几种水稻害虫Wolbachia的检测及全线粒体基因组的序列分析
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摘要
水稻二化螟Chilo suppressalis (Walker)、稻纵卷叶螟Cnaphalocrocis medialis (Guenee)和大螟Sesamia infer ens (Walker)是三种重要的水稻害虫,分别隶属鳞翅目、螟蛾科和夜蛾科。其中水稻二化螟和大螟为钻蛀性害虫,稻纵卷叶螟为远距离迁飞性害虫。本研究对水稻二化螟和稻纵卷叶螟内共生菌Wolbachia感染情况进行了检测；同时对水稻二化螟、稻纵卷叶螟和大螟的全线粒体基因组序列进行测序和分析,在全线粒体基因组水平上探讨部分鳞翅目昆虫的系统发育关系,丰富鳞翅目昆虫线粒体基因组数据。现将研究结果总结如下：
1、水稻二化螟23个地理种群的Wolbachia感染率为0-40.0%,平均感染率为14.3%。基于wsp基因片段序列,将水稻二化螟中检测到的Wolbahcia分为6个品系,分别命名为wChisupl-wChisup6(登陆序列号分别为HM165272、HQ336510、 HQ336514、HQ336511、HQ336512和HQ336513),其中品系wChisup1和wChisup2隶属A组,其它的隶属于B组；不同地理种群中的Wolbachia感染率和感染类群不具有明显的空间分布格局。通过序列比对发现水稻二化螟感染的wsp基因序列与其它物种的完全一致或相似性很高。
2、采自全国26个地区的稻纵卷叶螟种群的Wolbachia感染率为10%-90%,平均感染率为58.8%。通过序列比对发现,感染稻纵卷叶螟Wolbachia的wsp、ftsZ和16S rDNA基因在不同地区种群中的序列完全一致,而且与其它物种的也完全一致或具有很高的相似性。
3、水稻二化螟、稻纵卷叶螟和大螟的全线粒体基因组长度分别为15395bp、15388bp和15413bp,均包含37个基因和一个非编码的A+T富含区；各基因顺序和转录方向一致。这三种水稻害虫线粒体基因组均有较高的碱基A+T含量,都存在3个大于30bp的间隔区,而且在tRN ATrp和tRNACys重叠区均有8bp的保守序列,但基因间隔和重叠区数目及长度存在差异。此外,这三种水稻害虫线粒体基因组中的蛋白质编码基因的A+T碱基含量、AT-skew值和GC-skew值相似,而且大部分蛋白质编码基因都使用ATN和TAA作为起始密码子和终止密码子,但是密码子的第一位点至第三位点的A+T碱基含量存在很大差异。
4、三种水稻害虫线粒体基因组均包含22个tRNA基因,反密码子多为GNN或UNN；除tRNASer(AGN)缺失D臂外,其余的tRNA基因二级结构都可以折叠成典型的三叶草结构；大多数tRNA二级结构均存在不同程度的碱基错配现象,错配类型多为G-U。同时这三种螟虫线粒体基因组的lrRNA和srRNA的二级结构相似,其中lrRNA包含6个结构域,49个颈环结构；srRNA的二级结构包含3个结构域,33个颈环结构。三种水稻害虫线粒体基因组的A+T丰富区均包含ATAGA(T))序列和Poly-T序列,一些重复序列。稻纵卷叶螟和大螟线粒体基因组的A+T丰富区均含有一个茎环结构；此外,稻纵卷叶螟线粒体基因组的A+T丰富区还含有1个(TA)13序列。
5、基于线粒体基因组13个蛋白质编码基因的核苷酸序列及氨基酸序列的联合数据集,采用不同方法构建了36种鳞翅日昆虫的系统发育进化树。结果表明采用最大似然法(ML)和贝叶斯法(BI)所得拓扑结构一致,都显示出蚕蛾总科Bombycoidea、尺蛾总科Geometroidea、夜蛾总科Noctuoidea、螟蛾总科Pyraloidea和凤蝶总科Papilionoidea总科关系较近,该研究结果与其他学者的研究基本一致。
Chilo suppressalis (Walker)(Lepidoptera:Pyralidae) and Cnaphalocrocis medialis (Guenee)(Lepidoptera:Pyralidae), and Sesamia inferens (Walker)(Lepidoptera:Noctuidae) are famous rice pests, in which C. suppressalis and S. inferens are wood-boring insects, C. medialis is a migratory pest. In this study we investigate prevalence and diversity of Wolbachia infection in C. suppressalis and C medialis populations. Meanwhile, the complete mitochondrial genomes (mitogenomes) of C. suppressalis, C. medialis, and S. inferens were sequenced and analyzed, which can enrich the lepidopteran species data in Genbank and go further into declare the phylogenetic relationships among lepidopteran insects. The primary achievements of this dissertation were listed as follows:
1. Infection frequency of Wolbachia in23populations of C. suppressalis ranges from0-40.0%with an average infection rate at14.3%. Wolbachia was not detected in13populations, but six strains of Wolbachia (wChisupl-wChisup6) were identified based on wsp sequences isolated in other10populations (HM165272, HQ336510, HQ336514, HQ336511, HQ336512, HQ336513). Among these strains, wChisup1-wChisup2belong to Group-A and wChisup3-wChisup6belong to Group-B. There is no obvious geographical pattern for the prevalence and distribution of the six Wolbachia strains. Sequence alignment analysis indicates that wsp sequences found in C. suppressalis is high, and these sequences are also closely related to those in other species.
