Reconstructing intraordinal relationships in Lepidoptera using mitochondrial genome data with the description of two newly sequenced lycaenids, Spindasis takanonis and Protantigius superans (Lepidoptera: Lycaenidae)

Lepidoptera is one of the largest insect orders, but the phylogenetic relationships within this order, have yet to be adequately described. Among these unresolved relationships include those regarding the monophyly of the Macrolepidoptera and interfamilial relationships of the true butterflies superfamily Papilionoidea. We present two new mitochondrial genomes (mitogenomes) belonging to the butterfly family Lycaenidae to explore the phylogenetic relationships existing among lepidopteran superfamilies and true butterfly families from a mitogenome perspective, and to evaluate the characteristics of the lepidopteran mitogenomes. Our consensus phylogeny of the Lepidoptera largely supported the superfamilial relationships (((((Bombycoidea + Geometroidea) + Noctuoidea) + Pyraloidea) + Papilionoidea) + Tortricoidea), signifying a lack of support for a traditionally defined Macrolepidoptera. The familial relationships of the true butterflies concordantly recovered the previously proposed phylogenetic hypothesis (((Lycaenidae + Nymphalidae) + Pieridae) + Papilionidae). The test for the effect of optimization schemes (exclusion and inclusion of third codon position of PCGs and two rRNA genes, with and without partitions) on the resolution and relationships within the Lepidoptera have demonstrated that the majority of analyses did not substantially alter the relevant topology and node support, possibly as the result of relatively strong signal in mitogenomes for intraordinal relationships in Lepidoptera.     

The mitochondrial genome of the butterfly Papilio xuthus (Lepidoptera: Papilionidae) and related phylogenetic analyses

The nearly complete mitochondrial genome of the butterfly Papilio xuthus (Lepidoptera: Papilionidae) was sequenced for its nucleotide sequence of 13,964 bp. The genome has a typical gene order identical to other lepidopteran species. All tRNAs showed same stable canonical clover-leaf structure as those of other insects, except for tRNA^Ser (AGN), in which the dihydrouracil arm (DHU arm) could not form stable stem–loop structure. Anomalous initiation codons have been observed for the cox1 gene, where the ATTACG hexa-nucleotide was believed to be involved in the initiation signaling. Twelve mitochondrial protein-coding gene sequence data were used to infer the phylogenetic relationships among the insect orders. Even though the number of insect orders represented by complete mitochondrial genomes is still limited, several well-established relationships are evident in the phylogenetic analysis of the complete sequences. Monophyly of the Homometabola was not supported in this paper. Phylogenetic analyses of the available species of Bombycoidea, Pyraloidea, Papilionoidea and Tortricidea bolstered the current morphology-based hypothesis that Bombycoidea, Pyraloidea and Papilionoidea are monophyletic (Obtectomera). Bombycoidea (Bombyx mandarina and Antheraea pernyi) and Papilionoidea (P. xuthus and Coreana raphaelis) formed a sister group.     

Identifying two moth species (Lepidoptera: Ditrysia) from Saudi Arabia using mitochondrial 16S rRNA sequences

The mitochondrial genetic markers are considered useful tools for discrimination between more closely related lepidopteran taxa. Therefore, the present study aimed to investigate the role of mitochondrial (mt) 16 s rRNA gene in the determination of the taxonomic position for two moth species within Ditrysia clade. Maximum likelihood analysis has indicated a well-supported dendrogram based on the Tamura-Nei model for the recovered lepidopterans. The mt 16 s rRNA query sequences from 24 species within seven families were analyzed. This analysis and bootstrap confidence revealed two major clades representing Glossata suborder within Lepidoptera, with a close relationship of Noctuoidea + (Pyraloidea (Hesperioidea + Papilionoidea)). The subfamily Heliothinae forming a sister group with Risobinae (Noctinae + Hadeninae). In addition, there is a clear observation about the close relation between Phycitinae + Galleriinae within Pyraloidea and Cyrestinae + Limenitidinae within Papilionoidea. The present study supported that the Helicoverpa and Meroptera species are the first accounts of these genera inhabiting Saudi Arabia.     

