Repetitive sequence analysis and karyotyping reveals centromere-associated DNA sequences in radish (Raphanus sativus L.).
Repetitive sequence analysis and karyotyping reveals centromere-associated DNA sequences in radish (Raphanus sativus L.).
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DOI：
10.1186/s12870-015-0480-y
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发表时间：
2015-04-18
影响因子：
5.3
通讯作者：
Jin W
中科院分区：
文献类型：
--
作者：
He Q;Cai Z;Hu T;Liu H;Bao C;Mao W;Jin W
萝卜（Raphanus sativus L.，2n = 2x = 18）是一种主要的根类蔬菜作物，尤其是在东亚。萝卜根含有多种营养成分，对增强免疫力具有重要作用。重复元件是基因组序列的主要组成部分，也是高等真核生物基因组大小变化的最重要因素。迄今为止，关于萝卜重复元素的研究仍然有限。为了更好地了解萝卜的基因组结构，我们进行了一项研究来评估萝卜中重复元件的比例及其分布。我们通过低覆盖率基因组测序对萝卜中的重复元件进行了全基因组表征，然后进行了基于相似性的聚类分析。结果显示，大约 31% 的基因组由重复序列组成。卫星重复序列是基因组中最主要的元素。使用荧光原位杂交 (FISH) 表征了萝卜染色体上三个卫星重复序列（CL1、CL25 和 CL43）的分布模式。 CL1主要位于所有染色体的着丝粒区域，CL25位于亚端粒区域，CL43是端粒卫星。两个卫星重复序列 CL1 和 CL25 的 FISH 信号与 5S rDNA 和 45S rDNA 一起，提供有用的细胞遗传学标记来识别每个单独的体细胞中期染色体。着丝粒特异性组蛋白 H3 (CENH3) 已被用作识别着丝粒 DNA 序列的标记。从萝卜中鉴定并克隆了一种推定的 CENH3 (RsCENH3)。其推导的氨基酸序列与芸苔属物种CENH3的氨基酸序列高度相似。针对白菜CENH3 的抗体，专门对萝卜着丝粒进行染色。使用抗 BrCENH3 抗体进行的免疫染色和染色质免疫沉淀 (ChIP) 测试表明，着丝粒特异性逆转录转座子 (CR-Radish) 和卫星重复序列 (CL1) 与萝卜中的 RsCENH3 直接相关。对萝卜中重复元素的比例进行了估计，卫星重复是最主要的元素。精细核型分析的建立使我们能够轻松识别每个体细胞中期染色体。基于免疫荧光和 ChIP 的检测证明了着丝粒上卫星和着丝粒特异性逆转录转座子的功能意义。我们的研究为未来萝卜基因组研究提供了宝贵的基础。本文的在线版本 (doi:10.1186/s12870-015-0480-y) 包含补充材料，可供授权用户使用。
Radish (Raphanus sativus L., 2n = 2x = 18) is a major root vegetable crop especially in eastern Asia. Radish root contains various nutritions which play an important role in strengthening immunity. Repetitive elements are primary components of the genomic sequence and the most important factors in genome size variations in higher eukaryotes. To date, studies about repetitive elements of radish are still limited. To better understand genome structure of radish, we undertook a study to evaluate the proportion of repetitive elements and their distribution in radish. We conducted genome-wide characterization of repetitive elements in radish with low coverage genome sequencing followed by similarity-based cluster analysis. Results showed that about 31% of the genome was composed of repetitive sequences. Satellite repeats were the most dominating elements of the genome. The distribution pattern of three satellite repeat sequences (CL1, CL25, and CL43) on radish chromosomes was characterized using fluorescence in situ hybridization (FISH). CL1 was predominantly located at the centromeric region of all chromosomes, CL25 located at the subtelomeric region, and CL43 was a telomeric satellite. FISH signals of two satellite repeats, CL1 and CL25, together with 5S rDNA and 45S rDNA, provide useful cytogenetic markers to identify each individual somatic metaphase chromosome. The centromere-specific histone H3 (CENH3) has been used as a marker to identify centromere DNA sequences. One putative CENH3 (RsCENH3) was characterized and cloned from radish. Its deduced amino acid sequence shares high similarities to those of the CENH3s in Brassica species. An antibody against B. rapa CENH3, specifically stained radish centromeres. Immunostaining and chromatin immunoprecipitation (ChIP) tests with anti-BrCENH3 antibody demonstrated that both the centromere-specific retrotransposon (CR-Radish) and satellite repeat (CL1) are directly associated with RsCENH3 in radish. Proportions of repetitive elements in radish were estimated and satellite repeats were the most dominating elements. Fine karyotyping analysis was established which allow us to easily identify each individual somatic metaphase chromosome. Immunofluorescence- and ChIP-based assays demonstrated the functional significance of satellite and centromere-specific retrotransposon at centromeres. Our study provides a valuable basis for future genomic studies in radish. The online version of this article (doi:10.1186/s12870-015-0480-y) contains supplementary material, which is available to authorized users.
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影响因子：
1.7
作者：
Han, Y. H.;Zhang, Z. H.;Jin, W. W.
通讯作者：
Jin, W. W.
影响因子：
7.2
作者：
Lim, Ki-Byung;Yang, Tae-Jin;Park, Beom-Seok
通讯作者：
Park, Beom-Seok
影响因子：
5.6
作者：
GRELLET, F;DELCASSO, D;DELSENY, M
通讯作者：
DELSENY, M
DOI：
10.1093/dnares/dsu014
发表时间：
2014-10
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Kitashiba H;Li F;Hirakawa H;Kawanabe T;Zou Z;Hasegawa Y;Tonosaki K;Shirasawa S;Fukushima A;Yokoi S;Takahata Y;Kakizaki T;Ishida M;Okamoto S;Sakamoto K;Shirasawa K;Tabata S;Nishio T
通讯作者：
Nishio T
影响因子：
11.6
作者：
Jin, WW;Melo, JR;Jiang, JM
通讯作者：
Jiang, JM