Global ecological damage has heightened the demand for silk as 'a structural material made from sustainable resources'. Scientists have earnestly searched for stronger and tougher silks. Bagworm silk ...might be a promising candidate considering its superior capacity to dangle a heavy weight, summed up by the weights of the larva and its house. However, detailed mechanical and structural studies on bagworm silks have been lacking. Herein, we show the superior potential of the silk produced by Japan's largest bagworm, Eumeta variegata. This bagworm silk is extraordinarily strong and tough, and its tensile deformation behaviour is quite elastic. The outstanding mechanical property is the result of a highly ordered hierarchical structure, which remains unchanged until fracture. Our findings demonstrate how the hierarchical structure of silk proteins plays an important role in the mechanical property of silk fibres.
In 2008, the genome assembly and gene models for the domestic silkworm, Bombyx mori, were published by a Japanese and Chinese collaboration group. However, the genome assembly contains a ...non-negligible number of misassembled and gap regions due to the presence of many repetitive sequences within the silkworm genome. The erroneous genome assembly occasionally causes incorrect gene prediction. Here we performed hybrid assembly based on 140 × deep sequencing of long (PacBio) and short (Illumina) reads. The remaining gaps in the initial genome assembly were closed using BAC and Fosmid sequences, giving a new total length of 460.3 Mb, with 30 gap regions and an N50 comprising 16.8 Mb in scaffolds and 12.2 Mb in contigs. More RNA-seq and piRNA-seq reads were mapped on the new genome assembly compared with the previous version, indicating that the new genome assembly covers more transcribed regions, including repetitive elements. We performed gene prediction based on the new genome assembly using available mRNA and protein sequence data. The number of gene models was 16,880 with an N50 of 2154 bp. The new gene models reflected more accurate coding sequences and gene sets than old ones. The proportion of repetitive elements was also reestimated using the new genome assembly, and was calculated to be 46.8% in the silkworm genome. The new genome assembly and gene models are provided in SilkBase (http://silkbase.ab.a.u-tokyo.ac.jp).
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•Whole silkworm genome resequencing was performed using PacBio long-read and Illumina short-read sequencers.•High quality genome assembly (460.3 Mb) containing 696 scaffolds with an N50 size of 16.8 Mb was obtained.•Gene prediction using the newly assembled genome identified 16,880 genes with an N50 of 2154 bp.•The new genome assembly and the gene models were evaluated.•The new genome assembly and the gene models are available in SilkBase (http://silkbase.ab.a.u-tokyo.ac.jp).
The diamondback moth
Plutella xylostella
(L.) (Lepidoptera: Plutellidae) is one of the most destructive insect pests worldwide which has developed resistance to many insecticides. Previously, a point ...mutation (I4790K) in a ryanodine receptor gene, a target gene of diamides, was identified as a major factor of resistance of the diamondback moth to cyantraniliprole in Japan. Although the diamondback moths have not yet widely developed resistance to cyantraniliprole in Japan, increasing resistant diamondback moth populations with the I4790K mutation in the future is a concern. To simply and quickly monitor the frequency of the I4790K mutations in field populations, we developed a multiplex polymerase chain reaction (PCR)-based molecular diagnostic method that can identify a genotype of the I4790K mutation site. We evaluated the sensitivity and specificity of the diagnostic method by comparing its cyantraniliprole-resistant and cyantraniliprole-susceptible allele detection results with those by Illumina MiSeq sequencing data. The results show sufficiently high sensitivity and specificity. Moreover, cyantraniliprole-resistant allele frequencies calculated by the molecular diagnostic method were almost comparable with those by MiSeq sequencing data. The molecular diagnostic method would help in performing continuous monitoring of the cyantraniliprole resistance level of diamondback moth populations in the field.