The complete mitochondrial genome of <Emphasis Type="Italic">Vanessa indica</Emphasis> and phylogenetic analyses of the family Nymphalidae

Vanessa indica is a small butterfly lacking historical molecular and biological research. Vanessa indica belongs to the family Nymphalidae (Lepidoptera: Papilionoidea), which is the largest group of butterflies and are nearly ubiquitous. However, after more than a century of taxonomic and molecular studies, there is no consensus for family classification, and the phylogenetic relationships within Nymphalidae are controversial. The first objective was to sequence and characterize the complete mitochondrial genome of V. indica. The most important objective was to completely reconstruct the phylogenetic relationships for family members within Nymphalidae. The mitochondrial genomic DNA (mtDNA) of V. indica was extracted and amplified by polymerase chain reaction. The complete mitochondrial sequence was annotated and characterized by analyzing sequences with SeqMan program. The phylogenetic analyses were conducted on thirteen protein coding genes (PCGs) in 95 mtDNA of Nymphalidae downloaded from GenBank for reference using the maximum likelihood method and Bayesian inference to ensure the validity of the results. The complete mitogenome was a circular molecule with 15,191 bp consisting of 13 protein coding genes, two ribosomal RNA genes (16S rRNA and 12S rRNA), 22 transfer RNA (tRNA) genes, and an A?+?T-rich region (D-loop). The nucleotide composition of the genome was highly biased for A?+?T content, which accounts for 80.0% of the nucleotides. All the tRNAs have putative secondary structures that are characteristic of mitochondrial tRNAs, except tRNA^Ser(AGN). All the PCGs started with ATN codons, except cytochrome c oxidase subunit 1 (COX1), which was found to start with an unusual CGA codon. Four genes were observed to have unusual codons: COX1 terminated with atypical TT and the other three genes terminated with a single T. The A?+?T rich region of 327 bp consisted of repetitive sequences, including a ATAGA motif, a 19-bp poly-T stretch, and two microsatellite-like regions (TA)₈. The phylogenetic analyses consistently placed Biblidinae as a sister cluster to Heliconiinae and Calinaginae as a sister clade to Satyrinae. Moreover, the phylogenetic tree identified Libytheinae as a monophyletic group within Nymphalidae. The complete mitogenome of V. indica was 15,191 bp with mitochondrial characterizations common for lepidopteran species, which enriched the mitochondria data of Nymphalid species. And the phylogenetic analysis revealed different classifications and relationships than those previously described. Our results are significant because they would be useful in further understanding of the evolutionary biology of Nymphalidae.     

Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers

Phylogenetic relationships among major clades of butterflies and skippers have long been controversial, with no general consensus even today. Such lack of resolution is a substantial impediment to using the otherwise well studied butterflies as a model group in biology. Here we report the results of a combined analysis of DNA sequences from three genes and a morphological data matrix for 57 taxa (3258 characters, 1290 parsimony informative) representing all major lineages from the three putative butterfly super-families (Hedyloidea, Hesperioidea and Papilionoidea), plus out-groups representing other ditrysian Lepidoptera families. Recently, the utility of morphological data as a source of phylogenetic evidence has been debated. We present the first well supported phylogenetic hypothesis for the butterflies and skippers based on a total-evidence analysis of both traditional morphological characters and new molecular characters from three gene regions (COI, EF-1alpha and wingless). All four data partitions show substantial hidden support for the deeper nodes, which emerges only in a combined analysis in which the addition of morphological data plays a crucial role. With the exception of Nymphalidae, the traditionally recognized families are found to be strongly supported monophyletic clades with the following relationships: (Hesperiidae+(Papilionidae+(Pieridae+(Nymphalidae+(Lycaenidae+Riodinidae))))). Nymphalidae is recovered as a monophyletic clade but this clade does not have strong support. Lycaenidae and Riodinidae are sister groups with strong support and we suggest that the latter be given family rank. The position of Pieridae as the sister taxon to nymphalids, lycaenids and riodinids is supported by morphology and the EF-1alpha data but conflicted by the COI and wingless data. Hedylidae are more likely to be related to butterflies and skippers than geometrid moths and appear to be the sister group to Papilionoidea+Hesperioidea.     

