Gao Dongying, Caspersen Ann M, Hu Gongshe, Bockelman Harold E, Chen Xianming
Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, United States.
Wheat Health, Genetics, and Quality Research Unit, USDA-ARS, Pullman, WA, United States.
Front Plant Sci. 2022 May 23;13:904619. doi: 10.3389/fpls.2022.904619. eCollection 2022.
Mutator-like transposable elements (MULEs) represent a unique superfamily of DNA transposons as they can capture host genes and cause higher frequency of mutations in some eukaryotes. Despite their essential roles in plant evolution and functional genomics, MULEs are not fully understood yet in many important crops including barley (). In this study, we analyzed the barley genome and identified a new mutator transposon . This transposon is present at extremely high copy number in barley and shows unusual structure as it contains three open reading frames (ORFs) including one ORF (ORF1) encoding mutator transposase protein and one ORF (ORFR) showing opposite transcriptional orientation. We identified homologous sequences of in both monocots and dicots and grouped them into a large mutator family named . transposons from different species share significant sequence identity, but they exhibit distinct sequence structures. Unlike the transposase proteins which are highly conserved between transposons from different organisms, the ORFR-encoded proteins are quite different from distant species. Phylogenetic analysis indicated that transposons shared closer evolutionary relationships with the maize transposon than other reported MULEs. We also found phylogenetic incongruence for the transposons identified in rice and its wild species implying the possibility of horizontal transfer of transposon. Further comparison indicated that over 200 barley genes contain -related sequences. We analyzed the barley pan genomes and detected polymorphic transposons between the sequenced 23 wild and cultivated barley genomes. Our efforts identified a novel mutator transposon and revealed its recent transposition activity, which may help to develop genetic tools for barley and other crops.
类 Mutator 转座元件（MULEs）代表了一类独特的 DNA 转座子超家族，因为它们能够捕获宿主基因并在一些真核生物中导致更高频率的突变。尽管 MULEs 在植物进化和功能基因组学中具有重要作用，但在包括大麦在内的许多重要作物中，人们对其仍未完全了解。在本研究中，我们分析了大麦基因组并鉴定出一种新的 Mutator 转座子。这种转座子在大麦中以极高的拷贝数存在，并且呈现出不寻常的结构，因为它包含三个开放阅读框（ORFs），其中一个 ORF（ORF1）编码 Mutator 转座酶蛋白，另一个 ORF（ORFR）呈现相反的转录方向。我们在单子叶植物和双子叶植物中都鉴定出了 的同源序列，并将它们归为一个名为 的大型 Mutator 家族。来自不同物种的 转座子具有显著的序列同一性，但它们表现出不同的序列结构。与来自不同生物体的 转座子之间高度保守的转座酶蛋白不同，ORFR 编码的蛋白在亲缘关系较远的物种中差异很大。系统发育分析表明， 转座子与玉米 转座子的进化关系比其他已报道的 MULEs 更为密切。我们还发现水稻及其野生近缘种中鉴定出的 转座子存在系统发育不一致性，这意味着转座子水平转移的可能性。进一步比较表明，超过 200 个大麦基因包含与 相关的序列。我们分析了大麦泛基因组，并在测序的 23 个野生和栽培大麦基因组之间检测到多态性 转座子。我们的研究鉴定出一种新型 Mutator 转座子，并揭示了其近期的转座活性，这可能有助于开发用于大麦和其他作物的遗传工具。
