Intron gain and loss in segmentally duplicated genes in rice.
Intron gain and loss in segmentally duplicated genes in rice.
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DOI：
10.1186/gb-2006-7-5-r41
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发表时间：
2006
期刊：
影响因子：
12.3
通讯作者：
Buell CR
中科院分区：
文献类型：
--
作者：
Lin H;Zhu W;Silva JC;Gu X;Buell CR
对水稻中3,000多个共线性配对基因的分析表明，在片段重复后，内含子丢失比内含子获得更多。内含子受到的选择压力比外显子小，因此，内含子序列比外显子具有更高的增益和损失率。在许多植物物种中，基因组的大部分已经分段复制，产生了大量的重复基因。最近完成的水稻基因组中，节段性复制已被记录，使我们能够研究内含子的进化水稻，一个二倍体单子叶植物物种。对水稻片段重复的分析表明，371 Mb基因组中的159 Mb和43，719个非转座元件相关基因中的21，570个包含在一个重复区域内。在这些重复区域中，存在3，101个共线配对基因。利用这组片段重复的基因，我们研究了从全长cDNA支持的水稻非转座元件相关基因模型的内含子进化。使用在双子叶模式物种拟南芥中具有直系同源物的基因对，我们确定了更多的内含子丢失（35个基因对内的49个内含子）比内含子获得（5个基因对内的5个内含子）以下片段重复。我们不能证明优先内含子损失在3'端的基因，如以前报道的哺乳动物基因组。然而，我们确实发现缺失内含子侧翼的外显子的四个核苷酸具有较少使用的4聚体。我们观察到，在水稻内的内含子进化后，节段性重复在很大程度上占主导地位的内含子丢失。在五个内含子获得的情况下，在片段重复基因，获得的序列相似的转座因子。
Analysis of over 3,000 co-linear paired genes in rice shows more intron loss than intron gain following segmental duplication. Introns are under less selection pressure than exons, and consequently, intronic sequences have a higher rate of gain and loss than exons. In a number of plant species, a large portion of the genome has been segmentally duplicated, giving rise to a large set of duplicated genes. The recent completion of the rice genome in which segmental duplication has been documented has allowed us to investigate intron evolution within rice, a diploid monocotyledonous species. Analysis of segmental duplication in rice revealed that 159 Mb of the 371 Mb genome and 21,570 of the 43,719 non-transposable element-related genes were contained within a duplicated region. In these duplicated regions, 3,101 collinear paired genes were present. Using this set of segmentally duplicated genes, we investigated intron evolution from full-length cDNA-supported non-transposable element-related gene models of rice. Using gene pairs that have an ortholog in the dicotyledonous model species Arabidopsis thaliana, we identified more intron loss (49 introns within 35 gene pairs) than intron gain (5 introns within 5 gene pairs) following segmental duplication. We were unable to demonstrate preferential intron loss at the 3' end of genes as previously reported in mammalian genomes. However, we did find that the four nucleotides of exons that flank lost introns had less frequently used 4-mers. We observed that intron evolution within rice following segmental duplication is largely dominated by intron loss. In two of the five cases of intron gain within segmentally duplicated genes, the gained sequences were similar to transposable elements.
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DOI：
10.1073/pnas.0408274102
发表时间：
2005-01-18
影响因子：
11.1
作者：
Roy, SW;Gilbert, W
通讯作者：
Gilbert, W
影响因子：
7
作者：
Fedorov, A;Roy, S;Gilbert, W
通讯作者：
Gilbert, W
影响因子：
64.8
作者：
Matsumoto, T;Wu, JZ;Sugiura, M
通讯作者：
Sugiura, M
影响因子：
14.9
作者：
Chenna, R;Sugawara, H;Thompson, JD
通讯作者：
Thompson, JD
DOI：
10.1101/sqb.1987.052.01.098
发表时间：
1987-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
GILBERT, W
通讯作者：
GILBERT, W