Complete mitochondrial genomes of five skippers (Lepidoptera: Hesperiidae) and phylogenetic reconstruction of Lepidoptera

We sequenced mitogenomes of five skippers (family Hesperiidae, Lepidoptera) to obtain further insight into the characteristics of butterfly mitogenomes and performed phylogenetic reconstruction using all available gene sequences (PCGs, rRNAs, and tRNAs) from 85 species (20 families in eight superfamilies). The general genomic features found in the butterflies also were found in the five skippers: a high A + T composition (79.3%–80.9%), dominant usage of TAA stop codon, similar skewness pattern in both strands, consistently length intergenic spacer sequence between tRNA^Gln and ND2 (64–87 bp), conserved ATACTAA motif between tRNA^{Ser (UCN)} and ND1, and characteristic features of the A + T-rich region (the ATAGA motif, varying length of poly-T stretch, and poly-A stretch). The start codon for COI was CGA in four skippers as typical, but Lobocla bifasciatus evidently possessed canonical ATG as start codon. All species had the ancestral arrangement tRNA^Asn/tRNA^{Ser (AGN)}, instead of the rearrangement tRNA^{Ser (AGN)}/tRNA^Asn, found in another skipper species (Erynnis). Phylogenetic analyses using all available genes (PCGs, rRNAS, and tRNAs) yielded the consensus superfamilial relationships ((((((Bombycoidea + Noctuoidea + Geometroidea) + Pyraloidea) + Papilionoidea) + Tortricoidea) + Yponomeutoidea) + Hepialoidea), confirming the validity of Macroheterocera (Bombycoidea, Noctuoidea, and Geometroidea in this study) and its sister relationship to Pyraloidea. Within Rhopalocera (butterflies and skippers) the familial relationships (Papilionidae + (Hesperiidae + (Pieridae + ((Lycaenidae + Riodinidae) + Nymphalidae)))) were strongly supported in all analyses (0.98–1 by BI and 96–100 by ML methods), rendering invalid the superfamily status for Hesperioidea. On the other hand, current mitogenome-based phylogeny did not find consistent superfamilial relationships among Noctuoidea, Geometroidea, and Bombycoidea and the familial relationships within Bombycoidea between analyses, requiring further taxon sampling in future studies.     

The complete mitochondrial genome of Biston panterinaria (Lepidoptera: Geometridae), with phylogenetic utility of mitochondrial genome in the Lepidoptera

The complete mitochondrial genome (mitogenome) of the Chinese pistacia looper Biston panterinaria was sequenced and annotated (15,517 bp). It contains the typical 37 genes of animal mitogenomes and a high A + T content (79.5%). All protein coding genes (PCGs) use standard ATN initiation codons except for cytochrome c oxidase 1 (COX1) with CGA. Eleven PCGs use a common stop codon of TAA or TAG, whereas COX2 and NADH dehydrogenase 4 (ND4) use a single T. All transfer RNA (tRNA) genes have the typical clover-leaf structure with the exception of tRNA^Ser(AGN). We reconstructed a preliminary mitochondrial phylogeny of six ditrysian superfamilies and performed comparative analyses of inference methods (Bayesian Inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP)), dataset compositions (including and excluding 3rd codon positions), and alignment methods (Muscle, Clustal W, and MAFFT). Our analyses indicated that inference methods and dataset compositions more significantly affected the phylogenetic results than alignment methods. BI analysis consistently revealed uncontroversial relationships with all dataset compositions. By contrast, ML analysis failed to reconstruct stable phylogeny at two nodes, whereas MP analysis had more difficulties in the tree resolution and nodal support. Distinct from most previous studies, our analyses revealed that Geometroidea had a closer lineage relationship with Bombycoidea than Noctuoidea. Similar to previous molecular studies, our analyses revealed that Hesperiidae were nested in the Papilionoidea clade, providing further evidence to the previous concept that Papilionoidea was paraphyletic, and none of the butterflies were associated with the Macroheterocera.     

