四种蝗虫线粒体基因组测序及系统发生分析
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摘要
直翅目是昆虫包括两大类：一类为螽亚目,以螽斯和蟋蟀为代表,其触角长度长于身体的长角型昆虫,另一类为蝗亚目,以蝗虫和蚱为代表,其触角长度短于身体的短角型昆虫。
本研究选择了四种蝗虫进行了全线粒体测序,其中蹦蝗属和小蹦蝗属各一种,分别为贵州蹦蝗和峨眉小蹦蝗,其中根据形态从蹦蝗属中分出的小蹦蝗属能否成立是有争议的,太白秦岭蝗是中国特有属秦岭蝗属代表种类,仅分布于高寒的秦岭山脉。青海屹蝗是网翅蝗科一短翅型物种,在NCBI上提交的5种网翅蝗科物种中只有一种是短翅类型。
本研究采用长距离PCR(聚合酶链式反应)结合二次嵌套PCR技术对蝗总科的4种蝗虫的全线粒体基因组进行了测定,拼接和注释,对四种斑腿蝗科蝗虫峨眉小蹦蝗(Pedopodisma emiensis(Yin)),贵州蹦蝗(Sinopodisma guizhouensis Zheng)和太白秦岭蝗(Qinlinggacris taibiensis Yin et Chou)外,还结合了本实验室所测而未发表的霍山蹦蝗(Sinopodisma houshana)进行了比较基因组分析,对四种网翅蝗科蝗虫青海屹蝗Oreoptygonotus chinghaiensis之外,还结合了NCBI下载的黑膝异爪蝗Euchorthippus fusigeniculatus,中华雏蝗Chorthippus chinensis Tarbinsky和隆额网翅蝗Arcyptera coreana Shiraki的线粒体基因组对网翅蝗科线粒体基因组的一些特性进行了比较基因组分析,并结合NCBI中已收录的和本研究小组其他成员所测定的未公开的共计54种直翅目昆虫线粒体基因组全序列,采用PCGs、 rRNA和全线粒体37基因联合三种数据集用最大简约法,最大似然法和贝叶斯推论法重新构建了直翅目系统树。主要结论如下：
1.四种蝗总科昆虫分别为峨眉小蹦蝗(Pedopodisma emiensis(Yin))、贵州蹦蝗(Sinopodisma guizhouensis Zheng)、太白秦岭蝗(Qinlingacris taibaiensis Yin et Chou)和青海屹蝗(Oreoptygonotus chinghaiensis(Chnget Hang))。线粒体基因组全序列总长度分别为16014bp、16013bp.15631bp和15620bp。四种蝗虫均编码线粒体基因组中典型的37个基因,这37个基因分别为：13个蛋白编码基因,2个核糖体RNA基因和22个转运RNA基因。四种蝗虫线粒体基因排列次序和基因的转录方向同已经发表的蝗亚目昆虫一致。
2.四种蝗虫线粒体基因组碱基组成均具AT偏向性,其中峨眉小蹦蝗(Pedopodisma emiensis(Yin))AT含量为76.5%,贵州蹦蝗(Sinopodisma guizhouensis Zheng)AT含量为76.4%,太白秦岭蝗(Qinlingacris taibaiensis Yin et Chou) AT含量为76.3%,青海屹蝗(Oreoptygonotus chinghaiensis(Cheng et Hang)) AT含量为75.2%。
3.本研究所测定的线粒体基因组的A+T富集区均位于srRNA和trnI之间,长度和A+T含量分别为：峨眉小蹦蝗(Pedopodisma emiensis(Yin))为1123bp和85.8%,贵州蹦蝗(Sinopodisma guizhouensis Zheng)为1127bp和84.8%,太白秦岭蝗(Qinlingacris taibaiensis Yin et Chou)为778bp和88.7%,青海屹蝗(Oreoptygonotus chinghaiensis(Cheng et Hang))为711bp和82.1%。相对于4个主要部分(PCGs, rRNAs, tRNAs, A+T富集区),A+T富集区的AT含量是最高的区域。
4.四种蝗虫各自均具有22个转运RNA基因,核酸保守性具链间偏向性,分布于J链的所有tRNAs比位于N链的所有tRNAs的AT%略偏高。tRNASer(AGN)的DHU臂都存在缺失的现象,其他21个转运RNA均能形成典型的三叶草二级结构。绝大多数tRNA二级结构存在一定数目的错配。在tRNA的二级结构中氨基酸接受臂和反密码子环长度较保守,TψC臂和DHU臂的变异最大。
5.核糖体二级结构预测显示,四种蝗虫16s核糖体基因均不能形成H1臂。
6.斑腿蝗科四个物种线粒体基因组的13个蛋白编码基因中,有11种蛋白编码基因数目完全一致,仅有2种不一致,为cytb和nad3蛋白编码基因。
7.4种斑腿蝗氨基酸序列变异率中,cytb, cox1, cox2, cox3的氨基酸变异率最低(其中cytb的变异率为最低,AVE=0.049), nadl, nad4, nad4L和nad5的氨基酸变异率中等,atp8, nad3, nad2和nad6的氨基酸变异率偏高(其中nad3的变异率为最高,AVE=0.153)。
