Complete mitochondrial genome of Oxya chinensis （Orthoptera, Acridoidea）

The complete sequence of Oxya chinensis （0. chinensis） mitochondrial genome is reported here. It is 15,443 bp in length and contains 75.9% A＋T. The protein-coding genes have a similar A＋T content （75.2%）. The initiation codon of the cytochrome oxidase subunit I gene in the mitochondrial genome of O. chinensis appears to be ATC, instead of the tetranucleotides that have been reported in Locusta migratoria （L migratoria） mitochondrial genome. The sizes of the large and small ribosomal RNA genes are 1319 and 850 bp, respectively. The transfer RNA genes have been modeled and showed strong resemblance to the dipteran transfer RNAs, and all anticodons are identical to those of dipteran. The A＋T-rich region is 562 bp, shorter than that of other known Orthoptera insects. The six conserved domains were identified within the A＋T-rich region by comparing its sequence with those of other grasshoppers. The result of phylogenetic analysis based on the dataset containing 12 concatenated protein sequences confirms the close relation-ship of O. chinensis with L migratoria.     

斐豹蛱蝶线粒体基因组全序列的测定和分析(英文)

该研究对斐豹蛱蝶(Argyreus hyperbius)(鳞翅目:蛱蝶科)线粒体基因组全序列进行了测定和初步分析。结果表明:斐豹蛱蝶线粒体基因全序列全长为15156bp,包含13个蛋白质编码基因、22个tRNA和2个rRNA基因以及1个非编码的A+T富集区,基因排列顺序与其它鳞翅目种类一致;线粒体全序列核苷酸组成和密码子使用显示出明显的A+T偏好(80.8%)和轻微的AT偏移(AT skew,?0.019)。基因组中共存在11个2～52bp不等的基因间隔区,总长96bp;以及14个1～8bp不等的基因重叠区,总长34bp。除COI以CGA作为起始密码子外,13个蛋白质编码基因中的其余12个基因是以ATN作为起始密码子。除COI和COII基因是以单独的一个T为终止密码子,其余11个蛋白质编码基因都是以TAA结尾的。除了缺少DHU臂的tRNASer(AGN),其余的tRNA基因都显示典型的三叶草结构。tRNA(AGN)和ND1之间的基因间隔区包含一个ATACTAA结构域,这个结构域在鳞翅目中是保守的。A+T富集区没有较大的多拷贝重复序列,但是包含一些微小重复结构:ATAGA结构域下游的20bp poly-T结构,ATTTA结构域后的(AT)9重复,以及位于tRNAMet上游的5bp poly-A结构等。这项研究所揭示的斐豹蛱蝶的线粒体基因组特征,不仅为认识蛱蝶科的遗传多样性贡献数据,而且对于该物种的保护生物学、群体遗传学、谱系地理及演化研究等具有重要意义。     

云斑车蝗线粒体基因组全序列测定与分析

采用长距 PCR 扩增及保守引物步移法并结合克隆测序测定并注释了云斑车蝗 Gastrimargus marmoratus （Thunberg）的线粒体基因组全序列。结果表明：云斑车蝗线粒体基因组全序列为15 904 bp（GenBank登录号为EU527334）,A+T含量略高于非洲飞蝗Locusta migratoria,为76.04%,包括13个蛋白质编码基因,22个tRNA 基因,2个rRNA基因和一段1 057 bp的A+T富集区。蛋白质基因的起始密码子中,除COⅠ和ND5为TTG以外,均为昆虫典型的起始密码子ATN。ND5基因使用了不完全终止密码子T,其余基因均为典型的TAA或TAG。预测了22个tRNA基因的二级结构,发现tRNA^Ser（AGN）缺少DHU臂, tRNA^Ser（UGY）的反密码子环上有9个碱基。预测了云斑车蝗12S和16S rRNA二级结构,分别包括3个结构域30个茎环和6个结构域44个茎环。A+T富集区含有3个串联重复序列。     

残锷线蛱蝶线粒体基因组全序列及其系统学意义(英文)

