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DNA条形码技术在主要实蝇类害虫识别中的应用
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摘要
实蝇(Tephritid fruit fly)类昆虫属双翅目Diptera、实蝇科Tephritidae,遍布全世界的热带、亚热带和温带地区,种类多,寄主范围广,危害严重,为水果和蔬菜的重要经济作物害虫。COI基因是线粒体呼吸链上编码细胞色素氧化酶亚基I的基因,相对于其它分子标记其最大优势为,相对保守但又较容易被通用引物扩增,同时又有足够的变异能够将物种区别开来。DNA条形码技术,即通过对COI基因57端一段长度约为650bp的基因片段进行测序和序列分析,进而在DNA水平上成功地区分物种。本学位论文以口岸经常截获的实蝇类害虫的幼体(卵、幼虫、蛹)以及成虫残体(头部、胸部、腹部、足、翅)为靶标,采用DNA条形码技术,从口岸快速检疫检验和准确识别的角度,研究实蝇类害虫幼体及成虫残体的快速分子检测鉴定技术。并对口岸经常截获的离腹寡毛实蝇属的21种实蝇进行物种鉴定,探讨其系统发育关系,为离腹寡毛实蝇属昆虫进化关系的研究提供分子依据。最后通过构建实蝇类害虫DNA条形码识别数据库,为实蝇类害虫的远程检测和监测,防止其在我国进一步传播扩散提供技术支撑。
     主要研究结果如下:
     1.DNA条形码识别技术对实蝇类幼体及残体的识别鉴定
     实蝇类害虫多为国内外检疫对象,其鉴定识别方法主要依据成虫的外部形态特征,而传统的形态学识别法对口岸经常截获的幼体及残缺的虫体,则无能为力。本研究以桔小实蝇Bactrocera dorsalis的幼体(卵、幼虫、蛹)以及成虫残体(足、翅、头部、胸部、腹部)为对象,利用DNA条形码技术,构建实蝇类害虫快速鉴定技术体系,并以其他4种常见实蝇(包括番石榴实蝇B. correcta、瓜实蝇B.cucurbitae、南亚果实蝇B.tau、柑桔大实蝇B. minax,)为对象对该技术体系进行应用验证。结果显示,桔小实蝇幼体以及成虫残体的碱基序列与数据库中靶标种COI基因碱基序列的一致性为99.51%-99.84%,其他4种实蝇相应序列与数据库中靶标种COI基因序列的一致性分别为100%,100%,99.81%-99.83%和100%;以邻接法(NJ法)构建系统发育树,靶标种实蝇均与数据库中对应种实蝇聚为一支,且置信度均为100%。以K2-P模型计算种内及种间遗传距离得出,5种实蝇的种间遗传距离为0.0597~0.2363,平均为O.1693;种内遗传距离为0.0000~0.0041,平均为0.0019。表明,基于DNA条形码的物种识别技术完全可用于口岸截获的实蝇类害虫幼体及残体的准确鉴定。
     2.DNA条形码技术在离腹寡毛实蝇属常见实蝇中的应用及其系统发育分析
     本研究以离腹寡毛实蝇属常见的8个亚属21种具有重要经济意义的实蝇为对象,利用DNA条形码技术,通过对线粒体DNA细胞色素C氧化酶亚基I(mtDNACOI)基因(约650bp)片段的测序和比对,对其进行物种的识别鉴定与系统发育关系分析。NJ、MP、ML三种系统发育树结果基本一致,各物种都聚为一支,置信度为90%以上。以Kimura2-paramete双参数模型计算种内及种间遗传距离,得出,21种实蝇的种内遗传距离为0.0003~0.0068,平均为0.0043:种间遗传距离为0.0154~0.2395,平均为0.1540;种间遗传距离为种内遗传距离的35.8倍,而且,种内、种间遗传距离没有重叠区域。表明,基于COI基因的DNA条形码技术可以用于离腹寡毛实蝇属昆虫的快速鉴定识别,该技术体系的建立对实蝇类害虫的检测监测具有重要意义。
     3.构建实蝇类害虫DNA条形码识别系统
     本文通过自主研发并结合资料收集和整理经济性实蝇条形码相关信息,应用ASP.NET动态网页技术和C#编程语言,开发建立了包括地中海实蝇Ceratitis capitata、桔小实蝇Bactrocera dorsalis、橄榄果实蝇B. oleae、柑桔大实蝇B. minax等在内的实蝇类害虫DNA条形码识别系统,该系统为外来入侵生物预防和控制研究中心(CMIAS)中国主要外来入侵昆虫DNA条形码识别系统(DIASChttp://www.chinaias.cn)的重要组成部分。该系统包括标本库、DNA条形码库以及知识库。标本库拥有3属35种具有重要经济价值的实蝇类害虫,共计1932个样本,其中如桔小实蝇(561头)、具条实蝇(311头)、蜜柑实蝇(128)居多。DNA条形码数据库,共计收录了5属185种具有重要经济价值的实蝇类害虫2405条DNA条形码序列,其中3属29种291条序列为本研究获得,5属181种1696条序列来自NCBI数据库,5属100种417条序列来自BOLD数据库;本研究中的序列不仅来自不同的实蝇种类,尚包含同一种类不同地理种群的序列如桔小实蝇、瓜实蝇、南亚果实蝇、柑桔大实蝇等。知识库中包括物种的中文名、拉丁学名、同物异名、中文异名、英文俗名、分类地位、形态特征(包括形态特征描述及图片信息)、国内外分布,寄主植物种类及危害、原产地、传入和扩散途径,可能扩散区域、预防控制和管理措施等基础信息,涉及3属31常见并具有重要经济意义的实蝇种类,其中,本实验获得的29种中除迪奥实蝇外均包含知识库各种基础信息。实蝇类害虫DNA条形码数据库的初步应用显示,通过样品mtDNA COI序列,完全能实现实蝇类害虫的分子鉴定。实蝇类害虫DNA条形码识别系统的建立,对全面提升我国口岸检疫检验能力,保障我国国际贸易信誉具有重大意义。
Fruit flies of the family Tephritidae (Diptera:Tephritidae) are one of the important pests group of fruits and vegetables in tropical, subtropical and temperate areas all over the world, with a number of described species, a wide range of hosts and causes great damage. COI gene which lies in the respiratory chain of mitochondria encodes cytochrome oxidase subunit Ⅰ. COI gene has two important advantages over other molecular markers. Firstly, it is relatively conservative and easily amplified by universal primer. Secondly, the evolution of this gene is rapid enough to distinguish different species. DNA barcoding