Complete mitochondrial genome of the boreal digging frog Kaloula borealis (Anura, Microhylidae)

We sequenced the complete mitochondrial genome from the boreal digging frog Kaloula borealis. The genome sequence was 17,173 bp in size, and the gene order and contents were identical to those of previously reported amphibian mitochondrial genomes. Of 13 protein-coding genes (PCGs), 5 genes (CO2, ATPase 6, CO3, ND3, and ND4) had incomplete stop codons. Also ND1 gene used GTG as a start codon, while CO1 and ND5 genes used AGG as a stop codon. The base composition of K. borealis mitogenome showed a strong anti-G bias (6.11%) on the 3rd position of PCGs.     

Novel rearrangements of arthropod mitochondrial DNA detected with long-PCR: applications to arthropod phylogeny and evolution

Rearrangements of mitochondrial DNA gene order have been suggested as a tool for defining the pattern of evolutionary divergence in arthropod taxa. We have employed a combination of highly conserved insect-based polymerase chain reaction (PCR) primers with long-PCR to survey 14 noninsect arthropods for mitochondrial gene rearrangements. The size of the amplified fragments was used to order the primer containing genes. Five chelicerates exhibit amplicons that are consistent with the presumptive ancestral arthropod mtDNA gene order. These five species comprise two soft ticks, two prostriate hard ticks, and an opilionid. Six other chelicerates, all metastriate hard ticks, have a different arrangement that was originally discovered by this procedure and has been previously detailed in a complete mtDNA sequence. Three new arthropod mtDNA gene arrangements are described here. They were discovered in a terrestrial crustacean (Isopoda) and two myriapods (Chilopoda, centipede; Diplopoda, millipede). These rearrangements include major realignments of some of the large coding regions and two possible new positions for the tRNA(Met) (M) gene in arthropods. The long-PCR approach affords an opportunity to quickly screen divergent taxa for major rearrangements. Taxa exhibiting rearrangements can be targeted for DNA sequencing of gene boundaries to establish the details of the mtDNA organization.     

Two ancient bacterial endosymbionts have coevolved with the planthoppers (Insecta: Hemiptera: Fulgoroidea)

Background

Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes.

Results

We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis. The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13 mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites.

Conclusion

The well-supported phylogenetic placement of pseudoscorpions as sister to Acariformes differs from some previous analyses based on morphology. However, these two lineages share multiple molecular evolutionary traits, including substantial mitochondrial genome rearrangements, extensive nucleotide substitution, and loss of helices in their inferred tRNA and rRNA structures.     

Calibrating the chelicerate clock: a paleontological reply to Jeyaprakash and Hoy

Divergence times inferred for major lineages of Chelicerata (scorpions, spiders, mites, pycnogonids and xiphosurans) in a recent paper on mitochondrial phylogeny by Jeyaprakash and Hoy are compared to the known stratigraphical occurrences of these groups. Erroneous statements concerning fossil date estimates in the original study are corrected. We emphasize that the fossil record of chelicerates is more complete than is sometimes assumed, and that paleontology plays a key role in dating cladogenesis by setting minimum divergence times, which can and do falsify molecular clock estimates where the inferred divergence is substantially younger than the known fossil record. The oldest representatives of each chelicerate order are documented here, together with similar data for the major mite lineages down to family level. Through these, we hope to provide a robust framework and reference points for future molecular systematic studies of this nature.     

The complete mitochondrial genome of <Emphasis Type="Italic">Thrinchus schrenkii</Emphasis> (Orthoptera: Caelifera,Acridoidea, Pamphagidae)

Complete nucleotide sequences of mitochondrial genome (mitogenome) of Thrinchus schrenkii (Orthoptera: Acridoidea: Pamphagidae) were determined. It is 15672 bp in length and contains 71.2% A + T. All T. schrenkii protein-coding sequences except for the cytochrome oxidase subunit I (COI) start with a typical ATN codon. Instead, CCG, which is a rare but possible initiation codon, is located at the initiation context of COI. The usual termination codons (TAA and TAG) were found from 12 PCGs. However, the ND5 had incomplete termination codon (T). All tRNA genes could be folded into the typical cloverleaf secondary structure, excluding tRNA ^Ser(AGN) which forms another structure according to the Steinberg–Cedergren tertiary structure. The sizes of the large and small ribosomal RNA genes are 1319 and 848 bp, respectively. The A + T content of the A + T-rich region is 78.7%, which is the lowest among the known mitogenome of Acridoidea.     