2. Infection frequencies of Wolbachia in26geographical populations of C. medinalis range from10.0-90.0%with an average infection rate at58.8%by using wsp, ftsZ and16S rDNA sequences, respectively. Wolbachia was detected in all the geographically separate populations. The Wolbachia detected in different C. medinalis populations are100%identical to each other with its wsp, ftsZ, and16S rDNA sequences, which all belong to Group-B. Sequence alignment analysis indicates that wsp, jisZ and16S rDNA sequences found in C. medinalis are also closely related to those in other species.
3. All the mitogenomes of C. suppressalis (15395bp), C. medialis (15388bp), and S. inferens (15413bp) include37genes and an A+T-rich region. The gene order and transcription direction are the same to other lepidopteran species. All the nucleotide compositions show a high bias towards A and T. The number and length of the integenic regions and overlap regions are different, but they all exist three major integenic regions with over30bp and a conserved8-bp overlap region between tRNATrp and IRNA Most protein coding genes (PCGs) of the three mitogenomes start with a typical ATN codon and stop with TAA codon. The average A+T-content of the protein coding genes in S. inferens mitogenome is similar to other two species, so are AT-skews and GC-Skews. However, the position of the highest A+T-content of13PCGs is different among the three mitogenomes.
4. All the mitogenomes include22tRNA genes. The anticodons of most tRNAs are GNN and UNN. tRNA genes have the typical cloverleaf secondary structures except for the tRNASer(AGN) gene, which was found with the absence of a DHU arm. Most tRNAs exist mismatched base pairs in which the number of G-U pairs is usually the most. Meanwhile, the secondary structures of lrRNA and srRNA genes in S. inferens are similar to those of other two mitogenomes, in which there are49helices in lrRNA gene and33helices in srRNA gene. The A+T-rich regions of three mitogenomes contain some typical strtuctures:the conserved motif ATAGA(T) followed by a18-22bp poly-T stretch, some tandem reapeted units. Meanwhile, the similar potential stem-loop structure was found in S. inferens and C. medialis mitogenomes. In addition, there is a microsatellite (TA)n in C. medinalis.
5. Based on the combined data set of nucleotide and amino acid sequences of13protein coding genes, the phylogenetic relationships of36lepidopteran species was reconstructed using different methods. The result indicates similar topologies between the maxmium likelihood (ML) and Bayesian inference (BI) methods, and supports that the phylogenetic relationships are very close among Bombycoidea, Geometroidea, Noctuoidea, Pyraloidea, and Papilionoidea. The result basically supports the traditional view.
1、水稻二化螟23个地理种群的Wolbachia感染率为0-40.0%,平均感染率为14.3%。基于wsp基因片段序列,将水稻二化螟中检测到的Wolbahcia分为6个品系,分别命名为wChisupl-wChisup6(登陆序列号分别为HM165272、HQ336510、 HQ336514、HQ336511、HQ336512和HQ336513),其中品系wChisup1和wChisup2隶属A组,其它的隶属于B组；不同地理种群中的Wolbachia感染率和感染类群不具有明显的空间分布格局。通过序列比对发现水稻二化螟感染的wsp基因序列与其它物种的完全一致或相似性很高。
2、采自全国26个地区的稻纵卷叶螟种群的Wolbachia感染率为10%-90%,平均感染率为58.8%。通过序列比对发现,感染稻纵卷叶螟Wolbachia的wsp、ftsZ和16S rDNA基因在不同地区种群中的序列完全一致,而且与其它物种的也完全一致或具有很高的相似性。
3、水稻二化螟、稻纵卷叶螟和大螟的全线粒体基因组长度分别为15395bp、15388bp和15413bp,均包含37个基因和一个非编码的A+T富含区；各基因顺序和转录方向一致。这三种水稻害虫线粒体基因组均有较高的碱基A+T含量,都存在3个大于30bp的间隔区,而且在tRN ATrp和tRNACys重叠区均有8bp的保守序列,但基因间隔和重叠区数目及长度存在差异。此外,这三种水稻害虫线粒体基因组中的蛋白质编码基因的A+T碱基含量、AT-skew值和GC-skew值相似,而且大部分蛋白质编码基因都使用ATN和TAA作为起始密码子和终止密码子,但是密码子的第一位点至第三位点的A+T碱基含量存在很大差异。
4、三种水稻害虫线粒体基因组均包含22个tRNA基因,反密码子多为GNN或UNN；除tRNASer(AGN)缺失D臂外,其余的tRNA基因二级结构都可以折叠成典型的三叶草结构；大多数tRNA二级结构均存在不同程度的碱基错配现象,错配类型多为G-U。同时这三种螟虫线粒体基因组的lrRNA和srRNA的二级结构相似,其中lrRNA包含6个结构域,49个颈环结构；srRNA的二级结构包含3个结构域,33个颈环结构。三种水稻害虫线粒体基因组的A+T丰富区均包含ATAGA(T))序列和Poly-T序列,一些重复序列。稻纵卷叶螟和大螟线粒体基因组的A+T丰富区均含有一个茎环结构；此外,稻纵卷叶螟线粒体基因组的A+T丰富区还含有1个(TA)13序列。
5、基于线粒体基因组13个蛋白质编码基因的核苷酸序列及氨基酸序列的联合数据集,采用不同方法构建了36种鳞翅日昆虫的系统发育进化树。结果表明采用最大似然法(ML)和贝叶斯法(BI)所得拓扑结构一致,都显示出蚕蛾总科Bombycoidea、尺蛾总科Geometroidea、夜蛾总科Noctuoidea、螟蛾总科Pyraloidea和凤蝶总科Papilionoidea总科关系较近,该研究结果与其他学者的研究基本一致。