technology is able to identify species at DNA level successfully through sequencing and analyzing a fragment of about650bp which near the5' end of the cytochrome c oxidase Ⅰ (COI) mitochondrial gene. In this research, the immatures (including egg, larva and pupa) and adult debris (including leg. wing, head, thorax and abdomen) of common tephritid fruit fly pests were used to develop a rapid identification technique for tephritid fruit flies based on DNA barcoding technology. In addition, Twenty one species which belong to genus Bactrocera and frequently intercepted at port of entry were identified using DNA barcoding technology and analysed of molecular phylogenetic relationships, which provided evidence at molecular level to understand the evolution of genus Bactrocera. The general aim of this study is to establish DNA barcoding identification system to achive remote detection and monitoring of tephritid fruit flies to prevent them from further spreading in China. The main results are as follows:
     1Establishment and application of DNA barcoding technology for identification of the immatures and adult debris of Bactrocera dorsalis (Hendel)(Diptera:Tephritid)
     Many species in the family Tephritidae are quarantine pests worldwide. Usually, identification of the tephritid fruit flies is mainly based on external morphological characteristics of adults. In this research, the immatures (including egg, larva and pupa) and adult debris (including leg, wing, head, thorax and abdomen) of Bactrocera dorsalis were used to develop a rapid identification technique for tephritid fruit flies based on DNA barcoding technology. The other four tephritid fruit fly species, i.e., B. correcta, B. cucurbitae, B. tau and B. minax, were used to verify the feasibility of the tephritid fruit fly identification technique developed. The results showed that the nucleotide sequence identity of the partial COI gene between the immatures or adult debris of B. dorsalis with the target gene from GenBank database is99.51%-99.84%, and that of other four tephritid fruit fly species with the target gene from GenBank database is100%,100%,99.81%-99.83%and100%, respectively. Neighbor-joining tree was established based on the analysis of COI gene sequences. The target species and the corresponding species in the database clustered in the same branches. All bootstrap values of the original divergence within a same species are100%. The intra-and inter-species genetic distances were calculated with MEGA version5.0software using the Kimera2-Parameter model. The intra-species genetic distances are0.0000-0.0041, with an average of0.0019. The interspecies genetic distances are0.0597-0.2363, with an average of0.1693. There was no overlap between intra-and inter-species genetic distances. The results indicated that the developed DNA barcoding identification techniques based on the partial COI gene can provide a rapid and accurate method for identification of immatures or adult debris of tephritid tephritid fruit fly species.