Complete mitochondrial genome of the wild silkmoth,Saturnia boisduvalii (Lepidoptera: Saturniidae)

We sequenced mitochondrial genome (mitogenome) of the wild silkmoth, Saturnia boisduvalii (Lepidoptera: Saturniidae), which occurs in mainland Korea, and compared it with other species in Bombycoidea to characterize the genomic evolution of the superfamily. We found that the composition and arrangement of genes in the 15,257‐bp S. boisduvalii genome are typical of the majority of Lepidoptera, and the genome is biased toward A/T nucleotides, as previously reported. Comparison of individual gene divergence among bombycoid species showed that ND6 was most variable (p‐distance = 0.21), whereas COI and COII were most conserved, indicating that of all the protein‐coding genes (PCGs) ND6 appear to have evolved most rapidly. Thus, other PCGs beside COI are potential alternative markers, where scrutinized discrimination among species is required.     

丝带凤蝶线粒体基因组全序列及其系统学意义(英文)

锯凤蝶类与凤蝶科其他类群的系统发生关系及其分类学地位一直存在争议。本研究采用PCR和long PCR技术测定了属于锯凤蝶类的丝带凤蝶Sericinus montelus线粒体基因组全序列; 结合已有的其他凤蝶科物种的相应序列数据, 基于13个蛋白质编码基因重建了凤蝶科主要类群的系统发生树, 探讨了它们之间的系统发生关系。基因组分析结果表明： 丝带凤蝶线粒体基因组全长15 242 bp, 包括13个编码蛋白基因(ATP6, ATP8, COⅠ-Ⅲ, ND1-6, ND4L和Cytb)、 22个tRNA基因、 16S和12S rRNA基因以及非编码的控制区; 基因组A, T, G和C含量分别为40.1%, 40.8%, 7.4%和11.7%, 表现出明显的AT偏倚。所有的蛋白质编码基因都使用标准的起始密码子(ATN); 除ND4 和 ND4L基因使用单个的T作为终止密码子外, 其余蛋白编码基因都使用了标准的终止密码子(TAA)。除丝氨酸 tRNA的二氢尿苷突环缺失外, 所有tRNA基因都形成典型的三叶草型结构。基因组中共存在12个大小介于2~65 bp之间的基因间隔区以及15个大小介于1~8 bp之间的基因重叠区, 其中, 存在于COⅡ和tRNA^Lys之间的24 bp的间隔区在其他鳞翅目昆虫中未曾见到。以邻接法和最大简约法并基于13个蛋白质编码基因序列对凤蝶科进行了系统发生分析。结果显示, 丝带凤蝶和中华虎凤蝶Luehdorfia chinensis先构成一个支系, 再和冰清绢蝶Parnassius bremeri构成姊妹群; 表明锯凤蝶类应作为族级分类单元归于凤蝶科下的绢蝶亚科。     

The embryogenesis of the Tick Rhipicephalus (Boophilus) microplus: The establishment of a new chelicerate model system

Summary: Chelicerates, which include spiders, ticks, mites, scorpions, and horseshoe crabs, are members of the phylum Arthropoda. In recent years, several molecular experimental studies of chelicerates have examined the embryology of spiders; however, the embryology of other groups, such as ticks (Acari: Parasitiformes), has been largely neglected. Ticks and mites are believed to constitute a monophyletic group, the Acari. Due to their blood‐sucking activities, ticks are also known to be vectors of several diseases. In this study, we analyzed the embryonic development of the cattle tick, Rhipicephalus (Boophilus) microplus (Acari: Ixodidae). First, we developed an embryonic staging system consisting of 14 embryonic stages. Second, histological analysis and antibody staining unexpectedly revealed the presence of a population of tick cells with similar characteristics to the spider cumulus. Cumulus cell populations also exist in other chelicerates; these cells are responsible for the breaking of radial symmetry through bone morphogenetic protein signaling. Third, it was determined that the posterior (opisthosomal) embryonic region of R. microplus is segmented. Finally, we identified the presence of a transient ventral midline furrow and the formation and regression of a fourth leg pair; these features may be regarded as hallmarks of late tick embryogenesis. Importantly, most of the aforementioned features are absent from mite embryos, suggesting that mites and ticks do not constitute a monophyletic group or that mites have lost these features. Taken together, our findings provide fundamental common ground for improving knowledge regarding tick embryonic development, thereby facilitating the establishment of a new chelicerate model system. genesis 51:803–818. © 2013 Wiley Periodicals, Inc.     

