鳞翅目线粒体基因组分析及部分蛾类DNA条形码鉴定
摘要
线粒体基因组结构稳定、长度较小,较少发生重组,普遍为母性遗传,被广泛应用于种群遗传结构、基因漂流、谱系地理学和系统发育等研究。鳞翅目是昆虫纲四大目之一,种类繁多,全世界已知鳞翅目昆虫约达25万种,但目前已测定的鳞翅目线粒体基因组仅34种,对于庞大的鳞翅目种群来说,十分有限。加快鳞翅目线粒体基因组的测序和分析,对揭示鳞翅目线粒体基因组的进化和研究该类群复杂的系统发育关系有重要意义。
本文选取了鳞翅目2个种米蛾及旋纹潜叶蛾进行了线粒体基因组测序和注释,比较分析了鳞翅目34种昆虫的线粒体基因组结构、碱基组成特点、密码子使用情况、各蛋白质编码基因的进化速率。基于线粒体基因组进行了鳞翅目高阶元系统发育分析。
鳞翅目蛾类绝大多数是农、林业害虫,而且主要在幼虫时期进行危害,构建DNA条形码数据库,可确保对蛾类幼虫的快速准确鉴定,保证防控措施的有效实施。本文基于线粒体coxl基因对采自果园内的鳞翅目蛾类进行了调查鉴定,充实了鳞翅目DNA条形码数据库,检验了目前BOLD系统对农林害虫的鉴定成功率,检验了NJ树鉴定物种的准确度,对种内种间遗传距离进行了计算与讨论。
主要研究结果如下：
1.首次测定了螟蛾总科米蛾及巢蛾总科旋纹潜叶蛾线粒体全基因组序列,并分别进行了注释,预测了tRNA和rRNA基因的二级结构,分析了A+T富含区结构。米蛾及旋纹潜叶蛾的22个tRNA除了trns1 2.鳞翅目线粒体基因组的AT含量较高,各线粒体基因组H链上蛋白质基因编码区所有密码子位点的AT偏斜和GC偏斜均为负值,表示T含量高于A，C含量高于G。综合线粒体蛋白质编码基因的Ka/Ks比率、种间基因差异位点和基因变异分析,得出整个鳞翅目线粒体基因组进化速率比较快,其中脱氢酶亚基NADH基因进化速率通常快于细胞色素氧化酶基因。其中线粒体coX1基因进化速率居中,引物通用,适用于DNA条形码研究。
3.基于线粒体基因组所构建的鳞翅目系统发育树的基本结构为(巢蛾总科+(卷蛾总科+(凤蝶总科+(螟蛾总科+(夜蛾总科+(尺蛾总科+蚕蛾总科))))))。其中凤蝶总科、螟蛾总科和夜蛾总科的位置与传统形态分类不同,旋纹潜叶蛾所代表的巢蛾总科的位置与传统形态分类相同。
4.基于线粒体cox1基因所构建的NJ树,对果园采集的蛾类鉴定成功率为99.3%,证明线粒体coxl基因适用于鳞翅目蛾类鉴定。BOLD系统的鉴定成功率为75.1%,大蛾类比小蛾类成功率高,说明小蛾类数据欠缺。BOLD系统鉴定结果相似度在99%的鉴定成功率为94.6%；相似度在98-99%之间的鉴定成功率为89.6%；低于98%的鉴定成功率为12.2%。利用BOLD系统对鳞翅目蛾类进行鉴定时,建议常见种类以相似度大于99%为准确鉴定结果。种内种间遗传距离计算结果表明,86%的种类种内遗传距离低于1%,14%的种类在1-4.3%,同属种间遗传距离在1.3-15.3%,种内种间遗传距离有重叠,且无明显的种间阈值存在。
The mitochondrial genome is widely used for population genetic structure, gene flow, phylogeography and phylogenetic study, because of the structural stability, smaller length, less frequent reorganization and generally maternal inheritance. Lepidoptera is classified as Insecta, and widely distributed around the world with approximately250,000species. At present, there are34species mitochondrial genome sequenced successfully in Lepidoptera. But it is still very limited for large Lepidopteran populations. To reveal mitochondrial genome evolution and the phylogenetic relationship of Lepidoptera, it is very necessary that accelerating the Lepidopteran mitochondrial genome sequencing and analysis.
We selected two species (rice moth Corcyra cephalonica and leafminer moth Leucoptera malifoliella) to sequence and annotate the complete mitochondrial genome, and conducted a comparative analysis of the mitochondrial genomes in Lepidoptera, which mainly include the characteristics of base composition, codon usage, evolutionary rate of each protein-coding genes. Based on the mitochondrial genome we reconstructed phylogenetic relationship of Lepidoptera.
