五种螽蟖线粒体基因组的测定与直翅目谱系基因组学分析
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摘要
通过L-PCR结合二次嵌套PCR技术对5种螽蟖总科昆虫的线粒体基因组进行全序列测定,并联合NCBI中收录的和本研究小组其他成员所测定的直翅目昆虫线粒体基因组全序列,研究了直翅目主要类群之间的系统发育关系。获得的主要结果如下:
1.5种螽蟖总科昆虫,分别为疑钩额螽(Ruspolia dubia)、斑翅草螽(Conocephalusmaculates)、优雅蝈螽(Gampsocleis gratiosa)、北方棘螽(Deracantha onos)和陈氏掩耳螽(Elimaea cheni),与其它已发表的螽亚目昆虫的线粒体基因组,如:东方蝼蛄(Gryllotalpaorientalis)和摩门螽蟖(Anabrus simplex)拥有相同的基因次序。即其trnK和trnD的相对位置与已报道蝗亚目昆虫非洲飞蝗(Locusta migratoria migratoiodes)、短额负蝗(Atractomorphasinensis)和中华稻蝗(Oxya chinensis)相反,这表明trnK和trnD转位可能仅是蝗亚目昆虫的线粒体基因组基因排序特征。
2.斑翅草螽线粒体基因组中,除A+T丰富区以外,在trnS~(UCN)和nad1,nad1和trnL~(CUN)之间分别存在长度为78 bp和354 bp的基因间隔序列。
3.疑钩额螽线粒体基因组的A+T丰富区长度仅70 bp,是目前已报道的六足动物最短的A+T丰富区。
4.疑钩额螽和陈氏掩耳螽线粒体基因组的cox1均以罕见的TTA作为起始密码子。
5.5种螽蟖线粒体基因组的nad5均以不完全的终止密码子T作为终止信号。
6.线粒体基因组中同义密码子的使用与密码子第三位点的碱基组成紧密相关,而与基因组所编码的tRNA反密码子匹配情况关系不大,通常,密码子弟三位点为A/T的密码子使用频次高于G/C的密码子。
7.5种螽蟖线粒体基因组的tRNA二级结构均存在一定数量的碱基错配,且均以G-U弱配对为主,这可能暗示在线粒体基因组中G-U配对是一种正常的配对形式。
8.陈氏掩耳螽线粒体基因组中,A+T丰富区的A+T含量为70.6%,这一数值在基因组的各个组分中最低;在疑钩额螽和优雅蝈螽中,A+T丰富区的A+T含量(71.4%和67.4%)也仅略高于线粒体基因组全序列(70.8%和65.3%)和蛋白质编码基因(69.8%和63.5%)。这种现象在其他已报道的六足动物线粒体基因组全序列中同样存在,这可能暗示在六足动物中,高A+T含量并不是A+T丰富区的必要特征。
9.在斑翅草螽、优雅蝈螽和北方棘螽线粒体基因组A+T丰富区的J链和N链上均有连续的T簇分布,类似的结构在果蝇等全变态类昆虫中被认为是线粒体基因组复制的调控信号。
10.通过对30种直翅目昆虫线粒体谱系基因组学研究支持将直翅目划分为螽亚目和蝗亚目两支。螽亚目内部分支的拓扑结构比较稳定,分为三个分支:即由8种螽蟖总科昆虫形成的第一分支,由3种蟋蟀总科昆虫形成的第二小支,和由东方蝼蛄单独形成的第三小支,三个小支间的关系为(螽蟖总科,(蟋蟀总科,蝼蛄总科))。螽蟖总科内部的分支形式也基本可以确定,分支关系为((螽蟖科,硕螽科),(草螽科,露螽科))。蝗亚目分支内部差异较大,不过有以下几点基本可以确定:1)瘤锥蝗科、锥头蝗科和蚤蝼总科聚为一个与其它蝗总科昆虫平行的单系支。2)网翅蝗科、剑角蝗科、斑翅蝗科和斑腿蝗科的单系性都不被支持。3)网翅蝗科和剑角蝗科昆虫交替聚为一支,并形成较大的分支。
The complete mitochondrial genome(mitogenome) sequences for five species from Tettigonioidea,Ruspolia dubia,Conocephalus maculates,Gampsocleis gratiosa,Deracantha onos, and Elimaea cheni,were sequenced,assemblied,annotated,and compared with other known insect mitogenomes.An array of phylogenetic and phylogenomic techniques were used to infer the phylogenetic relationships among 30 orthopteran insects.Conclusions were showed below:
1.The gene arrangement of R.dubia,C.maculates,G gratiosa,D.onos,and E.cheni mitogenome is identical to that of Gryllotalpa orientalis,Anabrus simplex and Drosophila yakuba, which implying that the translocation from trnK-trnD to trnD-trnK occurring only in the suborder Caelifera.