Complete mitochondrial genome of the Amur stickleback Pungitius sinensis (Gasterosteiformes, Gasterosteidae)

The complete mitochondrial genome was sequenced from the Amur stickleback Pungitius sinensis. The genome sequence was 16,581 bp in size, and the gene order and contents were identical with those of previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), four genes (ND2, CO2, ND4, Cytb) had incomplete stop codons. The base composition of P. sinensis showed anti-G bias (9.53%) on the third position of PCGs.     

The effect of model choice on phylogenetic inference using mitochondrial sequence data: lessons from the scorpions

Chelicerates are a diverse group of arthropods, with around 65,000 described species occupying a wide range of habitats. Many phylogenies describing the relationships between the various chelicerate orders have been proposed. While some relationships are widely accepted, others remain contentious. To increase the taxonomic sampling of species available for phylogenetic study based on mitochondrial genomes we produced the nearly complete sequence of the mitochondrial genome of the scorpion Mesobuthus gibbosus. Mitochondrial gene order in M. gibbosus largely mirrors that in Limulus polyphemus but tRNA secondary structures are truncated. A recent analysis argued that independent reversal of mitochondrial genome strand-bias in several groups of arthropods, including spiders and scorpions, could compromise phylogenetic reconstruction and proposed an evolutionary model that excludes mutational events caused by strand-bias (Neutral Transitions Excluded, NTE). An arthropod dataset of six mitochondrial genes, when analyzed under NTE, yields strong support for scorpions as sister taxon to the rest of Chelicerata. We investigated the robustness of this result by exploring the effect of adding additional chelicerate genes and taxa and comparing the phylogenies obtained under different models. We find evidence that (1) placement of scorpions arising at the base of the Chelicerata is an artifact of model mis-specification and scorpions are strongly supported as basal arachnids and (2) an expanded chelicerate dataset finds support for several proposed interordinal relationships (ticks plus mites [Acari] and spiders plus whip spiders plus whip scorpions [Araneae+Pedipalpi]). Mitochondrial sequence data are subject to systematic bias that is positively misleading for evolutionary inference and thus extreme methodological care must be taken when using them to infer phylogenies.     

Complete mitochondrial genome of the Teinopalpus aureus guangxiensis (Lepidoptera: Papilionidae) and related phylogenetic analyses

In this study, we sequenced the complete mitochondrial genome of Teinopalpus aureus guangxiensis (Lepidoptera: Papilionidae), which is considered as an endemic species in China. It is listed as a vulnerable species by International Union for Conservation of Nature and Natural Resources Red List and also a first class endangered species in China. The complete mtDNA from T. aureus guangxiensis was 15,235 base pairs in length and contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. The T. aureus guangxiensis genes were in the same order and orientation as the completely sequenced mitogenomes of other lepidopteran species. All PCGs of T. aureus guangxiensis mitogenome start with a typical ATN codon and terminate in the common stop codon TAA, except that ND1 gene uses TTA, ND3 gene uses ATT, and ND4 and ND4L gene use TAA. The phylogenetic relationships were reconstructed with the concatenated sequences of the 13 PCGs of the mitochondrial genome, and phylogenetic results confirmed that Nymphalidae, Lycaenidae, Papilionidae, Pieridae are monophyletic clades.     

Complete mitochondrial genome of the marine medaka Oryzias melastigma (Beloniformes, Adrianichthyidae)

The complete mitochondrial genome was obtained from the assembled genome data sequenced by next-generation sequencer from the marine medaka Oryzias melastigma. The mitochondrial genome sequence was 16,864 bp in size, and the gene order and contents were identical with those of previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 4 genes (CO3, ND3, ND4, and Cytb) had incomplete stop codons. The base composition of O. melastigma mitogenome showed high A+T (59.65%) and anti-G bias (8.73%) on the 3rd position of PCGs.     

Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics

Only relatively recently have researchers turned to molecular methods for nematode phylogeny reconstruction. Thus, we lack the extensive literature on evolutionary patterns and phylogenetic usefulness of different DNA regions for nematodes that exists for other taxa. Here, we examine the usefulness of mtDNA for nematode phylogeny reconstruction and provide data that can be used for a priori character weighting or for parameter specification in models of sequence evolution. We estimated the substitution pattern for the mitochondrial ND4 gene from intraspecific comparisons in four species of parasitic nematodes from the family Trichostrongylidae (38-50 sequences per species). The resulting pattern suggests a strong mutational bias toward A and T, and a lower transition/transversion ratio than is typically observed in other taxa. We also present information on the relative rates of substitution at first, second, and third codon positions and on relative rates of saturation of different types of substitutions in comparisons ranging from intraspecific to interordinal. Silent sites saturate extremely quickly, presumably owing to the substitution bias and, perhaps, to an accelerated mutation rate. Results emphasize the importance of using only the most closely related sequences in order to infer patterns of substitution accurately for nematodes or for other taxa having strongly composition-biased DNA. ND4 also shows high amino acid polymorphism at both the intra- and interspecific levels, and in higher level comparisons, there is evidence of saturation at variable amino acid sites. In general, we recommend using mtDNA coding genes only for phylogenetics of relatively closely related nematode species and, even then, using only nonsynonymous substitutions and the more conserved mitochondrial genes (e.g., cytochrome oxidases). On the other hand, the high substitution rate in genes such as ND4 should make them excellent for population genetics studies, identifying cryptic species, and resolving relationships among closely related congeners when other markers show insufficient variation.      

枣食芽象甲线粒体基因组全序列测定与系统发育分析

【目的】从线粒体基因组水平上探讨枣食芽象甲Scythropus yasumatsui与近缘种的系统发育关系。【方法】利用Illumina MiSeq测序平台对枣食芽象甲线粒体基因组进行测序,对基因组序列进行拼装、注释和特征分析;利用贝叶斯法和最大似然法构建基于象甲科13个物种的线粒体基因组13个蛋白质编码基因核苷酸序列的系统发育树。【结果】结果表明,枣食芽象甲线粒体基因组全长为16 472 bp (GenBank登录号: MF807224),包含13个蛋白质编码基因、22个tRNA基因、2个rRNA基因和2个非编码控制区,37个基因的排列顺序与祖先昆虫的线粒体基因排列顺序一致。13个蛋白质编码基因的起始密码子为ATN,其中除了cob和nad1基因的完全终止密码子为TAG外,其余11个基因的完全终止密码子为TA(A)。22个tRNA基因中除了trnS1缺少DHU臂,反密码子由GCT变为TCT外,其余均能形成典型的三叶草结构。基于13个蛋白质编码基因序列构建的系统发育树结果显示,象甲科8个亚科系统发育关系为：(((隐喙象亚科(Cryptorhynchinae)+(象虫亚科(Curculioninae)+魔喙象亚科(Molytinae)))+长小蠹亚科(Platypodinae))+(粗喙象亚科(Entiminae)+Cyclominae亚科))+隐颏象亚科(Dryophthorinae)+小蠹亚科(Scolytinae))。【结论】在13种象甲科昆虫物种中,同属于粗喙象亚科的枣食芽象甲与南美果树象甲Naupactus xanthographus在系统发育树中聚为同一分支,表明基于线粒体基因组全序列的分子系统发育结果与传统的形态分类结果是一致的。     

Mity model: Tetranychus urticae, a candidate for chelicerate model organism

Chelicerates (scorpions, horseshoe crabs, spiders, mites and ticks) are the second largest group of arthropods and are of immense importance for fundamental and applied science. They occupy a basal phylogenetic position within the phylum Arthropoda, and are of crucial significance for understanding the evolution of various arthropod lineages. Chelicerates are vectors of human diseases, such as ticks, and major agricultural pests, such as spider mites, thus this group is also of importance for both medicine and agriculture. The developmental genetics of chelicerates is poorly understood and a challenge for the future progress for many aspects of chelicerate biology is the development of a model organism for this group. Toward this end, we are developing a chelicerate genetic model: the two-spotted spider mite Tetranychus urticae. T. urticae has the smallest genome of any arthropod determined so far (75 Mbp, 60% of the size of the Drosophila genome), undergoes rapid development and is easy to maintain in the laboratory. These features make T. urticae a promising reference organism for the economically important, poorly studied and species-rich chelicerate lineage.     

