The complete mitochondrial genome of Orthaga achatina (Lepidoptera: Pyralidae)

Name: The complete mitochondrial genome of Orthaga achatina (Lepidoptera: Pyralidae)
Creator: Zenodo
Published: 2020-10-30T06:07:33+08:00

Zenodo2020-10-30 更新2026-05-25 收录

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Pyralidae is the largest family in Lepidoptera, with more than 25,000 species in the world, some of which are pests of agricultural and forestry plants, such as Orthaga (Yang et al. 2020). Orthaga achatina Butler (Lepidoptera: Pyralidae) is the most serious pest of camphor trees (Cinnamomum camphora) in China, Korea, Japan, and Malaysia (Wu 2006). O. achatina can also feed on other Lauraceae plants, such as Lindera glauca and Cinnamomum cassia, causing serious defoliates (Long et al. 2017). The mitochondrial genomes have the potential to be “molecular clock” due to its high mutation rate and low DNA recombination rate (Gai et al. 2020; Yang et al. 2020). However, the mitochondrial genome of O. achatina has not been publicly reported. Therefore, we determined to sequence the complete mitochondrial genome of O. achatina using the de novo sequencing techniques strategy to understand the mitogenomic background and genetic evolution relationship of O. achatina. In the present study, samples of O. achatina were collected from camphor trees in July 2020 in Suzhou, Jiangsu Province, China (N31.16568o, E120.62638o). Some of these samples were immediately frozen at -80°C for sequencing analysis and others were preserved in the Entomological Lab of Nanjing Forestry University, and their specimen code is 2020NJEM1855-1860. The genomic DNA was extracted from O. achatina using CTAB (cetyltrimethylammonium Ammonium Bromide) method (Huanca-Mamani et al. 2015). Raw data generated by the Illumina HiSeq platform (Illumina Inc.; San Diego, CA, USA) were subject to de novo assembly by SPAdes version 3.14 (Bankevich et al. 2012). The complete mitochondrial genomes were annotated by MITOS WebServer (http://mitos.bioinf.uni-leipzig.de/index.py) (Bernt et al. 2013) and submitted to NCBI GenBank (GenBank accession number: MT916176). The mitochondrial genome of O. achatina was 15,150 bp in size, with a nucleotide composition of 38. 9% A, 41.8% T, 11.4% C and 7.9% G. The mitochondrial genome of O. achatina comprised the entire set of 37 typical invertebrate mitochondrial genes consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a control region (D-loop). The majority-coding strand encoded 23 genes (9 PCGs and 14 tRNAs), whereas the minority-coding strand encoded 14 genes (4 PCGs, 8 tRNAs, and 2 rRNAs). The sequence and arrangement of genes were highly conserved, suggesting the similarity with typical characteristics of the genome in Lepidoptera (Liu et al. 2018; Wu et al. 2016, 2020). A total of 44 overlapping nucleotides between genes in 6 locations with a length of 2 to 25 bp were found, whereas there were 857 bp intergenic nucleotides in 22 locations, ranging from 4 to 297 bp in length. All protein-coding genes (PCGs) were initiated with ATN as the start codon except the cox1, which is no justification for continued speculation about polynucleotide start codon similar to other Lepidoptera insects (Liu et al. 2018; Singh et al. 2017; Yang et al. 2020). Ten PCGs had canonical stop codons TAA or TAG, while three had incomplete termination codons single T (cox3 and atp6) or TA (nad4L). There were 22 tRNA genes with a length between 63 and 70 bp. All tRNA genes exhibited a typical clover-leaf secondary structure, except for tRNA-Ser(AGN) lacking the dihydrouridine (DHU) arm, which is common in Lepidoptera insects (Garey and Wolstenholme 1989). The lengths of lrRNA and srRNA were 1,362 bp and 780 bp, respectively. The control region was located between srRNA and tRNA-Met with a total length of 298 bp. In addition, the BLAST-based ortholog detector OrthoFinder v2.2.7 (Emms and Steven 2019) with default parameter values were used to identify ortholog among all the protein sequences of the 24 mitochondrial genomes. The phylogenetic relationship of O. achatina and 23 Lepidoptera species was inferred from phylogenetic analysis of the 13 protein-coding genes using MEGA7.0 software with maximum likelihood method and 1000 replicate sets on bootstrap analysis. The amino acid identity (AAI) of the 13 protein-coding genes of each Lepidoptera species and O. achatina were calculated by NCBI BLASTP. The phylogenetic tree and AAI heatmap of each protein was visualized using EVOLVIEW version 2 (https://evolgenius.info//evolview-v2) (He et al. 2016). Phylogenetic analyses showed similar relationships among sampled families as shown in Yang et al. (2020). Each clade showed a monophyletic cluster and the following clades were highly supported (Fig 1): (1) Pyralidae + Crambidae; and (2) (Pyralidae + Crambidae) + (Noctuidae + (Bombycidae + Geometridae)). We also found that O. achatina strains had the closest relationship with the genus Hypsopygia and Endotricha, which were located in a clade in the clade of Pyralidae. This study can provide a useful resource for the genetic evolution of O. achatina and underline the potential importance of mitochondrial genomes in comparative genomic analyses of Lepidoptera species.