对残锷线蛱蝶(Parathymasulpitia)(鳞翅目:蛱蝶科)线粒体基因组全序列进行了测定。结果表明:残锷线蛱蝶线粒体基因组全序列全长为15268bp,除了在trnS1(AGN)和trnE基因之间有一段121bp长的基因间隔外,其基因的排列顺序及排列方向与大多数已测鳞翅目物种基本一致。在蛋白质编码基因中,除cox1以CGA作为其起始密码子之外,其余12个蛋白质编码基因都以标准的ATN作为起始密码子。此外,除nad4基因以单独的T为终止密码子,其余12个蛋白质编码基因都以TAA结尾。除trnS1(AGN)缺少DHU臂之外,22个tRNA基因都显示典型的三叶草形二级结构。除A+T富集区外的非编码序列中,线粒体基因组共含有11个基因间隔区。其中,最长的一个121bp的基因间隔区位于trnS1(AGN)和trnE之间,其A+T含量高达100%。另外,和其他鳞翅目物种一样,在其A+T富集区的3’端有一段长达18bp的poly-T结构。A+T富集区内部没有明显的小卫星样多拷贝重复序列,而含有一些微卫星样的重复结构。本研究基于13种蛋白编码基因序列的组合数据,用最大似然法和贝叶斯法对蛱蝶科几个主要亚科间共9个代表物种间的系统发生关系进行了分析。结果表明,本研究的结果与前人的分子系统学研究结论基本吻合(其中,线蛱蝶亚科和釉蛱蝶亚科互为姐妹群),而与形态学的研究结论不一致。     

直翅目昆虫线粒体基因组研究进展

本文总结了本实验室对40余种直翅目昆虫的线粒体基因组序列的研究方法和主要结果.直翅目线粒体基因组研究中最重要的发现包括：（1）在直翅目昆虫线粒体基因组中发现了3种基因排列次序.蝗亚目除蜢总科外都具有DK排列.蜢总科的变色乌蜢为KD 排列,与蝗亚目其他总科不同,而与螽亚目昆虫的排序方式相同.已测出的螽亚目大多数昆虫的KD 排列顺序与典型节肢动物的完全相同,但在黄脸油葫芦Teleogryllus emma发生了tRNA^Glu,tRNA^Ser和tRNA^Asn的倒置;（2）在疑钩额螽Ruspolia dubia中发现了一种到目前为止具有最短控制区（70 bp）的线粒体基因组;（3）采用多种方法分析了昆虫A+T富集区存在的调控序列和二级结构特征,获得了昆虫A+T富集区保守序列的一致结构.采用Z曲线分析蝗虫的A+T富集区,表明也存在与原核生物复制起点类似的信号;（4）构建了30种蝗虫12S rRNA和16S rRNA的二级结构.在昆虫线粒体基因组非编码链中发现了一些类tRNA结构和tRNA异构体;（5）构建了基于线粒体基因组数据的直翅目昆虫主要亚科以上分类单元之间的系统发育关系.     

白纹佛蝗线粒体全基因组序列

通过长PCR扩增线粒体全基因组进行保守引物步移法结合克隆测序技术,对白纹佛蝗mtDNA 全序列进行了测定和分析.结果表明:白纹佛蝗线粒体基因组全长15 657 bp,包含13 个蛋白编码基因、22个tRNA 基因和2 个rRNA 基因以及1个非编码的控制区域,它们的长度分别是11 202 bp,1 486 bp,2 156 bp 和 728 bp.37个基因的位置与飞蝗的一致,有9对基因间存在41 bp重叠,重叠碱基数在 1～8 bp之间;基因间隔序列共计21处 126 bp,间隔长度从 1～20 bp不等,最大的基因间隔是20 bp,是在tRNALys 和 ATP8 基因之间.还对lrRNA和srRNA二级结构进行了预测,同时也对tRNA反密码子臂的碱基对类型以及不同链上蛋白编码基因的A/T,C/G组成偏向性进行了详细的讨论.     