Complete mitochondrial genome of Spilosoma lubricipedum (Noctuoidea: Erebidae) and implications for phylogeny of noctuid insects

Mitochondrial genomes (mitogenomes) have been widely used for studies on phylogenetic relationships and molecular evolutionary biology. Here, the complete mitogenome sequence of Spilosoma lubricipedum (Noctuoidea: Erebidae: Arctiinae) was determined (total length 15,375 bp) and phylogenetic analyses S. lubricipedum were inferred from available noctuid sequence data. The mitogenome of S. lubricipedum was found to be highly A + T-biased (81.39%) and exhibited negative AT- and GC-skews. All 13 protein-coding genes (PCGs) were initiated by ATN codons, except for cox1 with CGA. All tRNAs exhibited typical clover-leaf secondary structures, except for trnS1. The gene order of the S. lubricipedum mitogenome was trnM-trnI-trnQ-nad2. The A + T-rich region of S. lubricipedum contained several conservative features common to noctuid insects. Phylogenetic analysis within Noctuoidea was carried out based on mitochondrial data. Results showed that S. lubricipedum belonged to Erebidae and the Noctuoidea insects could be divided into five well-supported families (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))).     

The first complete mitochondrial genome from Bostrychus genus (Bostrychus sinensis) and partitioned Bayesian analysis of Eleotridae fish phylogeny

To understand the phylogenetic position of Bostrychus sinensis in Eleotridae and the phylogenetic relationships of the family, we determined the nucleotide sequence of the mitochondrial (mt) genome of Bostrychus sinensis. It is the first complete mitochondrial genome sequence of Bostrychus genus. The entire mtDNA sequence was 16508 bp in length with a standard set of 13 protein-coding genes, 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a noncoding control region. The mitochondrial genome of B. sinensis had common features with those of other bony fishes with respect to gene arrangement, base composition, and tRNA structures. Phylogenetic hypotheses within Eleotridae fish have been controversial at the genus level. We used the mitochondrial cytochrome b (cytb) gene sequence to examine phylogenetic relationships of Eleotridae by using partitioned Bayesian method. When the specific models and parameter estimates were presumed for partitioning the total data, the harmonic mean –lnL was improved. The phylogenetic analysis supported the monophyly of Hypseleotris and Gobiomorphs. In addition, the Bostrychus were most closely related to Ophiocara, and the Philypnodon is also the sister to Microphlypnus, based on the current datasets. Further, extensive taxonomic sampling and more molecular information are needed to confirm the phylogenetic relationships in Eleotridae.     

Filling the gaps in the classification of the Digenea Carus, 1863: systematic position of the Proterodiplostomidae Dubois, 1936 within the superfamily Diplostomoidea Poirier, 1886, inferred from nuclear and mitochondrial DNA sequences

The Diplostomida Olson, Cribb, Tkach, Bray & Littlewood, 2003 is the less diverse order of the two orders within the subclass Digenea Carus, 1863 and is currently classified into three superfamilies, i.e. Brachylaimoidea Joyeux & Foley, 1930, Diplostomoidea Poirier, 1886, and Schistosomatoidea Stiles & Hassall, 1898. Although the suprageneric-level relationships have been elucidated with the use of molecular markers, the lack of representation of some groups obscure the phylogenetic relationships among families, rendering the classification unstable. Here, we tested the phylogenetic position of the family Proterodiplostomidae Dubois, 1936 based on partial 28S rDNA and complete 18S rDNA sequences for Crocodilicola pseudostoma (Willemoes-Suhm, 1870), a crocodile parasite that has been found as a progenetic metacercaria parasitising the pale catfish Rhamdia guatemalensis (Günther) in Mexico and in other siluruforms in the Neotropics. We augmented the representation of the species, genera and families within the Diplostomida, including mostly representatives of the superfamily Diplostomoidea, and assembled a dataset that contains 49 species for the 28S rRNA gene, and 45 species for the 18S rRNA gene. Additionally, we explored the phylogenetic signal of the mitochondrial gene cox1 in reconstructing the phylogenetic relationships of selected members of the superfamily. Our analyses showed that the family Proterodiplostomidae is the sister taxon to the paraphyletic Diplostomidae Poirier, 1886 and Strigeidae Railliet, 1919, with Cyathocotylidae Mühling, 1898 + Brauninidae Wolf, 1903 as their sister group. Analysis of concatenated 18S + 28S sequences revealed the Liolopidae Odhner, 1912 as the basal group of the superfamily Diplostomoidea, although analyses of independent datasets showed that the position of this family remains uncertain. Analysis based on cox1 unequivocally resolved the Proterodiplostomidae as the sister taxon to the Diplostomidae and Strigeidae, although the Cyathocotylidae was nested in a different clade, along with brachylaimoids and schistosomatoids.     