8.4种斑腿蝗全线粒体mtDNA之间P-距离在贵州蹦蝗-霍山蹦蝗最小,为0.057, PCGs之间P-距离和mtDNA有相似的趋势,也是贵州蹦蝗-霍山蹦蝗最小,为0.056,说明两种蹦蝗在全线粒体mtDNA和PCGs之间差异很小。
9.4种斑腿蝗J-链的T含量均低于N-链,而A和C的含量均为J-链高于N-链。N-链上蛋白质编码基因第3位点显示了极低的G含量,而具有极高的T含量。
10.对PCGs、 rRNA和全线粒体37基因联合三种数据采用最大简约法,最大似然法和贝叶斯推论法重新构建的直翅目系统树,除基于rRNA用BI法所建树之外霍山蹦蝗和贵州蹦蝗均能优先聚成一支,再与峨眉小蹦蝗聚合,并结合形态学观察认为小蹦蝗属是成立的。
Orthoptera insects include two categories:one for the long-horned suborder to katydids and crickets, represented by its long antennae longer than the body angle of insects, the other for a short corner suborder to locust and grasshopper as the representative body of its antennae shorter than the short-corner type insects.
In this study, the mitochondrial DNA of four locusts was fully sequenced, including the genus of Sinopodisma and Pedopodisma. The possibility of establishing of genus Sinopodisma is controversial.
1. The Pedopodisma emiensis(Yin) mt genome was16014bp in size, the Sinopodisma guizhouensis Zheng mt genome was16013bp in size, the Qinlingacris taibaiensis Yin et Chou mt genome was15631bp in size and the Oreoptygonotus chinghaiensis(Cheng et Hang) was15620bp in size. The four mitochondrial genomes contain a identical set of13protein-coding genes,22transfer RNA genes, two ribosomal RNA genes and an A+T-rich region in the same arrangenment and orientation as those of the other analysed caeliferan species.
2. The nucleotide composition all showed A/T bias and the A+T content of four species mitogenomes showed little difference. The A+T content of Pedopodisma emiensis(Yin), Sinopodisma guizhouensis Zheng, Qinlingacris taibaiensis Yin et Chou and Oreoptygonotus chinghaiensis(Cheng et Hang)was76.5%,76.4%,76.3%and75.2%respectively.
3. The AT rich region between srRNA and trnl. The size of AT rich region of Pedopodisma emiensis (Yin), Sinopodisma guizhouensis Zheng, Qinlingacris taibaiensis Yin et Chou and Oreoptygonotus chinghaiensis (Cheng et Hang) was1123bp,1127bp,778bp and711bp. AT content of the AT rich region of Pedopodisma emiensis (Yin), Sinopodisma guizhouensis Zheng, Qinlingacris taibaiensis Yin et Chou and Oreoptygonotus chinghaiensis (Cheng et Hang) was85.8%,84.8%,82.1%and88.7%.
