| 武泽峰，于慧云，范三红.大麦基因组中Helitron转座元件的计算预测[J].麦类作物学报,2015,35(9):1183 |
| 大麦基因组中Helitron转座元件的计算预测 |
| Computational Prediction of Helitron Transposons in Hordeum vulgare Genome |
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| DOI：10.7606/j.issn.1009-1041.2015.09.01 |
| 中文关键词: 大麦 Helitron 转座子 基因捕获 LCV算法 |
| 英文关键词:Barley Helitron Transposon Gene capture LCV algorithm |
| 基金项目:中央高校基本科研业务费专项（2014YB032） |
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| 中文摘要: |
| Helitron是一类新发现的DNA转座元件，具有捕获宿主基因片段的能力，因而对植物基因及基因组的进化具有重要意义。为了研究麦类作物中这类元件对基因组的进化所起的作用，本研究采用一种改进的局部组合变量(LCV)方法对大麦基因组中的Helitron转座元件进行了预测，共鉴定了16 560个潜在的Helitron元件，去除假阳性后这些元件约占基因组的2.2%。基于序列分歧的计算发现，绝大多数Helitron形成于最近的900万年内，并且在大约250和550万年前各经历了一次剧烈扩张。在大麦基因组中发现了3个自主型Helitron元件，它们包含Rep和Helicase结构域的编码区。基因片段捕获分析发现，66.5%的元件平均捕获了1.9个基因片段，除了反转座和转座相关的基因外，参与发育调控的NAM家族转录因子和参与水分运输和环境胁迫响应的软木脂素合成酶基因也被高频捕获，表明Helitron转座元件不仅影响大麦基因组的结构，同时可以驱动特定功能基因的扩增。 |
| 英文摘要: |
| Helitron elements are a new class of DNA transposons. Because of the ability to capture gene fragments in the host genome, Helitron play a critical role in gene and genome evolution. To characterize the Helitron elements in Triticeae crops, a computational prediction based on the LCV algorithm was performed to identify putative Helitron in barley genome. Totally, 16 560 Helitron were identified which take up nearly 2.2% of barley genome after the removal of false positive elements. These elements were classified into 7 families containing 37 different subfamilies according to the sequence similarity of Helitron 5’ and 3’ ends. Based on the computation of sequence divergence, most of the elements have amplified in recent 9 million years, with two dramatic expansions 2.5 and 5.5 million years ago. Further more, three independent Helitron elements encoding Rep and Helicase domains were identified in barley genome. The analysis of gene capture showed that 66.5% Helitron captured gene fragments with mean of 1.9 per Helitron. In addition to those genes related to retrotranspose and transpose, the genes encoding NAM-family transcription factors which are involved in developmental regulation and suberin synthetase which are involved in transportation of water were captured with relative high frequency by Helitron elements, respectively, indicting Helitron elements can not only affect the genome structure but also drive the functional genes amplification in barely. |
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