Chilo suppressalis (Walker)(Lepidoptera:Pyralidae) and Cnaphalocrocis medialis (Guenee)(Lepidoptera:Pyralidae), and Sesamia inferens (Walker)(Lepidoptera:Noctuidae) are famous rice pests, in which C. suppressalis and S. inferens are wood-boring insects, C. medialis is a migratory pest. In this study we investigate prevalence and diversity of Wolbachia infection in C. suppressalis and C medialis populations. Meanwhile, the complete mitochondrial genomes (mitogenomes) of C. suppressalis, C. medialis, and S. inferens were sequenced and analyzed, which can enrich the lepidopteran species data in Genbank and go further into declare the phylogenetic relationships among lepidopteran insects. The primary achievements of this dissertation were listed as follows:
1. Infection frequency of Wolbachia in23populations of C. suppressalis ranges from0-40.0%with an average infection rate at14.3%. Wolbachia was not detected in13populations, but six strains of Wolbachia (wChisupl-wChisup6) were identified based on wsp sequences isolated in other10populations (HM165272, HQ336510, HQ336514, HQ336511, HQ336512, HQ336513). Among these strains, wChisup1-wChisup2belong to Group-A and wChisup3-wChisup6belong to Group-B. There is no obvious geographical pattern for the prevalence and distribution of the six Wolbachia strains. Sequence alignment analysis indicates that wsp sequences found in C. suppressalis is high, and these sequences are also closely related to those in other species.
2. Infection frequencies of Wolbachia in26geographical populations of C. medinalis range from10.0-90.0%with an average infection rate at58.8%by using wsp, ftsZ and16S rDNA sequences, respectively. Wolbachia was detected in all the geographically separate populations. The Wolbachia detected in different C. medinalis populations are100%identical to each other with its wsp, ftsZ, and16S rDNA sequences, which all belong to Group-B. Sequence alignment analysis indicates that wsp, jisZ and16S rDNA sequences found in C. medinalis are also closely related to those in other species.
3. All the mitogenomes of C. suppressalis (15395bp), C. medialis (15388bp), and S. inferens (15413bp) include37genes and an A+T-rich region. The gene order and transcription direction are the same to other lepidopteran species. All the nucleotide compositions show a high bias towards A and T. The number and length of the integenic regions and overlap regions are different, but they all exist three major integenic regions with over30bp and a conserved8-bp overlap region between tRNATrp and IRNA Most protein coding genes (PCGs) of the three mitogenomes start with a typical ATN codon and stop with TAA codon. The average A+T-content of the protein coding genes in S. inferens mitogenome is similar to other two species, so are AT-skews and GC-Skews. However, the position of the highest A+T-content of13PCGs is different among the three mitogenomes.
4. All the mitogenomes include22tRNA genes. The anticodons of most tRNAs are GNN and UNN. tRNA genes have the typical cloverleaf secondary structures except for the tRNASer(AGN) gene, which was found with the absence of a DHU arm. Most tRNAs exist mismatched base pairs in which the number of G-U pairs is usually the most. Meanwhile, the secondary structures of lrRNA and srRNA genes in S. inferens are similar to those of other two mitogenomes, in which there are49helices in lrRNA gene and33helices in srRNA gene. The A+T-rich regions of three mitogenomes contain some typical strtuctures:the conserved motif ATAGA(T) followed by a18-22bp poly-T stretch, some tandem reapeted units. Meanwhile, the similar potential stem-loop structure was found in S. inferens and C. medialis mitogenomes. In addition, there is a microsatellite (TA)n in C. medinalis.
5. Based on the combined data set of nucleotide and amino acid sequences of13protein coding genes, the phylogenetic relationships of36lepidopteran species was reconstructed using different methods. The result indicates similar topologies between the maxmium likelihood (ML) and Bayesian inference (BI) methods, and supports that the phylogenetic relationships are very close among Bombycoidea, Geometroidea, Noctuoidea, Pyraloidea, and Papilionoidea. The result basically supports the traditional view.
引文
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