Phylogenetic relationships of true butterflies (Lepidoptera: Papilionoidea) inferred from COI, 16S rRNA and EF-1α sequences

The molecular phylogenetic relationships among true butterfly families (superfamily Papilionoidea) have been a matter of substantial controversy; this debate has led to several competing hypotheses. Two of the most compelling of those hypotheses involve the relationships of (Nymphalidae + Lycaenidae) + (Pieridae + Papilionidae) and (((Nymphalidae + Lycaenidae) + Pieridae) + Papilionidae). In this study, approximately 3,500 nucleotide sequences from cytochrome oxidase subunit I (COI), 16S ribosomal RNA (16S rRNA), and elongation factor-1 alpha (EF-1α) were sequenced from 83 species belonging to four true butterfly families, along with those of three outgroup species belonging to three lepidopteran superfamilies. These sequences were subjected to phylogenetic reconstruction via Bayesian Inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP) algorithms. The monophyletic Pieridae and monophyletic Papilionidae evidenced good recovery in all analyses, but in some analyses, the monophylies of the Lycaenidae and Nymphalidae were hampered by the inclusion of single species of the lycaenid subfamily Miletinae and the nymphalid subfamily Danainae. Excluding those singletons, all phylogenetic analyses among the four true butterfly families clearly identified the Nymphalidae as the sister to the Lycaenidae and identified this group as a sister to the Pieridae, with the Papilionidae identified as the most basal linage to the true butterfly, thus supporting the hypothesis: (Papilionidae + (Pieridae + (Nymphalidae + Lycaenidae))).     

Mitochondrial genome characteristics of Somena scintillans (Lepidoptera: Erebidae) and comparation with other Noctuoidea insects

In this study, mitogenome of Somena scintillans (Lepidoptera: Erebidae) were sequenced and compared with other Noctuoidea species. The mitogenome is 15,410 base pairs in length. All 13 protein-coding genes (PCGs) are initiated by ATN codons except cox1 with CGA and all of PCGs terminate with TAA except nad4 with TAG. The codons ACG and CGC are absent. All the tRNA genes could be folded into the typical cloverleaf secondary structure except the trnS1 which not only loses dihydrouridine (DHU) arm but also mutates its anticodon into TCT. In the AT-rich region of the mitogenome the motif ‘ATAGA’ mutates to ‘ATATA’ and two copies of 161 bp-tandem repeats and two ‘TA’ short tandem repeats are founded. Phylogenetic analyses showed that S. scintillans is clustered into subfamily Lymatriinae. The phylogenetic relationships within Noctuoidea is (((Nolidae + (Euteliidae + Noctuidae)) + Erebidae) + Notodontidae)     

The complete mitochondrial genomes of two ghost moths, Thitarodes renzhiensis and Thitarodes yunnanensis: the ancestral gene arrangement in Lepidoptera

