大口鳒Psettodes erumei线粒体全序列的研究和鲽形目鱼类系统进化分析
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摘要
本研究测定大口鳒(Psettodes erumei)线粒体基因组全序列,其长度为17,315bp,共包含22种tRNA基因、2个rRNA基因、13个蛋白编码基因和2个非编码区。各基因在线粒体上的排列位置,与脊椎动物共有的基因次序相同,其中L链仅编码8个tRNA和ND6基因。
分析大口鳒基因组及各基因片段的碱基组成,整体来说A+T的含量大于G+C。tRNA和rRNA基因碱基组成偏倚较小,蛋白质编码基因呈现显著的反G偏倚,且主要表现在第三个密码子上。以L链为计算标准GC-skew=-0.32,AT-skew=0.08,符合脊椎动物的GC偏倚。
分析大口鳒各基因的序列特征:tRNA长度变异主要为插入和缺失;蛋白编码基因除COⅠ和COⅢ分别以GTG和CAC为起始密码子外,其余11个基因的起始密码子都为标准起始密码子ATG。终止密码子除TAA、TAG及它们相对应的不完全终止密码子T、TA外,ND1以AGG做为终止密码子,这种现象在鱼类中较少见;22个tRNA中,tRNAscan-SE只识别出21个tRNA的二级结构,tRNA-Set(GCT)则是用软件RNAstructure 4.5识别出其不规则的三叶草结构。在tRNA基因的二级结构中,碱基数目的变异主要存在于DHU环,而非配对碱基对主要存在于接受臂中;分析10中鲽形目鱼类的轻链起始复制区(O_L)的碱基组成和结构,大口鳒的A+T含量最少,仅为16.9%,牙鲆次之为36.5%,而其他种类均高于50%。同时在鲽形目鱼类中,O_L具有典型的“stem-loop”结构,茎区结构较保守。
设计两对引物扩增大口鳒左眼型和右眼型两个个体的控制区序列。两个个体均在5'端存在相同的56bp重复单元,3'端存在相同的8bp重复单元,只是重复数不同;左眼型个体在5'端有三个单倍型,重复次数分别为5.7:7.7;8.7;在3'端有两个单倍型,重复次数分别为8和23。右眼型个体在5'端有三个单倍型,重复次数分别为3.7;7.7;8.7。在3'端有两个单倍型,重复次数分别为6和25。同时通过与其它鲽形目鱼类比较,标识出大口鳒控制区结构:终止相关序列(TAS)、中央保守区序列(CSB-F、CSB-E、CSB-D),保守序列区序列(CSB-1、CSB-2、CSB-3)。比较8种鲽形目鱼类控制区全序列和只含有单拷贝重复单元的控制区碱基组成,结果显示前者的种间差异明显大于后者,变异系数约是后者的两倍。两者的差异是由于不同种类重复单元的碱基组成、长度及拷贝数不同。
建立两套系统树,其一为基于控制区部分序列,用BI法和ML法分析,对鲽形目12种鱼类进行系统分析,以鲈形目甲若鲹作为外类群。结果表明:在鲽形目内部大口鳒分类地位最原始;鲽亚目先与鳎亚目聚在一起,后与鳒亚目聚在一起,这与形态特征相符。
其二为基于mtDNA基因组(控制区除外),用BI法和ML法分析,构建鲽形目系统进化树,种类的选取包含10种鲽形目鱼类和其他与鲽形目进化关系较近30种鱼类,并以鲱形目(远东拟沙丁鱼和太平洋鲱)作为外类群。用DAMBE软件计算平均碱基含量为A 27.6%;C 29.4%,G 16.8%;T 26.2%,转换(Ts)/颠换(Tv)=1.18。系统树结果表明(1)大口鳒处于鲽形目系统分化的最原始位置,和其他学者研究的结果完全一致。大口鳒分类地位的确立,为今后研究鲽形目系统起源至关重要。(2)鲈形目在系统分类中别分为3、4个类群,鲽形目只和鲹科鱼类(鲈形目-Ⅰ)形成姐妹群,和鲈形目的其它类群关系较远。(3)本文虽选取的鲽形目种类很少,但是在目前的水平来看,仍支持鲽形目是单系起源的说法。
Amplified the mitochondrial(mt) genome of P.erumei.The whole sequence was 17,315bp.It contained 22 transfer RNA genes(tRNA),2 ribosomal RNA genes (rRNA),13 protein-coding,genes,2 dominating non-coding regions.Most genes were encoded by the H-strand,except for ND6 and eight tRNA genes.Organization of P. erumei was the same as the typical vertebrate arrangement.
