三種赤眼蜂線粒體基因級(jí)測(cè)定與分析
發(fā)布時(shí)間：2018-09-01 08:24
【摘要】：昆蟲(chóng)線粒體基因組因其結(jié)構(gòu)簡(jiǎn)單,遵循母系遺傳的原則、進(jìn)化速率快和重組發(fā)生率低等特點(diǎn),被廣泛的應(yīng)用到種群遺傳學(xué)、比較基因組學(xué)、系統(tǒng)發(fā)育分析以及基因組水平的分子進(jìn)化等領(lǐng)域的研究。本研究采用普通PCR和長(zhǎng)片段PCR(Long-PCR)相結(jié)合的實(shí)驗(yàn)方法,通過(guò)高通量測(cè)序技術(shù)測(cè)定了松毛蟲(chóng)赤眼蜂Trichogramma dendrolimi,玉米螟赤眼蜂Trichogramma ostriniae和稻螟赤眼蜂Trichogramma japonicum的線粒體基因組序列,并利用相關(guān)軟件和服務(wù)器進(jìn)行了組裝拼接、注釋和相關(guān)分析。通過(guò)整合在NCBI網(wǎng)站上的部分膜翅目線粒體基因組,基于線粒體基因組的13個(gè)編碼蛋白基因和2個(gè)rRNA基因序列,分別采用貝葉斯推論法(bayesian inference,BI)和最大似然法(maxmum-likelihood,ML)構(gòu)建了四種膜翅目的系統(tǒng)發(fā)育樹(shù)。主要的結(jié)論:1.本研究測(cè)定的3種赤眼蜂的線粒體基因組的全長(zhǎng)分別為:松毛蟲(chóng)赤眼蜂16877 bp,稻螟赤眼蜂15962 bp,玉米螟赤眼蜂16472bp。3種赤眼蜂的線粒體基因組各自包括包含37個(gè)基因(2個(gè)rRNA基因,22個(gè)tRNA基因和13個(gè)蛋白質(zhì)編碼基因)和一個(gè)A+T富集區(qū)。2.本研究的松毛蟲(chóng)赤眼蜂、稻螟赤眼蜂和玉米螟赤眼蜂3種赤眼蜂的蛋白質(zhì)編碼基因的起始密碼子均為ATN,除玉米螟赤眼蜂的基因nad4L的終止密碼子為TAG之外,其余終止密碼子均為TAA。3.線粒體基因組的22個(gè)tRNA基因都可以折疊成典型了三葉草二級(jí)結(jié)構(gòu),除了trnS1缺少D-loop,并且有tRNA的二級(jí)結(jié)構(gòu)存在一定數(shù)目的堿基錯(cuò)配。4.本研究的3種赤眼蜂都存在一個(gè)長(zhǎng)片段的非編碼區(qū),即A+T富集區(qū),長(zhǎng)度分別為松毛蟲(chóng)赤眼蜂1320 bp,稻螟赤眼蜂595 bp,玉米螟赤眼蜂830 bp。A+T含量分別為88%,91.1%,89.0%。三種赤眼蜂A+T富集區(qū)長(zhǎng)度的不同是它們線粒體基因組長(zhǎng)度不同的主要原因。A+T富集區(qū)內(nèi)部有一些典型的結(jié)構(gòu),其中包括類似poly-A結(jié)構(gòu)、poly-T結(jié)構(gòu),重復(fù)序列(AT)n和發(fā)卡結(jié)構(gòu)等。5.本研究的3種赤眼蜂的線粒體基因組基因排列具有相同的模式,但是和古老甲殼綱或者其他膜翅目的昆蟲(chóng)相比較發(fā)生了很大的重排。6.利用線粒體基因組蛋白質(zhì)編碼基因及去掉第三位點(diǎn)的蛋白質(zhì)編碼基因?qū)δこ崮坷ハx(chóng)進(jìn)行系統(tǒng)發(fā)育分析,(1)所有結(jié)果都支持針尾部為單系群。(2)針尾部及旗腹蜂總科(Aculeata + Evaniidae)與旗腹蜂類、姬蜂類及細(xì)蜂類(Evaniomorpha +Ichneumonomorpha + Proctotrupomorpha)為姊妹群關(guān)系。(3)癭蜂總科和細(xì)蜂總科的關(guān)系較為接近,為姊妹群的關(guān)系,而錘角細(xì)蜂總科則和小蜂總科為姊妹群的關(guān)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.
【學(xué)位授予單位】：南京農(nóng)業(yè)大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2016
【分類號(hào)】：S476.3
本文編號(hào)：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.
【學(xué)位授予單位】：南京農(nóng)業(yè)大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2016
【分類號(hào)】：S476.3
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