Characterization of the complete mitochondrial genome of Diaphania pyloalis (Lepidoptera: Pyralididae)

The complete mitochondrial genome (mitogenome) of Diaphania pyloalis (Lepidoptera: Pyralididae) was determined to be 15,298 bp and has the typical gene organization of mitogenomes from lepidopteran insects. It consists of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region. The A + T content of this mitogenome is 80.83% and the AT skew is slightly positive. All PCGs are initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which is initiated by CGA. Only the cox2 gene has an incomplete stop codon consisting of just a T. All the tRNA genes display a typical clover-leaf structure of mitochondrial tRNA. The A + T-rich region of the mitogenome is 332 bp in length, including several common features found in lepidopteran mitogenomes. Phylogenetic analysis showed that the D. pyloalis is close to Pyralididae.     

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.     

The complete mitochondrial genome of the Ailanthus silkmoth, Samia cynthia cynthia (Lepidoptera: Saturniidae)

The complete mitochondrial genome (mitogenome) of the Ailanthus silkmoth, Samia cynthia cynthia (Lepidoptera: Saturniidae) was determined. The circular genome is 15,345 bp long, and presents a typical gene organization and order for sequenced mitogenomes of Bombycidea species. The nucleotide composition of the genome is highly A+T biased, accounting for 79.86%. The AT skew of the genome is slightly negative, indicating the occurrence of more Ts than As, as found in other Saturniidae species. All protein-coding genes (PCGs) are initiated by ATN codons, except for COI and COII, which are tentatively designated by CGA and GTG, respectively, as observed in other insects. Four of 13 PCGs, including COI, COII, ATP6, and ND3, harbor the incomplete termination codons, T or TA. With an exception for tRNA^Ser(AGN), all other tRNAs can form a typical clover-leaf structure of mitochondrial tRNA. The 359 bp A+T-rich region of S. c. cynthia contains non-repetitive sequences, but harbors several features common to the Bombycidea insects, including the motif ATAGA followed by a poly-T stretch of 19 bp, a microsatellite-like (AT)₇ element preceded by the ATTTA motif, and a poly-A element upstream tRNA^Met. The phylogenetic analyses support the morphology-based current hypothesis that Bombycidae and Saturniidae are monophyletic. Our result confirms that Saturniini and Attacini form a reciprocal monophyletic group within Saturniidae.     

Molecular cloning,characterization and expression analysis of ATG1 in the silkworm, Bombyx mori

Atg1 is a Serine/Threonine protein kinase that plays a pivotal role in autophagy. A complete coding sequence of ATG1 is not available for the silkworm, Bombyx mori which is a good model for studying the autophagic process.     

Proteomic analysis of nucleopolyhedrovirus infection resistance in the silkworm, Bombyx mori (Lepidoptera: Bombycidae)

Silkworm hemolymph is an important defense tissue to resist bacteria and virus infections. To study the response of silkworm hemolymph in the resistance of Bombyx mori L. nucleopolyhedrovirus (BmNPV), we constructed a near-isogenic silkworm line with BmNPV resistance using highly resistant and highly susceptible parental strains. In this paper, two-dimensional gel electrophoresis (2-DE) and Matrix-Assisted Laser Desorption/Ionization (MALDI)-mass spectrometry were employed to investigate the differences of protein patterns in the hemolymph of the highly resistant, highly susceptible and near-isogenic silkworm strains after BmNPV was administrated to the larvae. A comparison between the proteomes of these three silkworm strains led us to identify two differentially expressed proteins, beta-N-acetylglucosaminidase 2 and aminoacylase. The expression levels of these proteins were higher in the BmNPV resistant strains.     

The complete mitochondrial genome of Sasakia funebris (Leech) (Lepidoptera: Nymphalidae) and comparison with other Apaturinae insects

Sasakia funebris, a member of the lepidopteran family, Nymphalidae (superfamily Papilionoidea) is a rare species and is found only in some areas of South China. In this study, the 15,233 bp long complete mitochondrial genome of S. funebris was determined, and harbors the gene arrangement identical to all other sequenced lepidopteran insects. The nucleotide composition of the genome is highly A + T biased, accounting for 81.2%. All protein-coding genes (PCGs) start with typical ATN codons, except for COI which begins with the CGA codon. All tRNAs have a typical clover-leaf secondary structure, except for tRNA^Ser(AGN), the dihydrouridine (DHU) arm of which forms a simple loop. The S. funebris A + T-rich region of 370 bp contains several features common to the Lepidoptera insects, including the motif ATAGA followed by a 19 bp poly-T stretch, and two tandem repeats consisting of 18 bp repeat units and 14 bp repeat units. The phylogenetic analyses of Apaturinae based on mitogenome sequences showed: (S. funebris + Sasakia charonda) + (Apatura metis + Apatura ilia). This result is consistent with the morphological classification.     