The Complete Mitochondrial Genome of the Beet Webworm,Spoladea recurvalis (Lepidoptera: Crambidae) and Its Phylogenetic Implications

The complete mitochondrial genome (mitogenome) of the beet webworm, Spoladea recurvalis has been sequenced. The circular genome is 15,273 bp in size, encoding 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes and containing a control region with gene order and orientation identical to that of other ditrysian lepidopteran mitogenomes. The nucleotide composition of the mitogenome shows a high A+T content of 80.9%, and the AT skewness is slightly negative (-0.023). All PCGs start with the typical ATN codons, except for COX1, which may start with the CGA codon. Nine of 13 PCGs have the common stop codon TAA; however, COX1, COX2 and ND5 utilize the T nucleotide and ND4 utilizes TA nucleotides as incomplete termination codons. All tRNAs genes are folded into the typical cloverleaf structure of mitochondrial tRNAs, except for the tRNA^Ser(AGY) gene, in which the DHU arm fails to form a stable stem-loop structure. A total of 157 bp intergenic spacers are scattered in 17 regions. The overlapping sequences are 42 bp in total and found in eight different locations. The 329 bp AT-rich region is comprised of non-repetitive sequences, including the motif ATAG, which is followed by a 14 bp poly-T stretch, a (AT₁₁ microsatellite-like repeat, which is adjacent to the motif ATTTA, and a 9 bp poly-A, which is immediately upstream from the tRNA^Met gene. Phylogenetic analysis, based on 13 PCGs and 13 PCGs+2 rRNAs using Bayesian inference and Maximum likelihood methods, show that the classification position of Pyraloidea is inconsistent with the traditional classification. Hesperioidea is placed within the Papilionoidea rather than as a sister group to it. The Pyraloidea is placed within the Macrolepidoptera with other superfamilies instead of the Papilionoidea.     

Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record

The phylum Cnidaria is comprised of remarkably diverse and ecologically significant taxa, such as the reef-forming corals, and occupies a basal position in metazoan evolution. The origin of this phylum and the most recent common ancestors (MRCAs) of its modern classes remain mostly unknown, although scattered fossil evidence provides some insights on this topic. Here, we investigate the molecular divergence times of the major taxonomic groups of Cnidaria (27 Hexacorallia, 16 Octocorallia, and 5 Medusozoa) on the basis of mitochondrial DNA sequences of 13 protein-coding genes. For this analysis, the complete mitochondrial genomes of seven octocoral and two scyphozoan species were newly sequenced and combined with all available mitogenomic data from GenBank. Five reliable fossil dates were used to calibrate the Bayesian estimates of divergence times. The molecular evidence suggests that cnidarians originated 741 million years ago (Ma) (95% credible region of 686-819), and the major taxa diversified prior to the Cambrian (543 Ma). The Octocorallia and Scleractinia may have originated from radiations of survivors of the Permian-Triassic mass extinction, which matches their fossil record well.     

Complete mitochondrial genome of the Amur stickleback Pungitius kaibarae (Gasterosteiformes, Gasterosteidae)

The complete mitochondrial genome was sequenced from the Amur stickleback Pungitius kaibarae. The genome sequence was 16,505 bp in size, and the gene order and contents were identical with the same genera Pungitius sinensis and other previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 3 genes (CO2, ND4, and Cytb) had incomplete stop codons. The base composition of P. kaibarae showed anti-G bias (8.86%) on the third position of PCGs.     

The complete mitochondrial genome of Diaphorina citri (Hemiptera: Psyllidae) and phylogenetic analysis

The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is the most serious pest of citrus as the vector of Huanglongbing (HLB), the citrus greening disease. In this study, the complete mitochondrial genome (mitogenome) of D. citri has been sequenced and annotated, and a comparative analysis is provided with known Psylloidea species. The mitogenome of D. citri is a typical circular molecular of 15,038 bp in length with an A + T content of 74.56%, contains the typical 37 genes and the gene order is identical to the other Psylloidea mitogenomes. The nucleotide composition and codon usage of D. citri are similar to the four Psylloidea species. All protein-coding genes (PCGs) use standard initiation codons (TAN), stop with TAA and TAG except ND2 and ND5 which stop with incomplete termination codon T. All tRNAs have the typical clover-leaf structure, with the exception of trnS1 lacking the dihydrouridine (DHU) arm. The control region is located between rrnL and the trnI gene with the highest A + T content among the five Psylloidea species. Phylogenetic analysis is conducted based on the 13 PCGs or/and 2 rRNAs of 23 Sternorrhycha mitogenomes. Both maximum likelihood (ML) and Bayesian inference (BI) analysis suggest a clear relationship of Psylloidea, Aleyrodoidea and Aphidoidea within Sternorrhycha, which support the traditional morphological classification.