2.The presence of 78 bp and 354 bp long intergenic spacer located between trnS~(UCN) and nadl,nadl and trnL~(CUN) is unique in the C.maculates mitogenome.
3.The length of A+T-rich region in the R.dubia mitogenome was determined to be 70 bp, which was the shortest among Hexapoda.
4.The putative initiation codon for coxl appears to be TTA in the R.dubia and E.cheni mitogenome.
5.All nad5 have incomplete termination codon(T) in the R.dubia,C.maculates,G. gratiosa,D.onos,and E.cheni mitogenome.
6.The usage of synonymous codon markedly correlated with the nucleotide composition at third codon position,and not the anticodon of tRNA in the mitogenome.Generally,the usage of codon that is A/T at the third codon position is higher than G/C.
7.Some unmatched base pairs occur in the R.dubia,C.maculates,G gratiosa,D.onos and E.cheni tRNAs,and overwhelming majority of them are G-U pairs.
8.The A+T content of the A+T-rich region was 70.6%,this value is lower than other regions in the E.cheni mitogenome.These values(71.4%and 67.4%) are slightly higher than the whole mitogenome and PCGs in the R.dubia and G gratiosa.This phenomenon indicated that the highly A+T content is not essential to A+T-rich region.
9.T-stretch was found on the J and N strand of A+T-rich region in the C.maculates,G gratiosa and D.onos mitogenome,which is involved in the recognition of the O_R of mtDNA at least among holometabolous insects.
10.Phylogenetic analysis confirmed a monophyletic Ensifera and Caelifera.Based on the comprehensive tree topologies,we can conclude that:1) the monophyly of Tettigonioidea, Grylloidea and Gryllotalpoidea was confirmed,and Grylloidea has a close relationship with Gryllotalpoidea than Tettigonioidea;2) the monophyly of Tettigoniidae was confirmed,and Tettigoniidae has a close relationship with Bradyporidae;3) there is disagreement in the monophyly of Conocephalidae,and additional samples or other molecular markers are needed to get further proof;4) the monophyly of Acridoidea was not supported;5) Chrotogonidae and Pyrgomorphidae has a close relationship with Tridactyloidea than other Acridoidea insects;6) the monophyly of Arcypteridae,Oedipodidae,Catantopidae and Acrididae was not be supported.
1.5种螽蟖总科昆虫,分别为疑钩额螽(Ruspolia dubia)、斑翅草螽(Conocephalusmaculates)、优雅蝈螽(Gampsocleis gratiosa)、北方棘螽(Deracantha onos)和陈氏掩耳螽(Elimaea cheni),与其它已发表的螽亚目昆虫的线粒体基因组,如:东方蝼蛄(Gryllotalpaorientalis)和摩门螽蟖(Anabrus simplex)拥有相同的基因次序。即其trnK和trnD的相对位置与已报道蝗亚目昆虫非洲飞蝗(Locusta migratoria migratoiodes)、短额负蝗(Atractomorphasinensis)和中华稻蝗(Oxya chinensis)相反,这表明trnK和trnD转位可能仅是蝗亚目昆虫的线粒体基因组基因排序特征。
2.斑翅草螽线粒体基因组中,除A+T丰富区以外,在trnS~(UCN)和nad1,nad1和trnL~(CUN)之间分别存在长度为78 bp和354 bp的基因间隔序列。
3.疑钩额螽线粒体基因组的A+T丰富区长度仅70 bp,是目前已报道的六足动物最短的A+T丰富区。
4.疑钩额螽和陈氏掩耳螽线粒体基因组的cox1均以罕见的TTA作为起始密码子。
5.5种螽蟖线粒体基因组的nad5均以不完全的终止密码子T作为终止信号。
6.线粒体基因组中同义密码子的使用与密码子第三位点的碱基组成紧密相关,而与基因组所编码的tRNA反密码子匹配情况关系不大,通常,密码子弟三位点为A/T的密码子使用频次高于G/C的密码子。
7.5种螽蟖线粒体基因组的tRNA二级结构均存在一定数量的碱基错配,且均以G-U弱配对为主,这可能暗示在线粒体基因组中G-U配对是一种正常的配对形式。
8.陈氏掩耳螽线粒体基因组中,A+T丰富区的A+T含量为70.6%,这一数值在基因组的各个组分中最低;在疑钩额螽和优雅蝈螽中,A+T丰富区的A+T含量(71.4%和67.4%)也仅略高于线粒体基因组全序列(70.8%和65.3%)和蛋白质编码基因(69.8%和63.5%)。这种现象在其他已报道的六足动物线粒体基因组全序列中同样存在,这可能暗示在六足动物中,高A+T含量并不是A+T丰富区的必要特征。
9.在斑翅草螽、优雅蝈螽和北方棘螽线粒体基因组A+T丰富区的J链和N链上均有连续的T簇分布,类似的结构在果蝇等全变态类昆虫中被认为是线粒体基因组复制的调控信号。