The complete sequence of the mitochondrial genome of the African Penguin (Spheniscus demersus)

The complete mitochondrial genome of the African Penguin (Spheniscus demersus) was sequenced. The molecule was sequenced via next generation sequencing and primer walking. The size of the genome is 17,346 bp in length. Comparison with the mitochondrial DNA of two other penguin genomes that have so far been reported was conducted namely; Little blue penguin (Eudyptula minor) and the Rockhopper penguin (Eudyptes chrysocome). This analysis made it possible to identify common penguin mitochondrial DNA characteristics. The S. demersus mtDNA genome is very similar, both in composition and length to both the E. chrysocome and E. minor genomes. The gene content of the African penguin mitochondrial genome is typical of vertebrates and all three penguin species have the standard gene order originally identified in the chicken. The control region for S. demersus is located between tRNA-Glu and tRNA-Phe and all three species of penguins contain two sets of similar repeats with varying copy numbers towards the 3′ end of the control region, accounting for the size variance. This is the first report of the complete nucleotide sequence for the mitochondrial genome of the African penguin, S. demersus. These results can be subsequently used to provide information for penguin phylogenetic studies and insights into the evolution of genomes.     

Characterization and identification of the integrin family in silkworm, Bombyx mori

As an important economic insect, Bombyx mori is also a useful model organism for lepidopteran insect. Integrins are evolutionarily conserved from sponges to humans, and play vital roles in many physiological and pathological processes. To explore their diverse functions of integrins in insect, eleven integrins including six α and five β subunits were cloned and characterized from silkworm. Our results showed that integrins from silkworm own more family members compared to other invertebrates. Among those α subunits, integrins α1, α2, and the other four subunits belong to PS1, PS2, and PS3 groups, respectively. The β subunits mainly gather in the insect βν group except the β1 subunit which belongs to the insect β group. Expression profiles demonstrated that the integrins exhibited distinct patterns, but were mainly expressed in hemocytes. α1 and β2 subunits are the predominant ones either in the embryogenesis or larva stages. Interestingly, integrins were significantly up-regulated after stimulated by 20-hydroxyecdysone (20-E) in vivo. These results indicate that integrins perform diverse functions in hemocytes of silkworm. Overall, our results provide a new insight into the functional and evolutionary features of integrins.     

The complete mitochondrial genome sequence analysis of Tibetan argali (Ovis ammon hodgsoni): Implications of Tibetan argali and Gansu argali as the same subspecies

The genus Ovis (Bovidae, Artiodactyla) includes six species, i.e. Ovis ammon, Ovis aries, Ovis canadensis, Ovis dalli, Ovis nivicola and Ovis vignei. Based on morphology, geographical location, habitat, etc., the species O. ammon is divided into nine subspecies. The near threatened Tibetan argali is distributed across the Tibetan Plateau and its peripheral mountains, and believed to be one of the O. ammon subspecies (O. a. hodgsoni). However, considering its morphological features and distributions, a question has been proposed by some researchers about the subspecies status of Tibetan argali. In this study, we employed complete mitochondrial DNA (mtDNA) to explore the phylogenetic relationship and population genetic structure of Tibetan argali. The results revealed that the nucleotide composition, gene arrangement and codon usage pattern of the mitochondrial genome of Tibetan argali are similar to those of other caprines. Phylogenetic analyses showed that Tibetan argali was clustered with O. ammon. Interestingly, five Tibetan argali individuals and one of the three Gansu argali (O. a. dalailamae) individuals were clustered in the same branch, which is a sister group to other two Gansu argali individuals. Together with morphological characteristics, our results suggested that Tibetan argali and Gansu argali may belong to the same subspecies (O. a. hodgsoni) of O. ammon, rather than two different subspecies.     