武铠蛱蝶线粒体基因组全序列测定和分析

【目的】了解闪蛱蝶亚科属间及种间的分子系统进化关系。【方法】采用PCR步移法对武铠蛱蝶 Chitoria ulupi 线粒体基因组全序列进行了测定和分析。基于线粒体基因组13个蛋白质编码基因的核苷酸序列构建了38种鳞翅目昆虫的系统发育树。【结果】分析结果表明,武铠蛱蝶线粒体基因组全长15 279 bp,包括13个蛋白质编码基因、22个tRNA基因、2个rRNA基因和一段长度为391 bp的A+T富含区,基因排列顺序与其他已知近缘种昆虫相同。武铠蛱蝶线粒体基因组中存在很高的A+T含量（79.9％）。13个蛋白质编码基因中,COII以TTG作为起始密码子,COI以CGA作为起始密码子外,其余均为昆虫典型的起始密码子ATN。COII和ND4基因使用了不完全终止密码子T,其余基因均以典型的TAA为终止密码子。在所测得的22个tRNA基因中,除tRNA^Ser(AGN)缺少DHU臂外,其余tRNA均能形成典型的三叶草结构。与其他多数鳞翅目昆虫一样,武铠蛱蝶的A+T富含区中有一段由ATAGAA引导的保守的多聚T结构,长度为21 bp,并散布着一些长短不一的串联重复单元。系统发育树结果显示,总科级别的系统发育关系为：卷蛾总科＋（凤蝶总科＋（螟蛾总科＋(夜蛾总科＋蚕蛾总科＋尺蛾总科)））;在蛱蝶科物种中,武铠蛱蝶与猫蛱蝶Timelaea maculate 亲缘关系最近。【结论】基于分子标记构建的鳞翅目昆虫系统发育关系与传统的形态学分类结果基本一致。     

Cloning and characterization of a microsatellite in the mitochondrial control region of the African side-necked turtle,Pelomedusa subrufa

The nucleotide sequence of the African side-necked turtle mitochondrial control region and its flanking tRNA genes was determined. This 73% A+T-rich region is 1194 bp long. Several conserved motifs involved in the regulation of the mitochondrial genome replication process, including one conserved sequence block (CSB1), and three termination-associated sequences were identified. The most remarkable feature found in this control region was the presence of six microsatellite-containing tandem repeats between the CSB1 motif and the tRNA^Phe gene. The potential usefulness of this microsatellite sequence for population-level studies is enhanced by its unique localization in the maternally inherited mitochondrial molecule.     

Complete mitochondrial genome of Locusta migratoria migratoria (Orthoptera: Oedipodidae): three tRNA-like sequences on the N-strand

The complete 16053 bp mitochondrial genome (mitogenome) sequence of Locusta migratoria migratoria has been determined. This mitogenome contains the base compositional biases and codon usage typical of metazoans, and the RSCU values indicate a negative correlation with the C and G contents in codon. The orientation and gene order of the L. migratoria migratoria is identical to Locusta migratoria migratoiodes. An unusual feature of the L. migratoria migratoria mitogenome is the presence of three tRNA-like structures on the N-strand: one tRNA(Ile)-like and two tRNA(Leu(CUN))-like sequences. The tRNA-like sequences have proper folding structures and anticodons sequences. Two repeated DNA sequences, Rpt I and Rpt II, were found in the A+T-rich region of the L. migratoria migratoria mitogenome. Both repeated sequences have various features. In the 5' region of Rpt I, a 51 bp fragment is localized in the srRNA gene; and there are two tandemly sub-repeated DNA sequences (sub-Rpts), Rpt 1-4, within Rpt I and Rpt II. One stem-loop structure on the N-strand that may be involved in the N-strand replication initiation was found in the A+T-rich region.     

