SINE jumping contributes to large-scale polymorphisms in the pig genomes.
SINE jumping contributes to large-scale polymorphisms in the pig genomes.
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正弦跳跃有助于猪基因组的大规模多态性
DOI：
10.1186/s13100-021-00246-y
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发表时间：
2021-06-28
期刊：
影响因子：
4.9
通讯作者：
Song C
中科院分区：
文献类型：
--
作者：
Chen C;D'Alessandro E;Murani E;Zheng Y;Giosa D;Yang N;Wang X;Gao B;Li K;Wimmers K;Song C
背景基于反转录转座子插入多态(RIPs)的分子标记已经被开发出来，并被广泛应用于动植物中。短散布核素(Sine)对基因活性乃至表型有广泛的影响。结果SINEA1基因插入频率最高(22.5% %，基因间26.5 %)，其次是SINEA2(10.5 %基因内和9 %基因间)和SINEA3(12.5 %基因内和5.0 %基因间)。我们开发了一种全基因组的正弦RIP挖掘方法，获得了大量的正弦RIP序列(36,284个)，准确率超过80%，在染色体上分布均匀(14.5/Mb)，SINEA1元件产生的正弦RIP序列的准确率为74.34 %。超过65 %的猪正弦序列与基因重叠，其中大部分(>； 95 %)位于内含子中。总体而言，大约四分之一(23.09 %)的基因包含正弦RIP。在蛋白质编码基因的转录本中观察到明显的正弦RIPs偏向。近一半的裂口在这些猪品种中很常见。对23个猪种的16个正弦重复序列进行了群体遗传分析，系统发育树和聚类分析结果与我国地方猪种的地理分布基本一致。结论SINEA1-3基因在不同猪种间具有较高的多态性，尤其是SINEA1基因在不同猪种间具有较高的多态性，并在猪基因组中产生了较大的结构变异。获得了35000多个正弦RIP标记。这些数据表明，年轻的正弦序列在创造新的遗传变异和塑造猪基因组的进化中发挥着重要作用，也为正弦片段作为遗传标记的巨大潜力提供了强有力的证据，可用于猪的群体遗传分析和数量性状基因座(QTL)定位。
BackgroundMolecular markers based on retrotransposon insertion polymorphisms (RIPs) have been developed and are widely used in plants and animals. Short interspersed nuclear elements (SINEs) exert wide impacts on gene activity and even on phenotypes. However, SINE RIP profiles in livestock remain largely unknown, and not be revealed in pigs.ResultsOur data revealed that SINEA1 displayed the most polymorphic insertions (22.5 % intragenic and 26.5 % intergenic), followed by SINEA2 (10.5 % intragenic and 9 % intergenic) and SINEA3 (12.5 % intragenic and 5.0 % intergenic). We developed a genome-wide SINE RIP mining protocol and obtained a large number of SINE RIPs (36,284), with over 80 % accuracy and an even distribution in chromosomes (14.5/Mb), and 74.34 % of SINE RIPs generated by SINEA1 element. Over 65 % of pig SINE RIPs overlap with genes, most of them (> 95 %) are in introns. Overall, about one forth (23.09 %) of the total genes contain SINE RIPs. Significant biases of SINE RIPs in the transcripts of protein coding genes were observed. Nearly half of the RIPs are common in these pig breeds. Sixteen SINE RIPs were applied for population genetic analysis in 23 pig breeds, the phylogeny tree and cluster analysis were generally consistent with the geographical distributions of native pig breeds in China.ConclusionsOur analysis revealed that SINEA1–3 elements, particularly SINEA1, are high polymorphic across different pig breeds, and generate large-scale structural variations in the pig genomes. And over 35,000 SINE RIP markers were obtained. These data indicate that young SINE elements play important roles in creating new genetic variations and shaping the evolution of pig genome, and also provide strong evidences to support the great potential of SINE RIPs as genetic markers, which can be used for population genetic analysis and quantitative trait locus (QTL) mapping in pig.
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影响因子：
2.4
作者：
Fang, M;Hu, X;Li, N
通讯作者：
Li, N
影响因子：
64.8
作者：
Carrieri, Claudia;Cimatti, Laura;Gustincich, Stefano
通讯作者：
Gustincich, Stefano
来自1,092个人基因组的遗传变异的综合图。
影响因子：
64.8
作者：
通讯作者：
--
DOI：
10.1111/tpj.12285
发表时间：
2013-10
期刊：
The Plant journal : for cell and molecular biology
影响因子：
--
作者：
Ben-David S;Yaakov B;Kashkush K
通讯作者：
Kashkush K
影响因子：
30.8
作者：
Dewannieux, M;Esnault, C;Heidmann, T
通讯作者：
Heidmann, T