Prevention of thermal aggregation of an allosteric protein by small molecules: some mechanistic insights

Detailed knowledge of conformation and dynamics of native, intermediate and unfolded states of a protein is essential in searching for effective small molecules to prevent its aggregation. In a recent study we have demonstrated how allosteric effectors may influence protein-protein interactions at high temperatures using glutamate dehydrogenase (GDH) as a model allosteric protein. In the present study, thermal aggregation of this well-characterized enzyme was investigated in the presence of a number of amino acids (including Gly, Glu, Trp, Pro, Lys, Arg), polyamines (putrescine and spermidine) and chaperone-like molecules (cyclodextrins and caseins) as non-specific effectors. It was shown that some amino acids and polyamines may suppress aggregation via interaction with native species and may preserve the activity of the enzyme while cyclodextrins and caseins may exert their anti-aggregation potential via binding to aggregation-prone intermediates, without having any capacity to protect its native structure from unfolding. Observations describing the similarities and differences between the specific ligands and non-specific small molecules related to their interaction with native and aggregation-prone states of GDH are presented and discussed. It is argued that the type of studies described in the present communication is useful for the development of effective strategies for prevention of aggregation by small molecules.     

Molecular cloning and expression in vitro of a carboxylesterase gene from the Glanville fritillary butterfly (Melitaea cinxia)

Carboxylesterase (EC 3.1.1.1) is a member of the carboxyl/cholinesterase (CCE) superfamily, which is widely distributed in animals, plants and microorganisms. This enzyme has been known to be associated with insecticide resistance and detoxification. Although CCEs have been extensively studied in insects, including lepidopterans, the research on butterflies, a major subgroup in Lepidoptera, is still poor. In the present study, we cloned a CCE gene (McCCE1) from the Glanville fritillary butterfly (Melitaea cinxia, Lepidoptera: Nymphalidae). The full-length cDNA encoding McCCE1 was 1786 bp, containing a 1641 bp open reading frame encoding 546 amino acids, a 38 bp 5′-untranslated region (5′-UTR), and a 107 bp 3′-UTR with a poly(A) tail. The functionally conserved amino acids in McCCE1 shared the 55% identity with the cytoplasmic esterase CCE017a in Helicoverpa armigera (Lepidoptera: Noctuidae), which has been associated with detoxification. Assays in vitro showed that the recombinant McCCE1 could hydrolyze α- and β-naphthyl acetate. Thus, the present study adds to the body of knowledge concerning the detoxification of pesticides by lepidopterans.     

A preliminary study for identification of candidate AFLP markers under artificial selection for shell color in pearl oyster Pinctada fucata

Pearl oyster Pinctada fucata is widely cultured to produce seawater pearl in South China, and the quality of pearl is significantly affected by its shell color. Thus the Pearl Oyster Selective Breeding Program (POSBP) was carried out for the shell color and growth traits. The black (B), gold (G), red (R) and white (W) shell strains with fast growth trait were achieved after five successive generation selection. In this study, AFLP technique was used to scan genome of four strains with different shell colors to identify the candidate markers under artificial selection. Eight AFLP primer combinations were screened and yielded 688 loci, 676 (98.26%) of which were polymorphic. In black, gold, red and white strains, the percentage of polymorphic loci was 90.41%, 87.79%, 93.60% and 93.31%, respectively, Nei's gene diversity was 0.3225, 0.2829, 0.3221 and 0.3292, Shannon's information index was 0.4801, 0.4271, 0.4825 and 0.4923, and the value of F_ST was 0.1805. These results suggested that the four different shell color strains had high genetic diversity and great genetic differentiation among strains, which had been subjected to the continuous selective pressures during the artificial selective breeding. Furthermore, six outlier loci were considered as the candidate markers under artificial selection for shell color. This study provides a molecular evidence for the inheritance of shell color of P. fucata.     