The mitochondrial genome of the quiet-calling katydids, <Emphasis Type="Italic">Xizicus fascipes</Emphasis> (Orthoptera: Tettigoniidae: Meconematinae)

To help determine whether the typical arthropod arrangement was a synapomorphy for the whole Tettigoniidae, we sequenced the mitochondrial genome (mitogenome) of the quiet-calling katydids, Xizicus fascipes (Orthoptera: Tettigoniidae: Meconematinae). The 16,166-bp nucleotide sequences of X. fascipes mitogenome contains the typical gene content, gene order, base composition, and codon usage found in arthropod mitogenomes. As a whole, the X. fascipes mitogenome contains a lower A+T content (70.2%) found in the complete orthopteran mitogenomes determined to date. All protein-coding genes started with a typical ATN codon. Ten of the 13 protein-coding genes have a complete termination codon, but the remaining three genes (COIII, ND5 and ND4) terminate with incomplete T. All tRNAs have the typical clover-leaf structure of mitogenome tRNA, except for tRNA(Ser(AGN)), in which lengthened anticodon stem (9 bp) with a bulged nuleotide in the middle, an unusual T-stem (6 bp in constrast to the normal 5 bp), a mini DHU arm (2 bp) and no connector nucleotides. In the A+T-rich region, two (TA)n conserved blocks that were previously described in Ensifera and two 150-bp tandem repeats plus a partial copy of the composed at 61 bp of the beginning were present. Phylogenetic analysis found: i) the monophyly of Conocephalinae was interrupted by Elimaea cheni from Phaneropterinae; and ii) Meconematinae was the most basal group among these five subfamilies.     

中华雏蝗（Chorthippus chinensis Tarb）线粒体基因组分析

采用Lon-PCR扩增线粒体全基因组和保守引物步移法结合克隆方法测定并拼接获得了中华雏蝗（Chorthippus chinensis Tarb）线粒体基因组全序列．序列的注释和分析结果表 明,中华雏蝗线粒体基因组序列全长15 599 bp,共有13个编码蛋白质基因、22个tRNA基因、2个rRNA基因和1个A+T富集区．基因顺序与非洲飞蝗（Locusta migratoria）相同,也发生了2个 tRNA Asp(D)和tRNALys(K)的倒置．13个编码蛋白质基因都使用了ATN作为起始密码子．除ND1以TAG和ND5的终止密码子为不完全的T外,其余11个编码蛋白质基因的终止密码子都为完整的TAA．6种直翅类昆虫13个蛋白质的氨基酸序列的联合数据集构建的系统树与形态分类系统一致,中华雏蝗与非洲飞蝗为姐妹群,并与东方蝼蛄构成一单系群．     

Complete mitochondrial genome of Chilo suppressalis (Walker) (Lepidoptera: Crambidae)

The complete sequence of the mitochondrial genome (mitogenome) of the rice stem borer Chilo suppressalis (Walker) (Lepidoptera: Crambidae) was determined to be 15,465 bp. It contains 13 protein-coding genes (PCGs), 22 tRNA genes, the large and small rRNA genes, and an A+T-rich region. The nucleotide composition of the mitogenome of C. suppressalis is highly A+T biased, accounting for 79.70% in whole mitogenome, 77.74% in PCGs, 84.70% in tRNAs, 81.20% in rRNAs and 94.19% in A+T-rich region, respectively. The PCGs have typical ATN start codons, except for cox1, which contains the unusual CGA. The C. suppressalis A+T-rich region contains a conserved structure combining the motif ATAGA and a 19-bp poly-T stretch, but absence of the 9-bp poly-A element upstream trnM.     

The complete mitochondrial genome of fall armyworm <Emphasis Type="Italic">Spodoptera frugiperda</Emphasis> (Lepidoptera:Noctuidae)

The mitochondrial genome (mitogenome) can provide important information for understanding molecular evolution and phylogenetic analyses. The complete mitogenome of Spodoptera frugiperda (Lepidoptera:Noctuidae) was determined to be 15,365 bp in length and has the typical gene order found in Noctuidae mitogenomes, it includes 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and a A+T-rich region. The nucleotide composition was biased toward A+T nucleotides (81.09 %) and the AT skew of this mitogenome was slightly positive (0.004). All PCGs were initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which was initiated by CGA. Eight of the 13 PCGs have the incomplete termination codon, T or TA. All the tRNA genes displayed the typical clover-leaf structure of mitochondrial tRNAs, with the exception of trnS1 (AGN). The A+T-rich region was 328 bp in length and consisted of several features common to the Noctuidae insects. Phylogenetic analysis showed that the S. frugiperda was within the Noctuidae.     

