白菜和甘蓝基因组转座子表达及其对基因调控的潜在影响

doi:10.3724/SP.J.1005.2013.01014

遗传 ›› 2013, Vol. 35 ›› Issue (8): 1014-1022.doi: 10.3724/SP.J.1005.2013.01014

白菜和甘蓝基因组转座子表达及其对基因调控的潜在影响

赵美霞^1,2, 张彪², 刘胜毅¹, 马渐新²

1. 中国农业科学院油料作物研究所, 农业部油料作物生物学重点实验室, 武汉 430062 2. 美国普渡大学农学系, 西拉法叶 47907

收稿日期:2013-03-11 修回日期:2013-04-16 出版日期:2013-08-20 发布日期:2013-08-25
通讯作者: 刘胜毅 E-mail:liusy@oilcrops.cn
基金资助:
国家自然科学基金项目(编号：30671119)资助

Transposon expression and potential effects on gene regulation of Brassica rapa and B. oleracea genomes

ZHAO Mei-Xia^{1, 2}, ZHANG Biao², LIU Sheng-Yi¹, MA Jian-Xin²

1. Key Laboratory of Oil Crops Biology and Genetic Breeding, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China 2. Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA

Received:2013-03-11 Revised:2013-04-16 Online:2013-08-20 Published:2013-08-25

摘要/Abstract

摘要：

转座子或转座元件是大多数真核生物基因组的主要组成成分。甘蓝(Brassica oleracea)基因组比白菜(B. rapa)大主要是转座子的扩增差异造成的。然而, 这两个芸薹属近缘物种转座子表达水平以及对基因的调控和功能的影响目前还不清楚。文章对白菜和甘蓝叶、根、茎3个器官的转录组数据进行了初步分析。结果显示, 转座子的表达量很低, 转录组reads中有1%来自转座子的转录本; 转座子的表达存在器官差异, 且不同类别和家族的转座子表达量相差很大, 相同类别和同一家族的转座子在白菜和甘蓝基因组中的表达活性也不相同。进一步鉴定到转录读出的LTR反转座子, 其与下游基因距离小于2 kb的有41个, 小于100 bp的有9个, 这些LTR的转录读出很可能通过正义或反义的转录本激活或干扰下游基因的表达。同时, 具有转录读出的intact LTR比solo LTR具有更强的读出活性。通过深入分析转座子的插入位点发现, 白菜基因组中转座子插入基因内部的频率比甘蓝基因组中的高; 与反转座子相比, DNA转座子更偏向于插入或保留在基因的内含子当中。这些结果为认识转座子对其他蛋白编码基因的影响提供了基础。

关键词: 甘蓝, 转座子, 转座子插入位点, 白菜, 转录组, 转录读出

Abstract:

Transposons or transposable elements (TEs) are ubiquitous and most abundant DNA components in higher eukaryotes. Recent sequencing of the Brassica rapa and B. oleracea genomes revealed that the amplification of TEs is one of the main factors inducing the difference in genome size. However, the expressions of TEs and the TE effects on gene regulation and functions of these two Brassica diploid species were unclear. Here, we analyzed the RNA sequencing data of leaves, roots, and stems from B. rapa and B. oleracea. Our data showed that overall TEs in either genome expressed at very low levels, and the expression levels of different TE categories and families varied among different organs. Moreover, even for the same TE category or family, the expression activities were distinct between the two Brassica diploids. Forty-one and nine LTR retrotransposons with the transcripts that read into their adjacent sequences have the distances shorter than 2 kb and 100 bp compared to the downstream genes. These LTR retrotransposon readout transcriptions may produce sense or antisense transcripts of nearby genes, with the effects on activating or silencing corresponding genes. Meanwhile, intact LTRs were detected at stronger readout activities than solo LTRs. Of the TEs inserted into genes, the frequencies were ob-served at a higher level in B. rapa than in B. oleracea. In addition, DNA transposons were prone to insert or retain in the intronic regions of genes in either Brassica genomes. These results revealed that the TEs may have potential effects on regulating protein coding genes.

Key words: Brassica rapa, transcriptome, transcription readout, B. oleracea, TE insertion, transposon

赵美霞张彪刘胜毅马渐新. 白菜和甘蓝基因组转座子表达及其对基因调控的潜在影响[J]. 遗传, 2013, 35(8): 1014-1022.

ZHAO Mei-Xia ZHANG Biao LIU Sheng-Yi MA Jian-Xin. Transposon expression and potential effects on gene regulation of Brassica rapa and B. oleracea genomes[J]. HEREDITAS, 2013, 35(8): 1014-1022.

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白菜和甘蓝基因组转座子表达及其对基因调控的潜在影响

Transposon expression and potential effects on gene regulation of Brassica rapa and B. oleracea genomes

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