than 20 elements were identified in the genome assemblies of the A, and C -genomes, supporting B-genome specific proliferation of these MITE families. Although apparently randomly distributed across the genome, 68 and 70% of the B-genome MITEs were present within 2 kb flanking regions of annotated genes suggesting they might influence gene expression and/or function. In addition, MITE derived microRNAs and transcription factor binding sites suggested a putative role in gene regulation. Age of insertion analysis revealed that the major proliferation of these elements occurred during 2-3 million years ago. Additionally, site-specific polymorphism analyses showed that 44% MITEs were undergoing active amplification into the B-genome. Overall, this study provides a comprehensive analysis of two high copy MITE families, which were specifically amplified in the B-genome, suggesting a potential role in shaping the B-genome.
微型反向重复转座元件（MITEs）是一类非自主的II类转座子，已被证明会影响基因组进化。亚麻荠（B基因组）是主要作为油料作物种植的三个二倍体之一，它含有对育种很重要的新等位基因。对来自B基因组的两个新的高拷贝hAT MITE家族（BniHAT-1和BniHAT-2）进行了特征分析，并评估了它们在相关二倍体亚麻荠（A基因组）和亚麻荠（C基因组）基因组中的流行情况。这两个新的MITE家族在B基因组中以高拷贝数存在，BniHAT-1和BniHAT-2分别有434个和331个拷贝。然而，在A基因组和C基因组的基因组组装中鉴定出的元件不到20个，这支持了这些MITE家族在B基因组中的特异性增殖。尽管这些MITEs显然在基因组中随机分布，但68%和70%的B基因组MITEs存在于注释基因的2 kb侧翼区域内，这表明它们可能影响基因表达和/或功能。此外，MITE衍生的微小RNA和转录因子结合位点表明其在基因调控中可能发挥作用。插入年龄分析表明，这些元件的主要增殖发生在200万至300万年前。此外，位点特异性多态性分析表明，44%的MITEs正在向B基因组进行活跃扩增。总体而言，本研究对两个在B基因组中特异性扩增的高拷贝MITE家族进行了全面分析，表明它们在塑造B基因组方面可能发挥作用。