The complete mitogenome of the Chinese bush cricket, Gampsocleis gratiosa （Orthoptera： Tettigonioidea）

The complete mitochondrial genome (mitogenome) of Gampsocleis gratiosa was determined. The 15, 929 bp in the size of G. gratiosa mitogenome contains a typical gene content, base composition, and codon usage found in metazoan. All 13 protein coding genes (PCGs) of the G. gratiosa mitogenome start with a typical ATN codon. The usual termination codons (TAA and TAG) were found from 10 PCGs. However, the atp6, nad4, and nad5 had incomplete termination codon (T). The anticodons of all tRNAs are identical to those observed in Drosophila yakuba and Locusta migratoria, and can be folded in the form of a typical clover leaf structure except for trnS (AGN). The secondary structure of trnS (AGN) was drawn according with the Steinberg-Cedergren tertiary structure. The A T content (67.4%) of the A T-rich region is relatively lower among the mitogenome regions, in contrast, it usually contains the highest A T content for most insects. Two isolated sequence repeat regions (202 bp) were found in the A T-rich region with mapping and secondary structure information.     

Complete mitochodrial genome of the crab spider Ebrechtella tricuspidata (Araneae: Thomisidae): A novel tRNA rearrangement and phylogenetic implications for Araneae

Mitochondrial genomes are widely used for phylogenetic and phylogeographic analyses among arthropods, but there is a lack of sufficient mitochondrial genome sequence data for spiders. Herein, we sequenced and characterized the complete mitochondrial genome of a crab spider Ebrechtella tricuspidata (Araneae: Thomisidae). The circular mitochondrial genome is 14,352 bp long, including a standard set of 37 genes and an A + T-rich region. Nucleotide composition is highly biased toward A + T nucleotides (77.3%). A novel gene order rearrangement is detected by a tRNA (trnL1) translocation. Tandem repeats are not identified in the A + T-rich region. Most of the tRNAs are greatly reduced in size and cannot be folded into typical cloverleaf-shaped secondary structures. The phylogenetic analysis confirms that the mitochondrial genome sequences are useful in resolving higher-level relationship of Araneae. Overall, our data present in this study will elevate our knowledge on the architecture and evolution of spider mitochondrial genome.     

The complete mitochondrial genome of grouse locust Tetrix japonica (Insecta: Orthoptera: Tetrigoidea)

We have determined the complete mitochondrial genome of a species of grouse locust, Tetrix japonica. The total length of the T. japonica mitogenome is 15,128 bp with 75.57% A+T content. It consists of 13 protein-coding, 22 transfer RNA (tRNA), and 2 ribosomal RNA (rRNA) genes, and an A+T-rich region. The A+T-rich region was located between the small rRNA and tRNA-Ile genes and is 531 bp in length.     

Characterization of the complete mitochondrial genomes of Cnaphalocrocis medinalis and Chilo suppressalis (Lepidoptera: Pyralidae)

The complete mitochondrial genomes (mitogenomes) of Cnaphalocrocis medinalis and Chilo suppressalis (Lepidoptera: Pyralidae) were determined and analyzed. The circular genomes were 15,388 bp long for C. medinalis and 15,395 bp long for C. suppressalis. Both mitogenomes contained 37 genes, with gene order similar to that of other lepidopterans. Notably, 12 protein-coding genes (PCGs) utilized the standard ATN, but the cox1 gene used CGA as the initiation codon; the cox1, cox2, and nad4 genes in the two mitogenomes had the truncated termination codons T, T, and TA, respectively, but the nad5 gene was found to use T as the termination codon only in the C. medinalis mitogenome. Additionally, the codon distribution and Relative Synonymous Codon Usage of the 13 PCGs in the C. medinalis mitogenome were very different from those in other pyralid moth mitogenomes. Most of the tRNA genes had typical cloverleaf secondary structures. However, the dihydrouridine (DHU) arm of the trnS1(AGN) gene did not form a stable stem-loop structure. Forty-nine helices in six domains, and 33 helices in three domains were present in the secondary structures of the rrnL and rrnS genes of the two mitogenomes, respectively. There were four major intergenic spacers, except for the A+T-rich region, spanning at least 12 bp in the two mitogenomes. The A+T-rich region contained an 'ATAGT(A)'-like motif followed by a poly-T stretch in the two mitogenomes. In addition, there were a potential stem-loop structure, a duplicated 25-bp repeat element, and a microsatellite '(TA)(13)' observed in the A+T-rich region of the C. medinalis mitogenome. A poly-T motif, a duplicated 31-bp repeat element, and a 19-bp triplication were found in the C. suppressalis mitogenome. However, there are many differences in the A+T-rich regions between the C. suppressalis mitogenome sequence in the present study and previous reports. Finally, the phylogenetic relationships of these insects were reconstructed based on amino acid sequences of mitochondrial 13 PCGs using Bayesian inference and maximum likelihood methods. These molecular-based phylogenies support the traditional morphologically based view of relationships within the Pyralidae.     