4. Each mitogenomes of four species has22tRNA. The pattern of nucleotide conservation in tRNA genes was majority strand-biased. AT content of tRNAs located on the majority strand were high than tRNAs that located on the minority strand. Each tRNA has the typical cloverleaf secondary structure found in most mt tRNA genes, except for tRNA-Ser(AGN), which lacks a DHU arm. Some unmatched base pairs occur in the Pedopodisma emiensis(Yi), Sinopodisma guizhouensis Zheng, Qinlingacris taibaiensis Yin et Chou, and Oreoptygonotus chinghaiensis(Cheng et Hang) tRNAs.
5. The secondary structure of16s ribosomal genes are not form H1arm, in addition, mitochondrial rRNA secondary structure of other parts of the very conservative, forming a plurality of sizes of stem-loop structure. Nucleotide substitution rate of the ring to the stem, and C-T is a common form of conversion. Stems mostly nucleotide substitution mutation compensation to ensure that the base to maintain the existence of secondary structure.
6.13protein-coding genes in four species of Catantopidae mitochondrial genome, there are11kinds of exactly the same size of protein-coding genes, only two different, cytb andnad3.
7. Variation rate of cytb, coxl, cox2, cox3are low (The lowest is cytb, AVE=0.049). Variation rate of nadl, nad4, nad4L and nad5are moderate. Variation rate of atp8, nad3, nad2and nad6are rapid (The fast is nad3, AVE=0.153).
8. The least P-distance between mtDNA is0.057(Sinopodisma guizhouensis Zheng to Sinopodisma houshana). The least P-distance between PCGs is0.056(Sinopodisma guizhouensis Zheng to Sinopodisma houshana). Indicate that two species in genus Sinopodisma is quite similar.
9. T content of the four species of Catantopidae in J strand lower than N strand, A and C content in the J strand are higher than that of in N strand. The third site of codon of protein-coding genes in N strand show a very low G content, and has a very high T content.
10. Based on PCGs, rRNA gene and whole37mitochondrial gene by using maximum parsimony, maximum likelihood and Bayesian inference method reconstructed phylogenetic tree Orthoptera, We consider that the exist of the genus Pedopodisma is reasonable.
本研究选择了四种蝗虫进行了全线粒体测序,其中蹦蝗属和小蹦蝗属各一种,分别为贵州蹦蝗和峨眉小蹦蝗,其中根据形态从蹦蝗属中分出的小蹦蝗属能否成立是有争议的,太白秦岭蝗是中国特有属秦岭蝗属代表种类,仅分布于高寒的秦岭山脉。青海屹蝗是网翅蝗科一短翅型物种,在NCBI上提交的5种网翅蝗科物种中只有一种是短翅类型。
