WildSilkbase: an EST database of wild silkmoths

Genome sequencing and assembly of Indian golden silkmoth, Antheraea assamensis Helfer (Saturniidae, Lepidoptera)

Muga silkworm (Antheraea assamensis), one of the economically important wild silkmoths, is unique among saturniid silkmoths. It is confined to the North-eastern part of India. Muga silk has the highest value among the other silks. Unlike other silkmoths, A. assamensis has a low chromosome number (n = 15), and ZZ/ZO sex chromosome system. Here, we report the first high-quality draft genome of A. assamensis, assembled by employing the Illumina and PacBio sequencing platforms. The assembled genome of A. assamensis is 501.18 Mb long, with 2697 scaffolds and an N50 of 683.23 Kb. The genome encompasses 18,385 protein-coding genes, 86.29% of which were functionally annotated. Phylogenetic analysis of A. assamensis revealed its divergence from other Antheraea species approximately 28.7 million years ago. Moreover, an investigation into detoxification-related gene families, CYP450, GST, and ABC-transporter, revealed a significant expansion in A. assamensis as compared to the Bombyx mori. This expansion is comparable to Spodoptera litura, suggesting adaptive responses linked to the polyphagous behavior observed in these insects. This study provides valuable insights into the molecular basis of evolutionary divergence and adaptations in muga silkmoth. The genome assembly reported in this study will significantly help in the functional genomics studies on A. assamensis and other Antheraea species along with comparative genomics analyses of Bombycoidea insects.

SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species

We introduce SilkBase as an integrated database for transcriptomic and genomic resources of the domesticated silkworm Bombyx mori and related species. SilkBase is the oldest B. mori database that was originally established as the expressed sequence tag database since 1999. Here, we upgraded the database by including the datasets of the newly assembled B. mori complete genome sequence, predicted gene models, bacterial artificial chromosome (BAC)-end and fosmid-end sequences, complementary DNA (cDNA) reads from 69 libraries, RNA-seq data from 10 libraries, PIWI-interacting RNAs (piRNAs) from 13 libraries, ChIP-seq data of 9 histone modifications and HP1 proteins and transcriptome and/or genome data of four B. mori-related species, i.e. Bombyx mandarina, Trilocha varians, Ernolatia moorei and Samia ricini. Our new integrated genome browser easily provides a snapshot of tissue- and stage-specific gene expression, alternative splicing, production of piRNAs and histone modifications at the gene locus of interest. Moreover, SilkBase is useful for performing comparative studies among five closely related lepidopteran insects.

Database URL: https://silkbase.ab.a.u-tokyo.ac.jp

In Vitro Culture of Human Corneal Endothelium on Non-Mulberry Silk Fibroin Films for Tissue Regeneration

Purpose

The purpose of this study was to determine if non-mulberry varieties of silk are suitable for the culture of corneal endothelium (CE).

Methods

Aqueous silk fibroin derived from Philosamia ricini (PR), Antheraea assamensis (AA), and Bombyx mori (BM) were cast as approximately 15 µm films with and without pores on which human CE cells were cultured. Tensile strength, elasticity, transmittance in visible range, and degradation properties of the films were characterised. Adhesion of CE to the silk films was quantified using MTT assay in addition to quantifying the number and area of focal adhesions using paxillin. Expression of CE markers was determined at the gene and protein levels using PCR and immunostaining, respectively. Barrier integrity of the cultured cells was measured as permeability to FITC dextran (10 kDa) in the presence or absence of thrombin.

Results

The films exhibited robust tensile strength, >95% transmittance and a refractive index comparable to the native cornea. BM degraded significantly faster when compared to PR and AA. A comparison between the three varieties of silk showed that significantly more cells were adhered to PR and AA than to BM. This was also reflected in the expression of stable focal adhesions on PR and AA, thus enabling the formation of intact monolayers of cells on these varieties unlike on BM. Treatment with thrombin significantly increased cellular permeability to dextran.

Conclusions

Our data shows that PR and AA varieties sufficiently support the growth and function of CE cells. This could be attributed to the presence of natural cell binding motifs (RGD) in these varieties.