Characterization of mitochondrial genome of Chinese wild mulberry silkworm, Bomyx mandarina (Lepidoptera: Bombycidae)

The complete mitochondrial genome of Chinese Bombyx mandarina(ChBm) was determined.The cir-cular genome is 15682 bp long, and contains a typical gene complement, order, and arrangement iden-tical to that of Bombyx mori(B.mori) and Japanese Bombyx mandarina(JaBm) except for two addi-tional tRNA-like structures:tRNASer(TGA)-like and tRNAIle(TAT)-like.All protein-coding sequences are initi-ated with a typical ATN codon except for the COI gene, which has a 4-bp TTAG putative initiator codon.Eleven of 13 protein-coding genes(PCGs) have a complete termination codon(all TAA), but the re-maining two genes terminate with incomplete codons.All tRNAs have the typical clover-leaf structures of mitochondrial tRNAs, with the exception of tRNASer(TGA)-like, with a four stem-and-loop structure.The length of the A T-rich region of ChBm is 484 bp, shorter than those of JaBm(747 bp) and B.mori(494―499 bp).Phylogenetic analysis among B.mori, ChBm, JaBm, and Antheraea pernyi(Anpe) showed that B.mori is more closely related to ChBm than JaBm.The earliest divergence time estimate for B.mori-ChBm and B.mori-JaBm is about 1.08±0.18―1.41±0.24 and 1.53±0.20―2.01±0.26 Mya, respec-tively.ChBm and JaBm diverged around 1.11±0.16―1.45±0.21 Mya.     

Population genetic structure of the migratory rice leaf roller, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), inferred from the mitochondrial A+T-rich region and nuclear ITS2 sequences

The population genetics of the migratory rice leaf roller, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), was characterized using the maternally inherited mitochondrial A+T-rich region and bi-parentally inherited nuclear internal transcribed spacer 2 (ITS2). One hundred and eighty-seven specimens of the rice leaf roller collected from 13 Korean and Chinese localities revealed 94 A+T-rich region haplotypes, ranging in sequence length from 339 to 348 bp and 129 ITS2 sequence types, ranging from 444 to 450 bp, with maximum sequence divergences of 4.55 and 4.43%, respectively. The finding of almost no significant F(ST), even among Chinese and Korean localities, except for one Chinese island population (ITS2 only), and the finding of genetic variance principally at the within-population level indicate the genetic structure characteristics of a migratory insect that is well connected among populations due to high gene flow. Detection of significant F(ST) estimates of one offshore island population in China (Haikou) compared to most others only by ITS2 rather than by the mitochondrial A+T-rich region, as well as the somewhat higher degree of genetic differentiation seen on ITS2, suggest the importance of female dispersal. Structural analysis of the A+T-rich region revealed a poly-T stretch (10-16 bp), a microsatellite-like AT repeat (10-14 repeats), and a 5-bp long-motif "ATTTA". The typical 5-bp long conserved motif sequence (ATAGA) previously detected in other lepidopterans was found to be ATAG in the C. medinalis A+T-rich region.