Lepidopteran moths mostly are agricultural and forestry pests, and mainly feeding on host plant during the larval stage. The DNA barcode database can ensure fast and accurate identification of moths'caterpillars, and provide accurate information for pest control. Based on mitochondrial coxl gene we surveyed and identified lepidopteran moths collected from an orchard, tested the successful rate of BOLD system and NJ tree for lepidopteran pests, calculated and discussed the inter-and intra-specific genetic distances.
The main results are as follows:
1. Nucleotide composition of C. cephalonica and L. malifoliella mitogenome genome are highly A+T biased (80.43%) and (82.57%),like other insects. Twelve PCGs start with a typical ATN codon, with the exception of cox1gene, which uses CGA as the initial codon.22tRNA genes evidence cloverleaf secondary structure, but trnS1(AGN) is found to lack the DHU stem. The secondary structure of rrnL and rrnS are generally similar to other lepidopterans with some minor differences. The L. malifoliella A+T-rich region includes the motif ATAGA, but the poly (T) stretch is replaced by a stem-loop structure, which may have a similar function to the poly (T) stretch. There is a high sequence identity between the intergenic spacer sequence trnQ-nad2and the neighboring nad2from most lepidopteran insects, this indicated that the intergenic spacer sequence trnQ-nad2may have originated from a partial duplication of the nad2gene.
2. The Lepidopteran mitochondrial genome have higher AT content, the AT skew and GC skew on the H chain of protein coding region are negative, which indicating that the T content is higher than A, the C content higher than G. Based on the Ka/Ks ratio, the interspecific gene loci divergence and gene mutation analysis, we found that evolutionary rate of dehydrogenase subunit the NADH gene usually faster than cytochrome oxidase gene. The coxl gene is moderate compared to other genes, and suitable for DNA barcode study.
3. The basic structure of the phylogenetic tree based the mitochondrial genomes is (Yponomeutoidea+(Tortricoidea+(Papilionoidea+(Pyraloidea+(Noctuoidea+(Geometroidea+Bombycoidea)))))). The positions of Papilionoidea, Pyraloidea and Noctuoidea are different from the traditional classification. The position of Yponomeutoidea represented by L.malifoliella, is same as traditional classification. Yponomeutoidea is sister group to the other lepidopteran superfamilies covered in the present study.
4. The NJ tree based on coxl gene shows identification successful rate is99.3%for moths collected from orchard, which prove that coxl gene is suitable for identification of Lepidopteran moths. The successful rate of the BOLD system is75.1%, and the the big moths have higher rates than the small moths,which shows the BOLD system lacked datas of small moths. The identification successful rate is94.6%when results similarity is greater than99%in the BOLD system, and successful rate is89.6%when the similarity in the range of98-99%, and successful rate is12.2%when the similarity less than98%. So it is accurate that the similarity of BOLD system identification is greater than99%for common species. Inter-and intra-specific genetic distances show that86%of the intraspecific genetic distances are less than1.0percent,14%are in the range of1.0-4.3percent. The interspecific genetic distances of the same genus are in the range of1.3-15.3percent, there are overlaps between inter-and intra-specific genetic distances, and not threshold value between inter-and intra-specific genetic distances.
本文选取了鳞翅目2个种米蛾及旋纹潜叶蛾进行了线粒体基因组测序和注释,比较分析了鳞翅目34种昆虫的线粒体基因组结构、碱基组成特点、密码子使用情况、各蛋白质编码基因的进化速率。基于线粒体基因组进行了鳞翅目高阶元系统发育分析。
鳞翅目蛾类绝大多数是农、林业害虫,而且主要在幼虫时期进行危害,构建DNA条形码数据库,可确保对蛾类幼虫的快速准确鉴定,保证防控措施的有效实施。本文基于线粒体coxl基因对采自果园内的鳞翅目蛾类进行了调查鉴定,充实了鳞翅目DNA条形码数据库,检验了目前BOLD系统对农林害虫的鉴定成功率,检验了NJ树鉴定物种的准确度,对种内种间遗传距离进行了计算与讨论。
主要研究结果如下：
1.首次测定了螟蛾总科米蛾及巢蛾总科旋纹潜叶蛾线粒体全基因组序列,并分别进行了注释,预测了tRNA和rRNA基因的二级结构,分析了A+T富含区结构。米蛾及旋纹潜叶蛾的22个tRNA除了trns1
3.基于线粒体基因组所构建的鳞翅目系统发育树的基本结构为(巢蛾总科+(卷蛾总科+(凤蝶总科+(螟蛾总科+(夜蛾总科+(尺蛾总科+蚕蛾总科))))))。其中凤蝶总科、螟蛾总科和夜蛾总科的位置与传统形态分类不同,旋纹潜叶蛾所代表的巢蛾总科的位置与传统形态分类相同。
4.基于线粒体cox1基因所构建的NJ树,对果园采集的蛾类鉴定成功率为99.3%,证明线粒体coxl基因适用于鳞翅目蛾类鉴定。BOLD系统的鉴定成功率为75.1%,大蛾类比小蛾类成功率高,说明小蛾类数据欠缺。BOLD系统鉴定结果相似度在99%的鉴定成功率为94.6%；相似度在98-99%之间的鉴定成功率为89.6%；低于98%的鉴定成功率为12.2%。利用BOLD系统对鳞翅目蛾类进行鉴定时,建议常见种类以相似度大于99%为准确鉴定结果。种内种间遗传距离计算结果表明,86%的种类种内遗传距离低于1%,14%的种类在1-4.3%,同属种间遗传距离在1.3-15.3%,种内种间遗传距离有重叠,且无明显的种间阈值存在。
The mitochondrial genome is widely used for population genetic structure, gene flow, phylogeography and phylogenetic study, because of the structural stability, smaller length, less frequent reorganization and generally maternal inheritance. Lepidoptera is classified as Insecta, and widely distributed around the world with approximately250,000species. At present, there are34species mitochondrial genome sequenced successfully in Lepidoptera. But it is still very limited for large Lepidopteran populations. To reveal mitochondrial genome evolution and the phylogenetic relationship of Lepidoptera, it is very necessary that accelerating the Lepidopteran mitochondrial genome sequencing and analysis.