螟蛾科（Pyralidae）是鳞翅目（Lepidoptera）中最大的一科，全球已知物种超过25000种，其中部分类群为农林业害虫，如Orthaga属物种（Yang et al. 2020）。 Orthaga achatina Butler（鳞翅目：螟蛾科）是中国、韩国、日本及马来西亚境内香樟（Cinnamomum camphora）发生最为严重的害虫之一（Wu 2006）。该虫还可取食其他樟科植物，如山苍子（Lindera glauca）和肉桂（Cinnamomum cassia），可造成严重的落叶现象（Long et al. 2017）。线粒体基因组因突变率高、DNA重组率低，具备成为“分子钟”的潜力（Gai et al. 2020；Yang et al. 2020）。然而目前尚未有关于O. achatina线粒体基因组的公开报道。因此，本研究采用de novo测序技术策略对O. achatina的完整线粒体基因组进行测序，以解析其线粒体基因组背景及遗传进化关系。本研究的O. achatina样本于2020年7月采集自中国江苏省苏州市的香樟树上（北纬31.16568°，东经120.62638°）。部分样本立即置于-80℃冷冻保存用于测序分析，其余样本保存于南京林业大学昆虫学实验室，标本编号为2020NJEM1855-1860。采用CTAB（十六烷基三甲基溴化铵，cetyltrimethylammonium Bromide）法从O. achatina体内提取基因组DNA（Huanca-Mamani et al. 2015）。Illumina HiSeq平台（Illumina公司；美国加利福尼亚州圣地亚哥）产出的原始数据通过SPAdes v3.14软件进行de novo组装（Bankevich et al. 2012）。完整线粒体基因组通过MITOS WebServer（http://mitos.bioinf.uni-leipzig.de/index.py）进行注释（Bernt et al. 2013），并提交至NCBI GenBank数据库（GenBank登录号：MT916176）。 O. achatina的线粒体基因组全长15150 bp，碱基组成为A：38.9%、T：41.8%、C：11.4%、G：7.9%。该线粒体基因组包含无脊椎动物线粒体基因组典型的37个基因，包括13个蛋白质编码基因（PCGs）、22个转运RNA基因（tRNAs）、2个核糖体RNA基因（rRNAs）以及1个控制区（D-loop）。多数编码链编码23个基因（9个PCGs和14个tRNAs），少数编码链编码14个基因（4个PCGs、8个tRNAs和2个rRNAs）。基因的序列与排列方式高度保守，与鳞翅目昆虫线粒体基因组的典型特征高度相似（Liu et al. 2018；Wu et al. 2016, 2020）。共在6个基因区域发现44 bp的重叠核苷酸，重叠长度为2~25 bp；同时在22个区域存在857 bp的基因间隔区，间隔长度范围为4~297 bp。所有蛋白质编码基因均以ATN作为起始密码子，仅cox1除外，其推测使用类似其他鳞翅目昆虫的多核苷酸起始密码子（Liu et al. 2018；Singh et al. 2017；Yang et al. 2020）。10个蛋白质编码基因具有标准的终止密码子TAA或TAG，其余3个基因具有不完全终止密码子单T（cox3和atp6）或TA（nad4L）。共包含22个tRNA基因，长度介于63~70 bp之间。除tRNA-Ser(AGN)缺失二氢尿嘧啶（DHU）臂外，所有tRNA基因均呈现典型的三叶草二级结构，这一现象在鳞翅目昆虫中较为常见（Garey and Wolstenholme 1989）。lrRNA与srRNA的长度分别为1362 bp和780 bp。控制区位于srRNA与tRNA-Met之间，全长298 bp。此外，本研究采用默认参数的OrthoFinder v2.2.7软件（Emms and Steven 2019）作为基于BLAST的同源基因检测工具，对24个线粒体基因组的全部蛋白质序列进行同源基因鉴定。基于13个蛋白质编码基因，使用MEGA7.0软件以最大似然法及1000次重复的bootstrap分析，对O. achatina与其他23种鳞翅目昆虫的系统发育关系进行推断。通过NCBI BLASTP计算每种鳞翅目昆虫与O. achatina的13个蛋白质编码基因的氨基酸一致性（AAI）。使用EVOLVIEW v2（https://evolgenius.info//evolview-v2）（He et al. 2016）可视化系统发育树与各蛋白的AAI热图。系统发育分析结果显示，采样类群间的亲缘关系与Yang等（2020）的研究结果一致。各分支均为单系群，且以下分支具有较高的支持率（图1）：(1) 螟蛾科（Pyralidae）+ 草螟科（Crambidae）；(2) (螟蛾科+草螟科) + (夜蛾科（Noctuidae）+ (家蚕蛾科（Bombycidae）+ 尺蛾科（Geometridae）))。本研究还发现，O. achatina与Hypsopygia属及Endotricha属物种的亲缘关系最近，三者共同聚在螟蛾科的一个分支中。本研究可为O. achatina的遗传进化研究提供宝贵的资源，并凸显了线粒体基因组在鳞翅目昆虫比较基因组学分析中的潜在重要价值。

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2020-10-30

The complete mitochondrial genome of Orthaga achatina (Lepidoptera: Pyralidae)

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