GingerRoot: A Novel DNA Transposon Encoding Integrase-Related Transposase in Plants and Animals
GingerRoot: A Novel DNA Transposon Encoding Integrase-Related Transposase in Plants and Animals
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姜根：一种新的转座子，编码植物和动物整合酶相关的转座酶
DOI：
10.1093/gbe/evz230
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发表时间：
2019-11-01
影响因子：
3.3
通讯作者：
Jiang, Ning
中科院分区：
文献类型：
--
作者：
Cerbin, Stefan;Wai, Ching Man;Jiang, Ning
转座因子是许多真核生物基因组中最大的组成部分，不同的基因组含有不同的转座因子组合。在这里，我们发现了一个新的DNA转座子在石松卷柏的基因组。进一步搜索保守DDE区域的相关序列，发现在鱼类，珊瑚，海葵和其他动物物种中存在这个超家族的元素。然而，这种元素似乎仅限于苔藓植物和石松植物。该转座子命名为GingerRoot，与6 bp（碱基对）靶位点重复和100-150 bp末端反向重复相关。转座酶序列的分析确定了DDE基序，催化结构域，这表明类似于吉普赛样长末端重复逆转录转座子，在植物基因组中最丰富的组成部分的整合酶。在S.鳞叶植物与吉普赛反转录转座子一样，姜根在基因附近缺乏插入偏好，这与约100 Mb的紧凑基因组大小形成对比。然而，相当一部分的姜根元件被发现携带基因片段，这表明复制基因序列的能力不太可能归因于基因的接近。携带基因片段的元件似乎甲基化程度更低，更趋分化，并且比没有基因片段的元件更远离基因，这表明它们优先保留在基因贫乏的区域。这项研究已经确定了一个广泛分布的，新的DNA转座子，和第一个植物DNA转座子与整合酶相关的转座酶，这表明在植物中从头形成Gypsy样元件的可能性。
Transposable elements represent the largest components of many eukaryotic genomes and different genomes harbor different combinations of elements. Here, we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla. Further searching for related sequences to the conserved DDE region uncovered the presence of this superfamily of elements in fish, coral, sea anemone, and other animal species. However, this element appears restricted to Bryophytes and Lycophytes in plants. This transposon, named GingerRoot, is associated with a 6 bp (base pair) target site duplication, and 100-150 bp terminal inverted repeats. Analysis of transposase sequences identified the DDE motif, a catalytic domain, which shows similarity to the integrase of Gypsy-like long terminal repeat retrotransposons, the most abundant component in plant genomes. A total of 77 intact and several hundred truncated copies of GingerRoot elements were identified in S. lepidophylla. Like Gypsy retrotransposons, GingerRoots show a lack of insertion preference near genes, which contrasts to the compact genome size of about 100Mb. Nevertheless, a considerable portion of GingerRoot elements was found to carry gene fragments, suggesting the capacity of duplicating gene sequences is unlikely attributed to the proximity to genes. Elements carrying gene fragments appear to be less methylated, more diverged, and more distal to genes than those without gene fragments, indicating they are preferentially retained in gene-poor regions. This study has identified a broadly dispersed, novel DNA transposon, and the first plant DNA transposon with an integrase-related transposase, suggesting the possibility of de novo formation of Gypsy-like elements in plants.