本研究采用长距离PCR(聚合酶链式反应)结合二次嵌套PCR技术对蝗总科的4种蝗虫的全线粒体基因组进行了测定,拼接和注释,对四种斑腿蝗科蝗虫峨眉小蹦蝗(Pedopodisma emiensis(Yin)),贵州蹦蝗(Sinopodisma guizhouensis Zheng)和太白秦岭蝗(Qinlinggacris taibiensis Yin et Chou)外,还结合了本实验室所测而未发表的霍山蹦蝗(Sinopodisma houshana)进行了比较基因组分析,对四种网翅蝗科蝗虫青海屹蝗Oreoptygonotus chinghaiensis之外,还结合了NCBI下载的黑膝异爪蝗Euchorthippus fusigeniculatus,中华雏蝗Chorthippus chinensis Tarbinsky和隆额网翅蝗Arcyptera coreana Shiraki的线粒体基因组对网翅蝗科线粒体基因组的一些特性进行了比较基因组分析,并结合NCBI中已收录的和本研究小组其他成员所测定的未公开的共计54种直翅目昆虫线粒体基因组全序列,采用PCGs、 rRNA和全线粒体37基因联合三种数据集用最大简约法,最大似然法和贝叶斯推论法重新构建了直翅目系统树。主要结论如下：
1.四种蝗总科昆虫分别为峨眉小蹦蝗(Pedopodisma emiensis(Yin))、贵州蹦蝗(Sinopodisma guizhouensis Zheng)、太白秦岭蝗(Qinlingacris taibaiensis Yin et Chou)和青海屹蝗(Oreoptygonotus chinghaiensis(Chnget Hang))。线粒体基因组全序列总长度分别为16014bp、16013bp.15631bp和15620bp。四种蝗虫均编码线粒体基因组中典型的37个基因,这37个基因分别为：13个蛋白编码基因,2个核糖体RNA基因和22个转运RNA基因。四种蝗虫线粒体基因排列次序和基因的转录方向同已经发表的蝗亚目昆虫一致。
2.四种蝗虫线粒体基因组碱基组成均具AT偏向性,其中峨眉小蹦蝗(Pedopodisma emiensis(Yin))AT含量为76.5%,贵州蹦蝗(Sinopodisma guizhouensis Zheng)AT含量为76.4%,太白秦岭蝗(Qinlingacris taibaiensis Yin et Chou) AT含量为76.3%,青海屹蝗(Oreoptygonotus chinghaiensis(Cheng et Hang)) AT含量为75.2%。
3.本研究所测定的线粒体基因组的A+T富集区均位于srRNA和trnI之间,长度和A+T含量分别为：峨眉小蹦蝗(Pedopodisma emiensis(Yin))为1123bp和85.8%,贵州蹦蝗(Sinopodisma guizhouensis Zheng)为1127bp和84.8%,太白秦岭蝗(Qinlingacris taibaiensis Yin et Chou)为778bp和88.7%,青海屹蝗(Oreoptygonotus chinghaiensis(Cheng et Hang))为711bp和82.1%。相对于4个主要部分(PCGs, rRNAs, tRNAs, A+T富集区),A+T富集区的AT含量是最高的区域。
4.四种蝗虫各自均具有22个转运RNA基因,核酸保守性具链间偏向性,分布于J链的所有tRNAs比位于N链的所有tRNAs的AT%略偏高。tRNASer(AGN)的DHU臂都存在缺失的现象,其他21个转运RNA均能形成典型的三叶草二级结构。绝大多数tRNA二级结构存在一定数目的错配。在tRNA的二级结构中氨基酸接受臂和反密码子环长度较保守,TψC臂和DHU臂的变异最大。
5.核糖体二级结构预测显示,四种蝗虫16s核糖体基因均不能形成H1臂。
6.斑腿蝗科四个物种线粒体基因组的13个蛋白编码基因中,有11种蛋白编码基因数目完全一致,仅有2种不一致,为cytb和nad3蛋白编码基因。
7.4种斑腿蝗氨基酸序列变异率中,cytb, cox1, cox2, cox3的氨基酸变异率最低(其中cytb的变异率为最低,AVE=0.049), nadl, nad4, nad4L和nad5的氨基酸变异率中等,atp8, nad3, nad2和nad6的氨基酸变异率偏高(其中nad3的变异率为最高,AVE=0.153)。
8.4种斑腿蝗全线粒体mtDNA之间P-距离在贵州蹦蝗-霍山蹦蝗最小,为0.057, PCGs之间P-距离和mtDNA有相似的趋势,也是贵州蹦蝗-霍山蹦蝗最小,为0.056,说明两种蹦蝗在全线粒体mtDNA和PCGs之间差异很小。
9.4种斑腿蝗J-链的T含量均低于N-链,而A和C的含量均为J-链高于N-链。N-链上蛋白质编码基因第3位点显示了极低的G含量,而具有极高的T含量。
10.对PCGs、 rRNA和全线粒体37基因联合三种数据采用最大简约法,最大似然法和贝叶斯推论法重新构建的直翅目系统树,除基于rRNA用BI法所建树之外霍山蹦蝗和贵州蹦蝗均能优先聚成一支,再与峨眉小蹦蝗聚合,并结合形态学观察认为小蹦蝗属是成立的。
Orthoptera insects include two categories:one for the long-horned suborder to katydids and crickets, represented by its long antennae longer than the body angle of insects, the other for a short corner suborder to locust and grasshopper as the representative body of its antennae shorter than the short-corner type insects.