ABSTRACT: BACKGROUND: Lepidoptera encompasses more than 160,000 described species that have been classified into 45-48 superfamilies. The previously determined Lepidoptera mitochondrial genomes (mitogenomes) are limited to six superfamilies of the most derived lepidopteran lineage Ditrysia. Compared with the ancestral insect gene order, these mitogenomes all contain a tRNA rearrangement. To gain new insights into Lepidoptera mitogenome evolution, we sequenced the mitogenomes of two ghost moths that belong to primitive lepidopteran lineages and conducted a comparative mitogenomic analysis across Lepidoptera. RESULTS: The mitogenomes of Thitarodes renzhiensis and T. yunnanensis are 16,173 bp and 15,814 bp long with an A+T content of 81.28% and 82.33%, respectively. Different tandem repeats in the A+T-rich region mainly account for the size difference between the two mitogenomes. Both mitogenomes include 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. The 1,584-bp sequence from rrnS to nad2 was also determined for Thitarodes sp.QL, which has no repetitive sequence in the A+T-rich region. All three Thitarodes species possess the ancestral gene order with trnI-trnQ-trnM located between the A+T-rich region and nad2, which is different from the gene order trnM-trnI-trnQ in all previously sequenced Lepidoptera species. The formerly identified conserved elements of Lepidoptera mitogenomes (i.e. the motif 'ATAGA' and poly-T stretch in the A+T-rich region and the long intergenic spacer upstream of nad2) are absent in the Thitarodes mitogenomes. The phylogenetic analysis supports that Hepialoidea, represented by T. renzhiensis and T. yunnanensis, occupies a basal position in the currently sampled seven superfamilies. The relationships of the other six superfamilies are (((((Bombycoidea + Geometroidea) + Noctuoidea) + Pyraloidea) + Papilionoidea) + Tortricoidea). CONCLUSION: The mitogenomes of T. renzhiensis and T. yunnanensis exhibit unusual features compared with the previously determined Lepidoptera mitogenomes. Their ancestral gene order indicates that the tRNA rearrangement event occurred after Lepidoptera diverged from other holometabolous insect orders. Phylogenetic analysis based on mitogenome sequences is a power tool for addressing phylogenetic relationships among major Lepidoptera superfamilies. Characterization of the two ghost moth mitogenomes has enriched our knowledge of Lepidoptera mitogenomes and contributed to our understanding of the mechanisms underlying mitogenome evolution, especially gene rearrangements.     

Complete mitochondrial genome sequence of <Emphasis Type="Italic">Cucullaea labiata</Emphasis> (Arcoida: Cucullaeidae) and phylogenetic implications

The complete mitochondrial genome of Cucullaea labiata (Arcoida: Cucullaeidae) was firstly determined in this study in order to better understand the phylogenetic relationship between Cucullaeidae and Arcidae. The C. labiata mitochondrial genome was 25,845 bp in size and contained 12 protein-coding genes, 2 rRNA and 22 tRNA genes. The number and the location of the tRNA genes were different from three Arcidae species (Scapharca broughtonii, Scapharca kagoshimensis and Tegillarca granosa). Gene arrangement also differed dramatically. The length of the non-coding regions was 10,559 bp, in which the largest one (6057 bp) included eight point nine copies of a 659 bp repeat motif. The number of repeated sequences was different in different individuals, similar to the findings from the mitochondrial genome of S. broughtonii and Placopecten magellanicus. One intron was found in cox1 gene both in CL_98 and in CL_99 individuals of C. labiata. The reason why mitochondrial introns are retained so scarcely in bivalve taxa needs further research. Phylogenetic analyses based on 12 concatenated amino acid sequences of protein-coding genes supported Cucullaeidae was the sister group of Arcidae.     

Complete mitochondrial genome of Saturnia jonasii (Lepidoptera: Saturniidae): Genomic comparisons and phylogenetic inference among Bombycoidea

The complete mitochondrial genome (mitogenome) of Saturnia jonasii (Lepidoptera: Saturniidae) was sequenced and compared to those of 19 other bombycoid species. Furthermore, the mitogenome sequences were used to infer phylogenetic relationships among bombycoid species. The 15,261-bp Saturnia jonasii mitogenome contained the typical sets of genes and gene arrangements found in majority of Lepidoptera. All Bombycoidea species, including Saturnia jonasii, have a 15–33-bp spacer sequence at the trnS₂-ND1 junction. The phylogenetic reconstruction of bombycoid species consistently and strongly supported monophylies of the families, Saturniidae, Bombycidae, and Sphingidae, based on Bayesian inference (BI) and maximum-likelihood (ML) methods. Among these families, the Bombycidae and Sphingidae species consistently showed a sister relationship, regardless of data partitions; the BI method strongly supported this relationship, whereas it was moderately supported using the ML method.     

