Investigation of loss and gain of introns in the compact genomes of pufferfishes (Fugu and Tetraodon)
Investigation of loss and gain of introns in the compact genomes of pufferfishes (Fugu and Tetraodon)
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DOI：
10.1093/molbev/msm278
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发表时间：
2008-03-01
影响因子：
10.7
通讯作者：
Venkatesh, Byrappa
中科院分区：
文献类型：
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作者：
Loh, Yong-Hwee;Brenner, Sydney;Venkatesh, Byrappa
我们研究了2种近缘的河豚物种——红河豚（Fugu rubripes）和黑病毒四齿鲨（Tetraodon nigroviridis）的紧凑基因组中的内含子进化，这两种物种大约在3200万年前（MYA）分化。对13547对基因对中的148028个内含子位置进行分析，发现四齿兽和河豚谱系中分别有57个和24个内含子缺失，两种谱系均未发现内含子缺失。为了进行比较，我们分析了人类和小鼠的12,866对同源基因中的144,545个内含子位置，以狗为外群，偏离约61 MYA，发现小鼠中有51个内含子丢失，人类中有3个内含子丢失，没有获得。四齿兽的内含子损失率高于河豚、小鼠和人类，但低于其他真核生物的损失率。在河豚和哺乳动物中丢失的内含子明显短于基因组中内含子的平均大小。河豚和四齿兽的一个内含子缺失分别留下了6个和3个核苷酸，这表明它们是由于基因组缺失而丢失的。与哺乳动物相比，这种内含子的丢失可能是河豚基因组中DNA缺失率更高的结果。与河豚相比，四齿鲨的世代时间较短，而河豚体内转座因子的多样性和活性高于哺乳动物，这可能是四齿鲨内含子丢失率较高的原因。我们的研究结果表明，在最近的进化过程中，河豚鱼和哺乳动物的内含子转换总体上很少发生，而内含子获得在脊椎动物进化中是极其罕见的事件。
We have investigated intron evolution in the compact genomes of 2 closely related species of pufferfishes, Fugu rubripes and Tetraodon nigroviridis, that diverged about 32 million years ago (MYA). Analysis of 148,028 aligned intron positions in 13,547 gene pairs using human as an outgroup identified 57 and 24 intron losses in Tetraodon and fugu lineages, respectively, and no gain in either lineage. For comparison, we analyzed 144,545 intron positions in 12,866 orthologous pairs of genes in human and mouse that diverged about 61 MYA using dog as an outgroup and identified 51 intron losses in mouse and 3 losses in human and no gain. The rate of intron loss in Tetraodon is higher than that in fugu, mouse, and human but lower than the previous estimates for other eukaryotes. The introns lost in pufferfishes and mammals are significantly shorter than the mean size of introns in the genome. One intron deleted in fugu and another in Tetraodon have left behind 6 and 3 nucleotides, respectively, suggesting that they were lost due to genomic deletions. Such losses of introns are likely to be the result of a higher rate of DNA deletions experienced by the genomes of pufferfishes compared with mammals. The shorter generation time of Tetraodon compared with fugu, and the rich diversity and higher activity of transposable elements in pufferfishes compared with mammals, may be responsible for the higher rate of intron loss in Tetraodon. Our findings indicate that overall very little intron turnover has occurred in pufferfishes and mammals during recent evolution and that intron gain is an extremely rare event in vertebrate evolution.