Nucleotide composition in mtDNA genome of P.erumei were A 27.8%,T 23.9%,G 16.3%,C 2.1%,A+T 51.7%,a strong bias against the use of'G'.GC-skew =-0.32,AT-skew=0.08,which were typical in vertebrates.P.erumei mt genome protein-coding genes used ATG as the initiation codons with the only exception of COⅠand COⅢ,which used GTG and CAC.Stop codons included TAA,TAG,TGG and incomplete stop codons T or TA.The base composition of Light-strand replication(O_L)exhibited unsimilarity to the corresponding region in the other flatfishes.The A+T of O_L of P.erumei was only 20.5%,this was much lower than 36.5%(Palichthys olivaceus) and other flatfishes(more than 50%).In flatfishes the secondary structure of O_L consisted of a conserve stem(TTCCC~*GCCT/ AAGGG~*CGGA) and loop structure.
Designed two primer pairs L-Pro/HLOOP and eru21/CX4 divided control region into 5' end and 3' end.There were 56bp tandemly repeated sequence in the 5' end and 8bp tandemly repeated sequence in the 3'end respectively.The 5'end in eyes sinistral specimen had three different clongs,the number copies were 8.7,7.7,5.7.And 3'end has two different clongs,the number copie were 8 and 23.The control region in eyes dextra specimen had three kinds of clongs in 5'end,the number copies were 7.7;8.7;3.7,there were two clongs in 3'end,the number copies 6 and 25.It also exhibited the typical tripartite structure with a central domain and two adjacent variable domains(ETAS and CSB).All blocks of conserved sequences,TAS, CSB-D,E,F,CSB-1,2,3could be identified.The difference of base composition of complete CR sequences was greater than that of CR sequence excluding the repeated regions in nine species of flatfishes,and the variation coefficient of the former was about twice of the latter,which was mainly due to the sequences variation in base composition,length and copy numbers of repeated regions.
Phylogenetic analysed of flatfishes with the Bayesian and ML method based on mtDNA genome(without CR) and CR.On both trees,P.erumei was the lowest group in the flatfishes,this was the same as morphological data.So maked sure evolutionary position of the P.erumei in flatfishes was very importantly to discuss the original of flatfishes in the future.At our level,the result considered that the hypothesis of monophyletic of flatfishes was stands,From our study it seemed to us that flatfishes's sister group was Carangidae(Perciformes-Ⅰ) with a high bootstrap support value.
分析大口鳒基因组及各基因片段的碱基组成,整体来说A+T的含量大于G+C。tRNA和rRNA基因碱基组成偏倚较小,蛋白质编码基因呈现显著的反G偏倚,且主要表现在第三个密码子上。以L链为计算标准GC-skew=-0.32,AT-skew=0.08,符合脊椎动物的GC偏倚。
分析大口鳒各基因的序列特征:tRNA长度变异主要为插入和缺失;蛋白编码基因除COⅠ和COⅢ分别以GTG和CAC为起始密码子外,其余11个基因的起始密码子都为标准起始密码子ATG。终止密码子除TAA、TAG及它们相对应的不完全终止密码子T、TA外,ND1以AGG做为终止密码子,这种现象在鱼类中较少见;22个tRNA中,tRNAscan-SE只识别出21个tRNA的二级结构,tRNA-Set(GCT)则是用软件RNAstructure 4.5识别出其不规则的三叶草结构。在tRNA基因的二级结构中,碱基数目的变异主要存在于DHU环,而非配对碱基对主要存在于接受臂中;分析10中鲽形目鱼类的轻链起始复制区(O_L)的碱基组成和结构,大口鳒的A+T含量最少,仅为16.9%,牙鲆次之为36.5%,而其他种类均高于50%。同时在鲽形目鱼类中,O_L具有典型的“stem-loop”结构,茎区结构较保守。
设计两对引物扩增大口鳒左眼型和右眼型两个个体的控制区序列。两个个体均在5'端存在相同的56bp重复单元,3'端存在相同的8bp重复单元,只是重复数不同;左眼型个体在5'端有三个单倍型,重复次数分别为5.7:7.7;8.7;在3'端有两个单倍型,重复次数分别为8和23。右眼型个体在5'端有三个单倍型,重复次数分别为3.7;7.7;8.7。在3'端有两个单倍型,重复次数分别为6和25。同时通过与其它鲽形目鱼类比较,标识出大口鳒控制区结构:终止相关序列(TAS)、中央保守区序列(CSB-F、CSB-E、CSB-D),保守序列区序列(CSB-1、CSB-2、CSB-3)。比较8种鲽形目鱼类控制区全序列和只含有单拷贝重复单元的控制区碱基组成,结果显示前者的种间差异明显大于后者,变异系数约是后者的两倍。两者的差异是由于不同种类重复单元的碱基组成、长度及拷贝数不同。