Translational Relevance

Development of a suitable carrier for engineering the CE to address a major clinical requirement of healthy donor tissues for transplantation.

CHARACTERIZATION OF TRYPSIN-LIKE AND CHYMOTRYPSIN-LIKE SERINE PROTEASES FROM MIDGUT OF Mythimna separata Walker

Two cDNA sequences encoding a trypsin-like and a chymotrypsin-like serine protease (MsT and MsCT, GenBank accession Nos. KP730443 and KP730444, respectively) were cloned from midgut of oriental armyworm, Mythimna separata Walker. Multiple alignments revealed that the deduced amino acid sequences of MsT and MsCT contained a serine protease catalytic motif GDSGGPL and catalytic triads (His, Asp, and Ser). Analyses of tissue and developmental expression of MsT and MsCT showed that they were mainly expressed in midguts and could be detected in first to sixth instar larvae, prepupal and pupal stages. Expressions of both MsT and MsCT were downregulated after 24 h of starvation and upregulated by subsequent insect refeeding. MsT expression in response to 20-hydroxyecdysone (20E) was dose dependent and upregulated after 24 h. However, MsCT expression in response to 20E was downregulated compared with controls. MsCT, but not MsT, transcripts were upregulated after 24 h of Cry1Ac protoxin exposure. These results suggested that MsT was most likely involved in food protein digestion and molting in M. separata whereas MsCT was most likely involved in food protein digestion and Bacillus thuringiensis (Bt) protoxin activation. RNA interference indicated that MsT and MsCT expression levels decreased 76.7 and 86.2% after treated with MsT and MsCT dsRNA, respectively. This study showed that M. separata expressed midgut proteases in line with known lepidopteran counterparts and contributed valuable sequence resource information regarding insect proteases.

A comprehensive view of the web-resources related to sericulture

Recent progress in the field of sequencing and analysis has led to a tremendous spike in data and the development of data science tools. One of the outcomes of this scientific progress is development of numerous databases which are gaining popularity in all disciplines of biology including sericulture. As economically important organism, silkworms are studied extensively for their numerous applications in the field of textiles, biomaterials, biomimetics, etc. Similarly, host plants, pests, pathogens, etc. are also being probed to understand the seri-resources more efficiently. These studies have led to the generation of numerous seri-related databases which are extremely helpful for the scientific community. In this article, we have reviewed all the available online resources on silkworm and its related organisms, including databases as well as informative websites. We have studied their basic features and impact on research through citation count analysis, finally discussing the role of emerging sequencing and analysis technologies in the field of seri-data science. As an outcome of this review, a web portal named SeriPort, has been created which will act as an index for the various sericulture-related databases and web resources available in cyberspace.Database URL: http://www.seriport.in/.

Genetic analysis of Indian tasar silkmoth (Antheraea mylitta) populations

Indian tasar silkmoth, Antheraea mylitta is an economically important wild silkmoth species distributed across India. A number of morphologically and ethologically well-defined ecotypes are known for this species that differ in their primary food plant specificity. Most of these ecotypes do not interbreed in nature, but are able to produce offspring under captive conditions. Microsatellite markers were developed for A. mylitta, and out of these, ten well-behaved microsatellite loci were used to analyze the population structure of different ecoraces. A total of 154 individual moths belonging to eight different ecoraces, were screened at each locus. Hierarchical analysis of population structure using Analysis of MOlecular VAriance (AMOVA) revealed significant structuring (F_ST = 0.154) and considerable inbreeding (F_IS = 0.505). A significant isolation by distance was also observed. The number of possible population clusters was investigated using distance method, Bayesian algorithm and self organization maps (SOM). The first two methods revealed two distinct clusters, whereas the SOM showed the different ecoraces not to be clearly differentiated. These results suggest that although there is a large degree of phenotypic variation among the different ecoraces of A. mylitta, genetically they are not very different, and the phenotypic differences may largely be a result of their respective ecology.