The tobacco cutworm, Spodoptera litura, is among the most widespread and destructive agricultural pests, feeding on over 100 crops throughout tropical and subtropical Asia. By genome sequencing, ...physical mapping and transcriptome analysis, we found that the gene families encoding receptors for bitter or toxic substances and detoxification enzymes, such as cytochrome P450, carboxylesterase and glutathione-S-transferase, were massively expanded in this polyphagous species, enabling its extraordinary ability to detect and detoxify many plant secondary compounds. Larval exposure to insecticidal toxins induced expression of detoxification genes, and knockdown of representative genes using short interfering RNA (siRNA) reduced larval survival, consistent with their contribution to the insect's natural pesticide tolerance. A population genetics study indicated that this species expanded throughout southeast Asia by migrating along a South India-South China-Japan axis, adapting to wide-ranging ecological conditions with diverse host plants and insecticides, surviving and adapting with the aid of its expanded detoxification systems. The findings of this study will enable the development of new pest management strategies for the control of major agricultural pests such as S. litura.
The RNA interference (RNAi) technology has been widely used in basic and applied research. It is known that RNAi works in some species but not in others, although the cause for this difference ...remains unclear. Here, we present inter- and intra-populational variations in RNAi sensitivity in the migratory locust Locusta migratoria, and provide information on the genetic background of such variations. In the four strains analyzed, originating from different Japanese localities, most individuals from two of the strains were sensitive to injections of double-stranded RNA (dsRNA) against the corazonin (CRZ) and ecdysone receptor genes, whereas those from the other two strains were resistant. Selection for individuals sensitive to dsCRZ produced a dramatic increase in the RNAi sensitivity in the following generations, although phenotypes also varied in the selected line, suggesting that several genes might control RNAi sensitivity. Reciprocal crosses between a sensitive and a resistant strain suggested that the resistant phenotype is dominant. The expression levels of nine RNAi-associated genes known for other organisms were not correlated with the variation in RNAi sensitivity observed in L. migratoria. Variations in RNAi sensitivity as the ones observed in this study should be considered when using RNAi in basic and applied research as well as in pest management.
•L. migratoria shows inter- and intra-populational variations in RNAi sensitivity.•The variation of RNAi sensitivity is a genetically based phenomenon.•The levels of nine RNAi-associated genes are not correlated with the variation.
Insect metamorphosis into an adult occurs after the juvenile hormone (JH) titer decreases at the end of the juvenile stage. This generally coincides with decreased transcript levels of JH-response ...transcription factors Krüppel homolog 1 (Kr-h1) and broad (br), and increased transcript levels of the adult specifier E93. Thrips (Thysanoptera) develop through inactive and non-feeding stages referred to as "propupa" and "pupa", and this type of distinctive metamorphosis is called neometaboly. To understand the mechanisms of hormonal regulation in thrips metamorphosis, we previously analyzed the transcript levels of Kr-h1 and br in two thrips species, Frankliniella occidentalis (Thripidae) and Haplothrips brevitubus (Phlaeothripidae). In both species, the transcript levels of Kr-h1 and br decreased in the "propupal" and "pupal" stages, and their transcription was upregulated by exogenous JH mimic treatment. Here we analyzed the developmental profiles of E93 in these two thrips species. Quantitative RT-PCR revealed that E93 expression started to increase at the end of the larval stage in F. occidentalis and in the "propupal" stage of H. brevitubus, as Kr-h1 and br mRNA levels decreased. Treatment with an exogenous JH mimic at the onset of metamorphosis prevented pupal-adult transition and caused repression of E93. These results indicated that E93 is involved in adult differentiation after JH titer decreases at the end of the larval stage of thrips. By comparing the expression profiles of Kr-h1, br, and E93 among insect species, we propose that the "propupal" and "pupal" stages of thrips have some similarities with the holometabolous prepupal and pupal stages, respectively.
LibSBML: an API Library for SBML Bornstein, Benjamin J.; Keating, Sarah M.; Jouraku, Akiya ...