10.通过对30种直翅目昆虫线粒体谱系基因组学研究支持将直翅目划分为螽亚目和蝗亚目两支。螽亚目内部分支的拓扑结构比较稳定,分为三个分支:即由8种螽蟖总科昆虫形成的第一分支,由3种蟋蟀总科昆虫形成的第二小支,和由东方蝼蛄单独形成的第三小支,三个小支间的关系为(螽蟖总科,(蟋蟀总科,蝼蛄总科))。螽蟖总科内部的分支形式也基本可以确定,分支关系为((螽蟖科,硕螽科),(草螽科,露螽科))。蝗亚目分支内部差异较大,不过有以下几点基本可以确定:1)瘤锥蝗科、锥头蝗科和蚤蝼总科聚为一个与其它蝗总科昆虫平行的单系支。2)网翅蝗科、剑角蝗科、斑翅蝗科和斑腿蝗科的单系性都不被支持。3)网翅蝗科和剑角蝗科昆虫交替聚为一支,并形成较大的分支。
The complete mitochondrial genome(mitogenome) sequences for five species from Tettigonioidea,Ruspolia dubia,Conocephalus maculates,Gampsocleis gratiosa,Deracantha onos, and Elimaea cheni,were sequenced,assemblied,annotated,and compared with other known insect mitogenomes.An array of phylogenetic and phylogenomic techniques were used to infer the phylogenetic relationships among 30 orthopteran insects.Conclusions were showed below:
1.The gene arrangement of R.dubia,C.maculates,G gratiosa,D.onos,and E.cheni mitogenome is identical to that of Gryllotalpa orientalis,Anabrus simplex and Drosophila yakuba, which implying that the translocation from trnK-trnD to trnD-trnK occurring only in the suborder Caelifera.
2.The presence of 78 bp and 354 bp long intergenic spacer located between trnS~(UCN) and nadl,nadl and trnL~(CUN) is unique in the C.maculates mitogenome.
3.The length of A+T-rich region in the R.dubia mitogenome was determined to be 70 bp, which was the shortest among Hexapoda.
4.The putative initiation codon for coxl appears to be TTA in the R.dubia and E.cheni mitogenome.
5.All nad5 have incomplete termination codon(T) in the R.dubia,C.maculates,G. gratiosa,D.onos,and E.cheni mitogenome.
6.The usage of synonymous codon markedly correlated with the nucleotide composition at third codon position,and not the anticodon of tRNA in the mitogenome.Generally,the usage of codon that is A/T at the third codon position is higher than G/C.
7.Some unmatched base pairs occur in the R.dubia,C.maculates,G gratiosa,D.onos and E.cheni tRNAs,and overwhelming majority of them are G-U pairs.
8.The A+T content of the A+T-rich region was 70.6%,this value is lower than other regions in the E.cheni mitogenome.These values(71.4%and 67.4%) are slightly higher than the whole mitogenome and PCGs in the R.dubia and G gratiosa.This phenomenon indicated that the highly A+T content is not essential to A+T-rich region.
9.T-stretch was found on the J and N strand of A+T-rich region in the C.maculates,G gratiosa and D.onos mitogenome,which is involved in the recognition of the O_R of mtDNA at least among holometabolous insects.
10.Phylogenetic analysis confirmed a monophyletic Ensifera and Caelifera.Based on the comprehensive tree topologies,we can conclude that:1) the monophyly of Tettigonioidea, Grylloidea and Gryllotalpoidea was confirmed,and Grylloidea has a close relationship with Gryllotalpoidea than Tettigonioidea;2) the monophyly of Tettigoniidae was confirmed,and Tettigoniidae has a close relationship with Bradyporidae;3) there is disagreement in the monophyly of Conocephalidae,and additional samples or other molecular markers are needed to get further proof;4) the monophyly of Acridoidea was not supported;5) Chrotogonidae and Pyrgomorphidae has a close relationship with Tridactyloidea than other Acridoidea insects;6) the monophyly of Arcypteridae,Oedipodidae,Catantopidae and Acrididae was not be supported.
引文
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