Extent of gene duplication in the genomes of Drosophila, nematode, and yeast
Extent of gene duplication in the genomes of Drosophila, nematode, and yeast
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DOI：
10.1093/oxfordjournals.molbev.a004079
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发表时间：
2002-03-01
影响因子：
10.7
通讯作者：
Li, WH
中科院分区：
文献类型：
--
作者：
Gu, ZL;Cavalcanti, A;Li, WH
我们对三个完整基因组中的重复基因进行了详细分析：酵母、果蝇和秀丽隐杆线虫。对于属于同一家族的两个蛋白质，我们使用标准 (1) 它们的相似性大于或等于 1（如果 L 大于或等于 150 个氨基酸，则 1 = 30%，并且如果 L < 150 个氨基酸，则 I = 0.01n + 4.8L(-0.321) (exp)。其中 n = 6，L 是可对齐区域的长度），以及 (2) 两个蛋白质之间的可对齐区域的长度两个序列大于或等于 对于 80% 的较长蛋白质，我们发现删除同种型（由选择性剪接引起）非常重要。相同的基因具有不同的名称。以及源自重复元素的蛋白质。我们估计酵母中有 Acre 530、674 和 1,219 个蛋白质家族。果蝇。和线虫，分别。因此，正如预期的那样，cast 的重复基因数量最少。然而。对于每个同义位点的取代数 (K-s) < 0.01 的重复对，果蝇只有七对。而野兽有 58 对，线虫有 153 对。在考虑密码子使用偏差和基因线圈版本的可能影响之后。这些数字分别变成了 6、55 和 147。因此。果蝇的年轻重复基因似乎比酵母和线虫要少得多。酵母和线虫中 K-s < 0.01 的大量重复对可能主要是由块重复引起的。好歹。很明显，果蝇的基因组经历了很少的基因复制。在最近的过去，其基因家族比秀丽隐杆线虫少得多。
We conducted a detailed analysis of duplicate genes in three complete genoms: yeast, Drosophila, and Caenorhabditis elegans. For two proteins belonging to the same family we used the criteria ( 1 ) their similarity is greater than or equal to1 ( 1 = 30% if L greater than or equal to 150 a.a. and I = 0.01n + 4.8L(-0.321) (exp) if L < 150 a.a.. where n = 6 and L is the length of the alignable region), and (2) the length of the alignable region between the two sequences is greater than or equal to80% of the longer protein, We found it very important to delete isoforms (caused by alternative splicing). same genes with different names. and proteins derived from repetitive elements. We estimated that there Acre 530, 674, and 1,219 protein families in yeast. Drosophila. and C. elegans, respectively. so, as expected, cast has the smallest number of duplicate genes. However. for the duplicate pairs with the number of substitutions per synonymous site (K-s) < 0.01, Drosophila has only seven pairs. whereas beast has 58 pairs and nematode has 153 pairs. After considering the possible effects of codon usage bias and gene coil version. these numbers became 6, 55, and 147, respectively. Thus. Drosophila appears to have much fewer young duplicate genes than do yeast and nematode. The larger numbers of duplicate pairs with K-s < 0.01 in yeast and C. elegans were probably largely caused by block duplications. At any rate. it is clear that the genome of Drosophila melanogaster has undergone few gene duplications. in the recent past and has much fewer gene families than C. elegans.