从野桑蚕到家蚕的基因突变与人工选择初步研究
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摘要
进化论研究的核心是描述生物进化的历史和探索进化过程的机制。自本世纪中叶以来，随着分子生物学的不断发展，进化论的研究也进入了分子水平。分子进化是达尔文进化论在分子水平上的延伸。分子进化一方面研究生命起源，另一方面研究天然化合物的生物合成途径，揭示通过DNA、RNA、糖和蛋白质等生物大分子的突变和选择来改变生物表型和性状进化的分子机制。当前分子进化的研究已是进化论研究的重要手段，并建立了一套依赖于核酸、蛋白质序列信息的理论方法。
过去十年中，基因组序列飞速积累，基因组学的研究手段也得到了进一步发展。这些都为进化学的研究了必要的条件，也催生了进化基因组学这门新生的交叉学科。进化基因组学的一个重要的研究内容就是以进化生物学的手段在基因组水平理解生物学的功能和生命现象。如比较不同物种的基因组或表达组，发现新的功能基因或结构，理解功能的遗传学基础。
近年来，以进化基因组学的观点来检测DNA编码区的进化选择受到了越来越多的关注。其中最常用的检测蛋白质编码区域的正选择的标准就是比较同义替换和非同义替换率。基因或密码子的进化压力可以通过比较同义替换率和非同义替换率来检测。同义替换率大于非同义替换率被认为是正选择的证据。
对于特定类群的编码蛋白质基因而言，根据密码子水平上的非同义替换率和同义替换率的比值ω=Ka／Ks，相应位点可以分为三类，即：负选择位点(ω＜1)、中性位点(ω=1)和正选择位点(ω＞1)。其中，中性位点的替换基本不影响蛋白质结构功能，因此不受选择作用。负选择位点对于维持蛋白质的正常结构具有关键作用，很难在被替代的情况下维持正常功能，因此受到负选择(削弱)，该位点的氨基酸替代速率ω很低；正选择能够赋予蛋白质新的结构或功能，有利于个体的生存和繁殖，因此受到正选择(加强)，该位点的氨基酸替代速率很高。正、负选择位点的检测和识别对于理解蛋白质的结构和功能具有重要意义。
家蚕起源于中国野桑蚕。家蚕与野桑蚕血缘亲近，野桑蚕作为丰富的野生蚕业资源，是可开发利用的宝贵基因库资源，同时也是研究家蚕分子进化的重要材料。几年来，随着分子生物学的发展，有关野桑蚕及家蚕的进化学研究也取得了许多进展，但大都围绕分子系统学的问题展开，探讨家蚕的起源问题。鲜有对进化选择的报道。因此，本研究利用现有的家蚕和野桑蚕的基因组数据和EST数据，用生物信息学的方法分析两者的进化选择关系，获得了一些初步的结论。
我们从整个家蚕基因组及野桑蚕EST数据中共筛选出343个直系同源基因(orthologous
gone)片段进行分析，同时选取黑腹果蝇(Drosophila melanogaster)和拟果蝇(Drosophila
simulans)作为对照，用同样的方法从果蝇中筛选出1328个直系同源基因。研究发现家蚕与野桑蚕的直系同源基因的Ka／Ks值与果蝇相比要高，显著偏大，而且无论是从均值或从分布上都呈现出同样的趋势，推测可能是强烈的人工选择导致的家蚕的进化比果蝇快。从表达组织上
The core of the evolution research is to describe the evolution history of the species and discover the mechanism of the process of evolution. Since the middle of this century, Molecular Biology developed fast, and the research of evolution has upgraded into the molecular level. On one side, the molecular research studies the origin of the lives; on the other side, it studies the synthesis mechanism of the natural chemical, to explain how the species' phenotype and traits changed via the changes of the DNA, RNA, protein and carbohydrate, and set up a series of theories and methods based on sequence information of nucleotides and proteins.
In the last decade, the genome sequences developed quickly, so are the research methods of genomics. They provide necessary conditions for evolution research, and also, fasten the development of the new interdisciplinary of genomics. One of the important research fields of evolution genomics is the evolution genomics.
The bloods relationship of the silkworm and wild silkworm is on intimate terms. As an abundant wild sericultural resource, wild silkworm is a treasure with much potential to exploit and also be used as an important material for the evolution on the origin of silkworm. These years, with the development of molecular biology, the evolution research related to Bombyx mandarina and Bombyx Mori has got much progress; however, most of the results are focused on Molecular Systematics. Few reports are related to artificial selection. So, in this investigation, based on the genome data of Bombyx mori and the EST data of Bombyx mandarina, we did some comparison and analyse.
We selected 343 orthologs from the genome of Bombyx mori and EST of Bombyx mandaina. In order to do comparable analysis, we also select 1328 orthologs from Drosophila melanogaster and Drosophila simulans. Via genomics analysis, we found the value of Ka/Ks of bombyx is higher than drosophila, and the difference is significant. No matter caring about the median or the distribution, the data always tells the same thing. We consider it should due to the intensively artificial selection, which lead to the fast evolution speed of the Bombyx..
Refer to the expression level, we studied the genes expressing specifically in one tissue. We found that the genes expressing specifically in the silk grand have much higher Ka/Ks. It may due to the artificial selection on the silk excreting by bombyx which made the genes expressing specifically in silk grand suffered a greater selection pressure. As a result, these genes have a higher evolution speed.