建立两套系统树,其一为基于控制区部分序列,用BI法和ML法分析,对鲽形目12种鱼类进行系统分析,以鲈形目甲若鲹作为外类群。结果表明:在鲽形目内部大口鳒分类地位最原始;鲽亚目先与鳎亚目聚在一起,后与鳒亚目聚在一起,这与形态特征相符。
其二为基于mtDNA基因组(控制区除外),用BI法和ML法分析,构建鲽形目系统进化树,种类的选取包含10种鲽形目鱼类和其他与鲽形目进化关系较近30种鱼类,并以鲱形目(远东拟沙丁鱼和太平洋鲱)作为外类群。用DAMBE软件计算平均碱基含量为A 27.6%;C 29.4%,G 16.8%;T 26.2%,转换(Ts)/颠换(Tv)=1.18。系统树结果表明(1)大口鳒处于鲽形目系统分化的最原始位置,和其他学者研究的结果完全一致。大口鳒分类地位的确立,为今后研究鲽形目系统起源至关重要。(2)鲈形目在系统分类中别分为3、4个类群,鲽形目只和鲹科鱼类(鲈形目-Ⅰ)形成姐妹群,和鲈形目的其它类群关系较远。(3)本文虽选取的鲽形目种类很少,但是在目前的水平来看,仍支持鲽形目是单系起源的说法。
Amplified the mitochondrial(mt) genome of P.erumei.The whole sequence was 17,315bp.It contained 22 transfer RNA genes(tRNA),2 ribosomal RNA genes (rRNA),13 protein-coding,genes,2 dominating non-coding regions.Most genes were encoded by the H-strand,except for ND6 and eight tRNA genes.Organization of P. erumei was the same as the typical vertebrate arrangement.
Nucleotide composition in mtDNA genome of P.erumei were A 27.8%,T 23.9%,G 16.3%,C 2.1%,A+T 51.7%,a strong bias against the use of'G'.GC-skew =-0.32,AT-skew=0.08,which were typical in vertebrates.P.erumei mt genome protein-coding genes used ATG as the initiation codons with the only exception of COⅠand COⅢ,which used GTG and CAC.Stop codons included TAA,TAG,TGG and incomplete stop codons T or TA.The base composition of Light-strand replication(O_L)exhibited unsimilarity to the corresponding region in the other flatfishes.The A+T of O_L of P.erumei was only 20.5%,this was much lower than 36.5%(Palichthys olivaceus) and other flatfishes(more than 50%).In flatfishes the secondary structure of O_L consisted of a conserve stem(TTCCC~*GCCT/ AAGGG~*CGGA) and loop structure.
Designed two primer pairs L-Pro/HLOOP and eru21/CX4 divided control region into 5' end and 3' end.There were 56bp tandemly repeated sequence in the 5' end and 8bp tandemly repeated sequence in the 3'end respectively.The 5'end in eyes sinistral specimen had three different clongs,the number copies were 8.7,7.7,5.7.And 3'end has two different clongs,the number copie were 8 and 23.The control region in eyes dextra specimen had three kinds of clongs in 5'end,the number copies were 7.7;8.7;3.7,there were two clongs in 3'end,the number copies 6 and 25.It also exhibited the typical tripartite structure with a central domain and two adjacent variable domains(ETAS and CSB).All blocks of conserved sequences,TAS, CSB-D,E,F,CSB-1,2,3could be identified.The difference of base composition of complete CR sequences was greater than that of CR sequence excluding the repeated regions in nine species of flatfishes,and the variation coefficient of the former was about twice of the latter,which was mainly due to the sequences variation in base composition,length and copy numbers of repeated regions.
Phylogenetic analysed of flatfishes with the Bayesian and ML method based on mtDNA genome(without CR) and CR.On both trees,P.erumei was the lowest group in the flatfishes,this was the same as morphological data.So maked sure evolutionary position of the P.erumei in flatfishes was very importantly to discuss the original of flatfishes in the future.At our level,the result considered that the hypothesis of monophyletic of flatfishes was stands,From our study it seemed to us that flatfishes's sister group was Carangidae(Perciformes-Ⅰ) with a high bootstrap support value.
引文
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