Bioinformatics,
2008-Mar-15, Letnik:
24, Številka:
6
Journal Article
Recenzirano
Odprti dostop
LibSBML is an application programming interface library for reading, writing, manipulating and validating content expressed in the Systems Biology Markup Language (SBML) format. It is written in ISO ...C and C++, provides language bindings for Common Lisp, Java, Python, Perl, MATLAB and Octave, and includes many features that facilitate adoption and use of both SBML and the library. Developers can embed libSBML in their applications, saving themselves the work of implementing their own SBML parsing, manipulation and validation software. Availability: LibSBML 3 was released in August 2007. Source code, binaries and documentation are freely available under LGPL open-source terms from http://sbml.org/software/libsbml. Contact: sbml-team@caltech.edu
Using PCR-Restriction Fragment Length Polymorphism (RFLP) with mitochondrial cytochrome c oxidase subunit I sequences, we examined the reproductive modes of female adults of Thrips tabaci collected ...at 54 sites across Japan. Results showed the presence of heteroplasmic insects harboring mitochondria associated with arrhenotoky and thelytoky. Using the insects, we also applied PCR-RFLP to examine the genotypes for the amino acid mutation (T929I) site involved in pyrethroid resistance. Findings showed the presence of thelytokous heterozygotes under the circumstance that most arrhenotokous insects are resistant homozygotes, and many thelytokous insects are susceptible homozygotes. These results suggest that, in the field, genetic exchange occurs between insects through of both reproductive modes. A survey of the genotypes for the other amino acid mutations using nucleotide sequencing showed a decline of insects with an M918T and L1014F pair and an increase of insects with M918L. These results suggest the evolutional progression of amino acid mutations associated with pyrethroid resistance in T. tabaci.
Development of a reliable method for RNA interference (RNAi) by orally-delivered double-stranded RNA (dsRNA) is potentially promising for crop protection. Considering that RNAi efficiency ...considerably varies among different insect species, it is important to seek for the practical conditions under which dsRNA-mediated RNAi effectively works against each pest insect. Here we investigated RNAi efficiency in the brown-winged green stinkbug Plautia stali, which is notorious for infesting various fruits and crop plants. Microinjection of dsRNA into P. stali revealed high RNAi efficiency-injection of only 30 ng dsRNA into last-instar nymphs was sufficient to knockdown target genes as manifested by their phenotypes, and injection of 300 ng dsRNA suppressed the gene expression levels by 80% to 99.9%. Knockdown experiments by dsRNA injection showed that multicopper oxidase 2 (MCO2), vacuolar ATPase (vATPase), inhibitor of apoptosis (IAP), and vacuolar-sorting protein Snf7 are essential for survival of P. stali, as has been demonstrated in other insects. By contrast, P. stali exhibited very low RNAi efficiency when dsRNA was orally administered. When 1000 ng/μL of dsRNA solution was orally provided to first-instar nymphs, no obvious phenotypes were observed. Consistent with this, RT-qPCR showed that the gene expression levels were not affected. A higher concentration of dsRNA (5000 ng/μL) induced mortality in some cohorts, and the gene expression levels were reduced to nearly 50%. Simultaneous oral administration of dsRNA against potential RNAi blocker genes did not improve the RNAi efficiency of the target genes. In conclusion, P. stali shows high sensitivity to RNAi with injected dsRNA but, unlike the allied pest stinkbugs Halyomorpha halys and Nezara viridula, very low sensitivity to RNAi with orally-delivered dsRNA, which highlights the varied sensitivity to RNAi across different species and limits the applicability of the molecular tool for controlling this specific insect pest.
The smaller tea tortrix,
Adoxophyes honmai
Yasuda (Lepidoptera: Tortricidae), is one of the most common pests that affect the tea plant,
Camellia sinensis
(L.) O. Kuntze. Diacylhydrazine-analog ...insect growth regulators, such as tebufenozide, have been used as controls; however, the species began showing resistance to this compound in approximately 2004. Previously, we identified an amino acid mutation (A415V) in the ecdysone receptor gene (
EcR
) as a principal factor in tebufenozide resistance and developed a molecular diagnostic method to detect the
EcR
A415V mutation through polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP). However, for the continuous management of tebufenozide resistance in
A. honmai
, a simple and quick genetic diagnostic method that does not require specialized equipment is preferable. In this study, we developed a novel technique to detect the mutation using allele-specific loop-mediated isothermal amplification (AS-LAMP). This method enables the monitoring and detection of tebufenozide-resistance alleles much faster than PCR–RFLP and with moderate accuracy. Therefore, it could be a powerful tool for the early detection of tebufenozide-resistant
A. honmai
in tea plantations.
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