过去十年中，基因组序列飞速积累，基因组学的研究手段也得到了进一步发展。这些都为进化学的研究了必要的条件，也催生了进化基因组学这门新生的交叉学科。进化基因组学的一个重要的研究内容就是以进化生物学的手段在基因组水平理解生物学的功能和生命现象。如比较不同物种的基因组或表达组，发现新的功能基因或结构，理解功能的遗传学基础。
近年来，以进化基因组学的观点来检测DNA编码区的进化选择受到了越来越多的关注。其中最常用的检测蛋白质编码区域的正选择的标准就是比较同义替换和非同义替换率。基因或密码子的进化压力可以通过比较同义替换率和非同义替换率来检测。同义替换率大于非同义替换率被认为是正选择的证据。
对于特定类群的编码蛋白质基因而言，根据密码子水平上的非同义替换率和同义替换率的比值ω=Ka／Ks，相应位点可以分为三类，即：负选择位点(ω＜1)、中性位点(ω=1)和正选择位点(ω＞1)。其中，中性位点的替换基本不影响蛋白质结构功能，因此不受选择作用。负选择位点对于维持蛋白质的正常结构具有关键作用，很难在被替代的情况下维持正常功能，因此受到负选择(削弱)，该位点的氨基酸替代速率ω很低；正选择能够赋予蛋白质新的结构或功能，有利于个体的生存和繁殖，因此受到正选择(加强)，该位点的氨基酸替代速率很高。正、负选择位点的检测和识别对于理解蛋白质的结构和功能具有重要意义。
家蚕起源于中国野桑蚕。家蚕与野桑蚕血缘亲近，野桑蚕作为丰富的野生蚕业资源，是可开发利用的宝贵基因库资源，同时也是研究家蚕分子进化的重要材料。几年来，随着分子生物学的发展，有关野桑蚕及家蚕的进化学研究也取得了许多进展，但大都围绕分子系统学的问题展开，探讨家蚕的起源问题。鲜有对进化选择的报道。因此，本研究利用现有的家蚕和野桑蚕的基因组数据和EST数据，用生物信息学的方法分析两者的进化选择关系，获得了一些初步的结论。
我们从整个家蚕基因组及野桑蚕EST数据中共筛选出343个直系同源基因(orthologous
gone)片段进行分析，同时选取黑腹果蝇(Drosophila melanogaster)和拟果蝇(Drosophila
simulans)作为对照，用同样的方法从果蝇中筛选出1328个直系同源基因。研究发现家蚕与野桑蚕的直系同源基因的Ka／Ks值与果蝇相比要高，显著偏大，而且无论是从均值或从分布上都呈现出同样的趋势，推测可能是强烈的人工选择导致的家蚕的进化比果蝇快。从表达组织上
The core of the evolution research is to describe the evolution history of the species and discover the mechanism of the process of evolution. Since the middle of this century, Molecular Biology developed fast, and the research of evolution has upgraded into the molecular level. On one side, the molecular research studies the origin of the lives; on the other side, it studies the synthesis mechanism of the natural chemical, to explain how the species' phenotype and traits changed via the changes of the DNA, RNA, protein and carbohydrate, and set up a series of theories and methods based on sequence information of nucleotides and proteins.
In the last decade, the genome sequences developed quickly, so are the research methods of genomics. They provide necessary conditions for evolution research, and also, fasten the development of the new interdisciplinary of genomics. One of the important research fields of evolution genomics is the evolution genomics.
The bloods relationship of the silkworm and wild silkworm is on intimate terms. As an abundant wild sericultural resource, wild silkworm is a treasure with much potential to exploit and also be used as an important material for the evolution on the origin of silkworm. These years, with the development of molecular biology, the evolution research related to Bombyx mandarina and Bombyx Mori has got much progress; however, most of the results are focused on Molecular Systematics. Few reports are related to artificial selection. So, in this investigation, based on the genome data of Bombyx mori and the EST data of Bombyx mandarina, we did some comparison and analyse.
We selected 343 orthologs from the genome of Bombyx mori and EST of Bombyx mandaina. In order to do comparable analysis, we also select 1328 orthologs from Drosophila melanogaster and Drosophila simulans. Via genomics analysis, we found the value of Ka/Ks of bombyx is higher than drosophila, and the difference is significant. No matter caring about the median or the distribution, the data always tells the same thing. We consider it should due to the intensively artificial selection, which lead to the fast evolution speed of the Bombyx..
Refer to the expression level, we studied the genes expressing specifically in one tissue. We found that the genes expressing specifically in the silk grand have much higher Ka/Ks. It may due to the artificial selection on the silk excreting by bombyx which made the genes expressing specifically in silk grand suffered a greater selection pressure. As a result, these genes have a higher evolution speed.
引文
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[2] Kimura, M. Evolutionary rate at the molecular level. Nature, 1968, 217: 624~626
[3] JL King, TH Jukes. Non-Darwinian evolution: random fixation of selectively neutral mutation s. Science, 1969, 164: 788~798
[5] 吕宝忠．王健，王顺德．从中性学说到非线性分子进化．自然杂志，1998，20(3)：163~167．
[6] Duty, GH. Neocatastrophism? A further look. Progress in Physical Geography 4, 1980, 391~413
[7] Gould, S. J. Punctuated equilibrium in fact and theory. Journal of Social Biological Structure, 1989, 12: 117~136
[8] H. Haken, Synergetics-An Introduction Nonequilibrium Phase Transitions & Self-Organization in Physics, Chemistry, and Biology. Berlin: Springer-Verlag, 1977
[9] Marc Kirschner, John Gerhart. Evolvability. Proceedings of the National Academy of Sciences of the United States of America, Vol. 95, No. 15: 8420~8427
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