In this study, the mitochondrial DNA of four locusts was fully sequenced, including the genus of Sinopodisma and Pedopodisma. The possibility of establishing of genus Sinopodisma is controversial.
1. The Pedopodisma emiensis(Yin) mt genome was16014bp in size, the Sinopodisma guizhouensis Zheng mt genome was16013bp in size, the Qinlingacris taibaiensis Yin et Chou mt genome was15631bp in size and the Oreoptygonotus chinghaiensis(Cheng et Hang) was15620bp in size. The four mitochondrial genomes contain a identical set of13protein-coding genes,22transfer RNA genes, two ribosomal RNA genes and an A+T-rich region in the same arrangenment and orientation as those of the other analysed caeliferan species.
2. The nucleotide composition all showed A/T bias and the A+T content of four species mitogenomes showed little difference. The A+T content of Pedopodisma emiensis(Yin), Sinopodisma guizhouensis Zheng, Qinlingacris taibaiensis Yin et Chou and Oreoptygonotus chinghaiensis(Cheng et Hang)was76.5%,76.4%,76.3%and75.2%respectively.
3. The AT rich region between srRNA and trnl. The size of AT rich region of Pedopodisma emiensis (Yin), Sinopodisma guizhouensis Zheng, Qinlingacris taibaiensis Yin et Chou and Oreoptygonotus chinghaiensis (Cheng et Hang) was1123bp,1127bp,778bp and711bp. AT content of the AT rich region of Pedopodisma emiensis (Yin), Sinopodisma guizhouensis Zheng, Qinlingacris taibaiensis Yin et Chou and Oreoptygonotus chinghaiensis (Cheng et Hang) was85.8%,84.8%,82.1%and88.7%.
4. Each mitogenomes of four species has22tRNA. The pattern of nucleotide conservation in tRNA genes was majority strand-biased. AT content of tRNAs located on the majority strand were high than tRNAs that located on the minority strand. Each tRNA has the typical cloverleaf secondary structure found in most mt tRNA genes, except for tRNA-Ser(AGN), which lacks a DHU arm. Some unmatched base pairs occur in the Pedopodisma emiensis(Yi), Sinopodisma guizhouensis Zheng, Qinlingacris taibaiensis Yin et Chou, and Oreoptygonotus chinghaiensis(Cheng et Hang) tRNAs.
5. The secondary structure of16s ribosomal genes are not form H1arm, in addition, mitochondrial rRNA secondary structure of other parts of the very conservative, forming a plurality of sizes of stem-loop structure. Nucleotide substitution rate of the ring to the stem, and C-T is a common form of conversion. Stems mostly nucleotide substitution mutation compensation to ensure that the base to maintain the existence of secondary structure.
6.13protein-coding genes in four species of Catantopidae mitochondrial genome, there are11kinds of exactly the same size of protein-coding genes, only two different, cytb andnad3.
7. Variation rate of cytb, coxl, cox2, cox3are low (The lowest is cytb, AVE=0.049). Variation rate of nadl, nad4, nad4L and nad5are moderate. Variation rate of atp8, nad3, nad2and nad6are rapid (The fast is nad3, AVE=0.153).
8. The least P-distance between mtDNA is0.057(Sinopodisma guizhouensis Zheng to Sinopodisma houshana). The least P-distance between PCGs is0.056(Sinopodisma guizhouensis Zheng to Sinopodisma houshana). Indicate that two species in genus Sinopodisma is quite similar.
9. T content of the four species of Catantopidae in J strand lower than N strand, A and C content in the J strand are higher than that of in N strand. The third site of codon of protein-coding genes in N strand show a very low G content, and has a very high T content.
10. Based on PCGs, rRNA gene and whole37mitochondrial gene by using maximum parsimony, maximum likelihood and Bayesian inference method reconstructed phylogenetic tree Orthoptera, We consider that the exist of the genus Pedopodisma is reasonable.
引文
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