The complete mitochondrial genome of Eterusia aedea (Lepidoptera,Zygaenidae) and comparison with other zygaenid moths

Zygaenidae comprises >1036 species, including many folivorous pests in agriculture. In the present study, the complete mitochondrial genome (mitogenome) of a major pest of tea trees, Eterusia aedea was determined. The 15,196-bp circular genome contained the common set of 37 mitochondrial genes (including 13 protein-coding genes, two rRNA genes, and 22 tRNA genes) and exhibited the similar genomic features to reported Zygaenidae mitogenome. Comparative analyses of Zygaenidae mitogenomes showed a typical evolutionary trend of lepidopteran mitogenomes. In addition, we also investigated the gene order of lepidopteran mitogenomes and proposed that the novel gene order trnA-trnR-trnN-trnE-trnS-trnF from Zygaenidae and Gelechiidae and most other gene rearrangements of this tRNA cluster evolved independently. Finally, the mitogenomic phylogeny of Lepidoptera was reconstructed based on multiple mitochondrial datasets. And all the phylogenetic results revealed the sister relationships of Cossoidea and Zygaenoidea with both BI and ML methods, which is the first stable mitogenomic evidence for this clade.     

The complete mitochondrial genome of the fall webworm,Hyphantria cunea (Lepidoptera: Arctiidae)

The complete mitochondrial genome (mitogenome) of the fall webworm, Hyphantria cunea (Lepidoptera: Arctiidae) was determined. The genome is a circular molecule 15 481 bp long. It presents a typical gene organization and order for completely sequenced lepidopteran mitogenomes, but differs from the insect ancestral type for the placement of tRNA^Met. The nucleotide composition of the genome is also highly A + T biased, accounting for 80.38%, with a slightly positive AT skewness (0.010), indicating the occurrence of more As than Ts, as found in the Noctuoidea species. All protein-coding genes (PCGs) are initiated by ATN codons, except for COI, which is tentatively designated by the CGA codon as observed in other lepidopterans. Four of 13 PCGs harbor the incomplete termination codon, T or TA. All tRNAs have a typical clover-leaf structure of mitochondrial tRNAs, except for tRNA^Ser(AGN), the DHU arm of which could not form a stable stem-loop structure. The intergenic spacer sequence between tRNA^Ser(AGN) and ND1 also contains the ATACTAA motif, which is conserved across the Lepidoptera order. The H. cunea A+T-rich region of 357 bp is comprised of non-repetitive sequences, but harbors several features common to the Lepidoptera insects, including the motif ATAGA followed by an 18 bp poly-T stretch, a microsatellite-like (AT)₈ element preceded by the ATTTA motif, an 11 bp poly-A present immediately upstream tRNA^Met. The phylogenetic analyses support the view that the H. cunea is closerly related to the Lymantria dispar than Ochrogaster lunifer, and support the hypothesis that Noctuoidea (H. cunea, L. dispar, and O. lunifer) and Geometroidea (Phthonandria atrilineata) are monophyletic. However, in the phylogenetic trees based on mitogenome sequences among the lepidopteran superfamilies, Papillonoidea (Artogeia melete, Acraea issoria, and Coreana raphaelis) joined basally within the monophyly of Lepidoptera, which is different to the traditional classification.     

Complete mitochondrial genome of the Eurasian flying squirrel Pteromys volans (Sciuromorpha, Sciuridae) and revision of rodent phylogeny

In this study, the complete mitochondrial genome of the Eurasian flying squirrel Pteromys volans (Rodentia, Sciuromorpha, Sciuridae) was sequenced and characterized in detail. The entire mitochondrial genome of P. volans consisted of 16,513 bp and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. Its gene arrangement pattern was consistent with the mammalian ground pattern. The overall base composition and AT contents were similar to those of other rodent mitochondrial genomes. The light-strand origin generally identified between tRNA ^Asn and tRNA ^Cys consisted of a secondary structure with an 11-bp stem and an 11-bp loop. The large control region was constructed of three characteristic domains, ETAS, CD, and CSB without any repeat sequences. Each domain contained ETAS1, subsequences A, B, and C, and CSB1, respectively. In order to examine phylogenetic contentious issues of the monophyly of rodents and phylogenetic relationships among five rodent suborders, here, phylogenetic analyses based on nucleotide sequence data of the 35 rodent and 3 lagomorph mitochondrial genomes were performed using the Bayesian inference and maximum likelihood method. The result strongly supported the rodent monophyly with high node confidence values (BP 100 % in ML and BPP 1.00 in BI) and also monophylies of four rodent suborders (BP 85–100 % in ML and BPP 1.00 in BI), except for Anomalumorpha in which only one species was examined here. Also, phylogenetic relationships among the five rodent suborders were suggested and discussed in detail.