三种赤眼蜂线粒体基因级测定与分析
发布时间：2018-09-01 08:24
【摘要】：昆虫线粒体基因组因其结构简单,遵循母系遗传的原则、进化速率快和重组发生率低等特点,被广泛的应用到种群遗传学、比较基因组学、系统发育分析以及基因组水平的分子进化等领域的研究。本研究采用普通PCR和长片段PCR(Long-PCR)相结合的实验方法,通过高通量测序技术测定了松毛虫赤眼蜂Trichogramma dendrolimi,玉米螟赤眼蜂Trichogramma ostriniae和稻螟赤眼蜂Trichogramma japonicum的线粒体基因组序列,并利用相关软件和服务器进行了组装拼接、注释和相关分析。通过整合在NCBI网站上的部分膜翅目线粒体基因组,基于线粒体基因组的13个编码蛋白基因和2个rRNA基因序列,分别采用贝叶斯推论法(bayesian inference,BI)和最大似然法(maxmum-likelihood,ML)构建了四种膜翅目的系统发育树。主要的结论:1.本研究测定的3种赤眼蜂的线粒体基因组的全长分别为:松毛虫赤眼蜂16877 bp,稻螟赤眼蜂15962 bp,玉米螟赤眼蜂16472bp。3种赤眼蜂的线粒体基因组各自包括包含37个基因(2个rRNA基因,22个tRNA基因和13个蛋白质编码基因)和一个A+T富集区。2.本研究的松毛虫赤眼蜂、稻螟赤眼蜂和玉米螟赤眼蜂3种赤眼蜂的蛋白质编码基因的起始密码子均为ATN,除玉米螟赤眼蜂的基因nad4L的终止密码子为TAG之外,其余终止密码子均为TAA。3.线粒体基因组的22个tRNA基因都可以折叠成典型了三叶草二级结构,除了trnS1缺少D-loop,并且有tRNA的二级结构存在一定数目的碱基错配。4.本研究的3种赤眼蜂都存在一个长片段的非编码区,即A+T富集区,长度分别为松毛虫赤眼蜂1320 bp,稻螟赤眼蜂595 bp,玉米螟赤眼蜂830 bp。A+T含量分别为88%,91.1%,89.0%。三种赤眼蜂A+T富集区长度的不同是它们线粒体基因组长度不同的主要原因。A+T富集区内部有一些典型的结构,其中包括类似poly-A结构、poly-T结构,重复序列(AT)n和发卡结构等。5.本研究的3种赤眼蜂的线粒体基因组基因排列具有相同的模式,但是和古老甲壳纲或者其他膜翅目的昆虫相比较发生了很大的重排。6.利用线粒体基因组蛋白质编码基因及去掉第三位点的蛋白质编码基因对膜翅目昆虫进行系统发育分析,(1)所有结果都支持针尾部为单系群。(2)针尾部及旗腹蜂总科(Aculeata + Evaniidae)与旗腹蜂类、姬蜂类及细蜂类(Evaniomorpha +Ichneumonomorpha + Proctotrupomorpha)为姊妹群关系。(3)瘿蜂总科和细蜂总科的关系较为接近,为姊妹群的关系,而锤角细蜂总科则和小蜂总科为姊妹群的关系。
[Abstract]:Insect mitochondrial genome has been widely used in population genetics and comparative genomics because of its simple structure, following the principle of maternal inheritance, rapid evolution rate and low incidence of recombination. Phylogenetic analysis and molecular evolution at genome level. In this study, the mitochondrial genome sequences of Trichogramma Dendrolimus Trichogramma dendrolimi, Trichogramma Trichogramma ostriniae and Trichogramma japonicum of Trichogramma oryzae were determined by high throughput sequencing with the combination of common PCR and long fragment PCR (Long-PCR). And the related software and server are used to assemble, annotate and related analysis. By integrating part of the Hymenoptera mitochondrial genome on the NCBI website, 13 encoded protein genes and 2 rRNA gene sequences were derived from the mitochondrial genome. Four phylogenetic trees of Hymenoptera were constructed by Bayesian inference (bayesian inference,BI) and maximum likelihood method (maxmum-likelihood,ML), respectively. The main conclusion is: 1. The mitochondrial genomes of three Trichogramma species were as follows: Trichogramma pine caterpillar, Trichogramma punctatus 16877 bp, Trichogramma oryzae, 15962 bp, Trichogramma oryzae, 16472bp.3 species, Trichogramma oryzae, including 37 genes (2 RRNA gene, 22 tRNA genes and 13 protein coding genes) and A T rich region. In this study, the initial codon of protein coding genes of Trichogramma Dendrolimus, Trichogramma oryzae and Trichogramma oryzae were all ATN, except TAG for the nad4L gene of Trichogramma furnacalis, and TAA.3. was the other codon. The 22 tRNA genes of mitochondrial genome can be folded into typical secondary structure of clover, except for the lack of D-loop in trnS1 and the existence of a certain number of base mismatch. 4 in the secondary structure of tRNA. All three species of Trichogramma in this study have a long non-coding region, that is, A T rich region, the length of which is 1320 bp, Trichogramma Dendrolimus 1320 bp, Trichogramma oryzae 595 bp, Trichogramma, 830 bp.A T content of Trichogramma oryzae is 8891.1% and 89.0, respectively. The difference in length of T-rich region of three Trichogramma species is the main reason for the difference in the length of mitochondrial genome. There are some typical structures in the A-T rich region, including poly-A structure, repeat sequence (AT) n and hairpin structure, etc. The mitochondrial genomes of the three species of Trichogramma in this study have the same pattern, but there is a large rearrangement of .6in comparison with the old crustacean or other Hymenoptera insects. The phylogenetic analysis of Hymenoptera insects using mitochondrial genome protein coding gene and protein coding gene without the third site was carried out. (1) all the results showed that the needle tail was a monophyletic group. (2) the needle tail and Aculeata. Evaniidae) and the flagella, (3) the relationship between the general family of gall wasps and the general family of the pachyceridae is close, which is the relationship of the sister group, while the relationship between the general family of Apodemycidae and the general family of small wasps is the relationship of the sister group.