Complete mitochondrial genome of the atlas moth, Attacus atlas (Lepidoptera: Saturniidae) and the phylogenetic relationship of Saturniidae species

Mitochondrial genome (mitogenome) can provide information for genomic structure as well as for phylogenetic analysis and evolutionary biology. In this study, we present the complete mitogenome of the atlas moth, Attacus atlas (Lepidoptera: Saturniidae), a well-known silk-producing and ornamental insect with the largest wing surface area of all moths. The mitogenome of A. atlas is a circular molecule of 15,282 bp long, and its nucleotide composition shows heavily biased towards As and Ts, accounting for 79.30%. This genome comprises 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A + T-rich region. It is of note that this genome exhibits a slightly positive AT skew, which is different from the other known Saturniidae species. All PCGs are initiated by ATN codons, except for COI with CGA instead. Only six PCGs use a common stop codon of TAA or TAG, whereas the remaining seven use an incomplete termination codon T or TA. All tRNAs have the typical clover-leaf structure, with an exception for tRNA^Ser(AGN). The A. atlas A + T-rich region contains non-repetitive sequences, but harbors several features common to the Bombycoidea insects. The phylogenetic relationships based on Maximum Likelihood method provide a well-supported outline of Saturniidae, which is in accordance with the traditional morphological classification and recent molecular works.     

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.     

The complete chloroplast genome of Origanum vulgare L. (Lamiaceae)

Oregano (Origanum vulgare L., Lamiaceae) is a medicinal and aromatic plant maybe best known for flavouring pizza. New applications e.g. as natural antioxidants for food are emerging due to the plants' high antibacterial and antioxidant activity. The complete chloroplast (cp) genome of Origanum vulgare (GenBank/EBML/DDBJ accession number: JX880022) consists of 151,935 bp and includes a pair of inverted repeats (IR) of 25,527 bp separated by one small and one large single copy region (SSC and LSC) of 17,745 and 83,136 bp, respectively.     

Characterization of the complete mitochondrial genome of the giant silkworm moth, Eriogyna pyretorum (Lepidoptera: Saturniidae)

The complete mitochondrial genome (mitogenome) of Eriogyna pyretorum (Lepidoptera: Saturniidae) was determined as being composed of 15,327 base pairs (bp), including 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. The arrangement of the PCGs is the same as that found in the other sequenced lepidopteran. The AT skewness for the E. pyretorum mitogenome is slightly negative (-0.031), indicating the occurrence of more Ts than As. The nucleotide composition of the E. pyretorum mitogenome is also biased toward A + T nucleotides (80.82%). All PCGs are initiated by ATN codons, except for cytochrome c oxidase subunit 1 and 2 (cox1 and cox2). Two of the 13 PCGs harbor the incomplete termination codon by T. All tRNA genes have a typical clover-leaf structure of mitochondrial tRNA, with the exception of trnS1(AGN) and trnS2(UCN). Phylogenetic analysis among the available lepidopteran species supports the current morphology-based hypothesis that Bombycoidea, Geometroidea, Notodontidea, Papilionoidea and Pyraloidea are monophyletic. As has been previously suggested, Bombycidae (Bombyx mori and Bombyx mandarina), Sphingoidae (Manduca sexta) and Saturniidae (Antheraea pernyi, Antheraea yamamai, E. pyretorum and Caligula boisduvalii) formed a group.     

The complete mitochondrial genome of the sycamore lace bug Corythucha ciliata (Hemiptera: Tingidae)

The complete mitochondrial genome of the sycamore lace bug, Corythucha ciliata, was sequenced in this study. It represents the first sequenced mitogenome of family Tingidae in Heteroptera. The mitogenome of C. ciliata is 15,257 bp and contains 37 genes including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and a large non-coding region. Gene arrangement, nucleotide content, codon usage, and amino acid composition and asymmetry indicate a high degree of conservation with six other species of Cimicomorpha. The 13 PCGs initiated with ATN as the start codon and terminated with TAA, TA or T as stop codon. The evolutionary rate of each PCG was different, among which ATP8 showed the highest rate while ATP6 indicated the lowest rate. The 22 tRNAs genes apparently fold into a typical cloverleaf structure; however, the anticodon (TTC) of trnSer (AGN) differs from other Heteropteran insects. Secondary structure modeling of rRNA genes revealed similarity to other insects, except for two incomplete helices (H1648 and H2735) in lrRNA. The predicted secondary structure of lrRNA indicates 45 helices in six domains, whereas srRNA has 27 helices in three domains. Three potential stem–loops and two tandem repeats (–TCTAAT–) were identified in the A+T-rich region. Phylogenetic analysis indicated that C. ciliata is a sister group to other Heteroptera species based on analysis of the 13 PCGs.