     2. Identification and Molecular phylogeny analysis of genus Bactrocera by DNA barcoding technology
     Twenty one species belonged to eight subgenus of genus Bactrocera were identified using DNA barcoding technology. Sequenced the partial mitochondrial cytochrome c oxidase subunit I (COI) gene (about650bp) which used to identify species and analyze the relationship of the molecular phylogeny. The phylogenetic tree was established by three types of phylogenetic (NJ, MP, ML) method. The intra-and inter-species genetic distances were calculated with MEGA version5.0software using the Kimura2-parameter model. The clustering analysis of phylogenetic tree was consistent with the published morphological analyses in twenty one Bactrocera species. Each branch corresponded to one species and all bootstrap values were over95%. The intra-species genetic distances are0.0003to0.0068, with an average of0.0043. The inter-species genetic distances are0.0154to0.2395, with an average of0.1540. The genetic distance between species in these21species was35.8times higher than the corresponding values within species (0.1540vs.0.0043). There was no overlap between inter-and intra-species genetic distances. The results indicated that the DNA barcoding based on partial COI gene can provide rapid and accurate identification of Bactrocera species.Develop this technology will play a important role in tephritid fruit fly pest identifying and monitoring.
     3. Establishment of DNA barcoding recognition system for tephritid fruit fly pests
     The work was supported by the National Basic Research Program of China. The DNA barcode identification system for tephritid fruit fly pests (including Ceratitis capitata, Bactrocera dorsalis, B. oleae, B. minax etc), a significant part of the Database of Invasive Alien Species in China (DIASC) developed by Centre for Management of Invasive Alien Species of Ministry of Agriculture(CMIAS), was established by collecting the barcode information about economical tephritid fruit fly pests and applying ASPNET technology and C#programming language. The DNA barcode identification system contains about2405mtDNA COI sequences of185species of5genus of Tephritid which were obtained from NCBI, BOLD and DIASC. The system has three genus thirty six species tephritid fruit fly (1932samples), such as B. dorsalis (561samples), B. scutellata (296samples), B. tsuneonis (128samples). There were291sequences of29species of3genus fruit flies from DIASC,1696sequences of181species of5genus fruit flies from NCBI and417sequences of100species of5genus fruit flies from BOLD. The species in this study such as B. dorsalis, B. cucurbitae, B. tau, B. mianx which are from different geographic populations. In the database, related information for3genus31most common tephritid fruit fly species was available, including Chinese name, scientific name, synonym, common name, classification status, morphology (illustration with images), distribution both in home and abroad, host plants and damage, country of origin, pathway for introduction and spread, intended spreading areas, measures for control and management. The DNA barcoding database was applied preliminarily, molecular identification of tephritid fruit fly pests was performed successfully via mtDNA COI sequences from samples. The establishment of DNA barcoding recognition system for tephritid fruit flies will play a very important role in improving quarantine capability at ports and international trade in China.
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