【学位授予单位】：南京农业大学
【学位级别】：硕士
【学位授予年份】：2016
【分类号】：S476.3
本文编号：2216636
[Abstract]:Insect mitochondrial genome has been widely used in population genetics and comparative genomics because of its simple structure, following the principle of maternal inheritance, rapid evolution rate and low incidence of recombination. Phylogenetic analysis and molecular evolution at genome level. In this study, the mitochondrial genome sequences of Trichogramma Dendrolimus Trichogramma dendrolimi, Trichogramma Trichogramma ostriniae and Trichogramma japonicum of Trichogramma oryzae were determined by high throughput sequencing with the combination of common PCR and long fragment PCR (Long-PCR). And the related software and server are used to assemble, annotate and related analysis. By integrating part of the Hymenoptera mitochondrial genome on the NCBI website, 13 encoded protein genes and 2 rRNA gene sequences were derived from the mitochondrial genome. Four phylogenetic trees of Hymenoptera were constructed by Bayesian inference (bayesian inference,BI) and maximum likelihood method (maxmum-likelihood,ML), respectively. The main conclusion is: 1. The mitochondrial genomes of three Trichogramma species were as follows: Trichogramma pine caterpillar, Trichogramma punctatus 16877 bp, Trichogramma oryzae, 15962 bp, Trichogramma oryzae, 16472bp.3 species, Trichogramma oryzae, including 37 genes (2 RRNA gene, 22 tRNA genes and 13 protein coding genes) and A T rich region. In this study, the initial codon of protein coding genes of Trichogramma Dendrolimus, Trichogramma oryzae and Trichogramma oryzae were all ATN, except TAG for the nad4L gene of Trichogramma furnacalis, and TAA.3. was the other codon. The 22 tRNA genes of mitochondrial genome can be folded into typical secondary structure of clover, except for the lack of D-loop in trnS1 and the existence of a certain number of base mismatch. 4 in the secondary structure of tRNA. All three species of Trichogramma in this study have a long non-coding region, that is, A T rich region, the length of which is 1320 bp, Trichogramma Dendrolimus 1320 bp, Trichogramma oryzae 595 bp, Trichogramma, 830 bp.A T content of Trichogramma oryzae is 8891.1% and 89.0, respectively. The difference in length of T-rich region of three Trichogramma species is the main reason for the difference in the length of mitochondrial genome. There are some typical structures in the A-T rich region, including poly-A structure, repeat sequence (AT) n and hairpin structure, etc. The mitochondrial genomes of the three species of Trichogramma in this study have the same pattern, but there is a large rearrangement of .6in comparison with the old crustacean or other Hymenoptera insects. The phylogenetic analysis of Hymenoptera insects using mitochondrial genome protein coding gene and protein coding gene without the third site was carried out. (1) all the results showed that the needle tail was a monophyletic group. (2) the needle tail and Aculeata. Evaniidae) and the flagella, (3) the relationship between the general family of gall wasps and the general family of the pachyceridae is close, which is the relationship of the sister group, while the relationship between the general family of Apodemycidae and the general family of small wasps is the relationship of the sister group.
【学位授予单位】：南京农业大学
【学位级别】：硕士
【学位授予年份】：2016
【分类号】：S476.3
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