We selected two species (rice moth Corcyra cephalonica and leafminer moth Leucoptera malifoliella) to sequence and annotate the complete mitochondrial genome, and conducted a comparative analysis of the mitochondrial genomes in Lepidoptera, which mainly include the characteristics of base composition, codon usage, evolutionary rate of each protein-coding genes. Based on the mitochondrial genome we reconstructed phylogenetic relationship of Lepidoptera.
Lepidopteran moths mostly are agricultural and forestry pests, and mainly feeding on host plant during the larval stage. The DNA barcode database can ensure fast and accurate identification of moths'caterpillars, and provide accurate information for pest control. Based on mitochondrial coxl gene we surveyed and identified lepidopteran moths collected from an orchard, tested the successful rate of BOLD system and NJ tree for lepidopteran pests, calculated and discussed the inter-and intra-specific genetic distances.
The main results are as follows:
1. Nucleotide composition of C. cephalonica and L. malifoliella mitogenome genome are highly A+T biased (80.43%) and (82.57%),like other insects. Twelve PCGs start with a typical ATN codon, with the exception of cox1gene, which uses CGA as the initial codon.22tRNA genes evidence cloverleaf secondary structure, but trnS1(AGN) is found to lack the DHU stem. The secondary structure of rrnL and rrnS are generally similar to other lepidopterans with some minor differences. The L. malifoliella A+T-rich region includes the motif ATAGA, but the poly (T) stretch is replaced by a stem-loop structure, which may have a similar function to the poly (T) stretch. There is a high sequence identity between the intergenic spacer sequence trnQ-nad2and the neighboring nad2from most lepidopteran insects, this indicated that the intergenic spacer sequence trnQ-nad2may have originated from a partial duplication of the nad2gene.
2. The Lepidopteran mitochondrial genome have higher AT content, the AT skew and GC skew on the H chain of protein coding region are negative, which indicating that the T content is higher than A, the C content higher than G. Based on the Ka/Ks ratio, the interspecific gene loci divergence and gene mutation analysis, we found that evolutionary rate of dehydrogenase subunit the NADH gene usually faster than cytochrome oxidase gene. The coxl gene is moderate compared to other genes, and suitable for DNA barcode study.
3. The basic structure of the phylogenetic tree based the mitochondrial genomes is (Yponomeutoidea+(Tortricoidea+(Papilionoidea+(Pyraloidea+(Noctuoidea+(Geometroidea+Bombycoidea)))))). The positions of Papilionoidea, Pyraloidea and Noctuoidea are different from the traditional classification. The position of Yponomeutoidea represented by L.malifoliella, is same as traditional classification. Yponomeutoidea is sister group to the other lepidopteran superfamilies covered in the present study.
4. The NJ tree based on coxl gene shows identification successful rate is99.3%for moths collected from orchard, which prove that coxl gene is suitable for identification of Lepidopteran moths. The successful rate of the BOLD system is75.1%, and the the big moths have higher rates than the small moths,which shows the BOLD system lacked datas of small moths. The identification successful rate is94.6%when results similarity is greater than99%in the BOLD system, and successful rate is89.6%when the similarity in the range of98-99%, and successful rate is12.2%when the similarity less than98%. So it is accurate that the similarity of BOLD system identification is greater than99%for common species. Inter-and intra-specific genetic distances show that86%of the intraspecific genetic distances are less than1.0percent,14%are in the range of1.0-4.3percent. The interspecific genetic distances of the same genus are in the range of1.3-15.3percent, there are overlaps between inter-and intra-specific genetic distances, and not threshold value between inter-and intra-specific genetic distances.
引文
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