Identification and evolution of the orphan genes in the domestic silkworm, Bombyx mori

Orphan genes (OGs) which have no recognizable homology to any sequences in other species could contribute to the species specific adaptations. In this study, we identified 738 OGs in the silkworm genome. About 31% of the silkworm OGs is derived from transposable elements, and 5.1% of the silkworm OGs emerged from gene duplication followed by divergence of paralogs. Five de novo silkworm OGs originated from non-coding regions. Microarray data suggested that most of the silkworm OGs were expressed in limited tissues. RNA interference experiments suggested that five de novo OGs are not essential to the silkworm, implying that they may contribute to genetic redundancy or species-specific adaptation. Our results provide some new insights into the evolutionary significance of the silkworm OGs.

Molecular architecture of silk fibroin of Indian golden silkmoth, Antheraea assama

The golden silk spun by Indian golden silkmoth Antheraea assama, is regarded for its shimmering golden luster, tenacity and value as biomaterial. This report describes the gene coding for golden silk H-fibroin (AaFhc), its expression, full-length sequence and structurally important motifs discerning the underlying genetic and biochemical factors responsible for its much sought-after properties. The coding region, with biased isocodons, encodes highly repetitious crystalline core, flanked by a pair of 5′ and 3′ non-repetitious ends. AaFhc mRNA expression is strictly territorial, confined to the posterior silk gland, encoding a protein of size 230 kDa, which makes homodimers making the elementary structural units of the fibrous core of the golden silk. Characteristic polyalanine repeats that make tight β-sheet crystals alternate with non-polyalanine repeats that make less orderly antiparallel β-sheets, β-turns and partial α-helices. Phylogenetic analysis of the conserved N-terminal amorphous motif and the comparative analysis of the crystalline region with other saturniid H-fibroins reveal that AaFhc has longer, numerous and relatively uniform repeat motifs with lower serine content that assume tighter β-crystals and denser packing, which are speculated to be responsible for its acclaimed properties of higher tensile strength and higher refractive index responsible for golden luster.

Identification and Characterization of a Novel Microvitellogenin from the Chinese Oak Silkworm Antheraea pernyi

Microvitellogenin (mVg) is a relatively small vitellogenic protein only characterized in the eggs of the lepidopteran insects Manduca sexta and Bombyx mori. In the present study, we report a novel mVg (ApmVg) isolated from the Chinese oak silkworm Antheraea pernyi. The obtained ApmVg cDNA sequence contains an open reading frame of 783 bp encoding a protein of 260 amino acids with a predicted molecular weight of 29.96 kDa. This gene does not contain introns. Structural analysis revealed that this protein shares putative conserved domains with the lepidopteran low-molecular weight lipoprotein, which belongs to the lipoprotein_11 superfamily. The protein sequence of ApmVg exhibits 48% sequence identity with mVg from M. sexta and 40–47% sequence identity with the 30K lipoproteins from B. mori. Phylogenetic analysis suggests that ApmVg is a novel member of the lepidopteran low-molecular weight lipoproteins. Transcriptional analysis indicated that ApmVg mRNA is mainly expressed in the fat body (both female and male) during post-diapause development of the pupal stage, and it was also detected in ovaries and spermaries in smaller amounts. RT-PCR and Western blot analyses revealed that ApmVg is synthesized by the fat body and secreted into hemolymph and ultimately accumulates in eggs. The ApmVg transcript can be detected in the fat bodies of female pupae four days after treatment with 20-hydroxyecdysone and shows an expression pattern distinct from that of vitellogenin (Vg), which is detectable throughout diapausing and in post-diapause development. ApmVg decreased dramatically during embryonic development. These results represent the first study of mVg outside M. sexta and B. mori and provide insight into the physiological role and evolution of mVgs.

Comparative transcriptome analyses on silk glands of six silkmoths imply the genetic basis of silk structure and coloration

BACKGROUND

Silk has numerous unique properties that make it a staple of textile manufacturing for several thousand years. However, wider applications of silk in modern have been stalled due to limitations of traditional silk produced by Bombyx mori. While silk is commonly produced by B. mori, several wild non-mulberry silkmoths--especially members of family Saturniidae--produce silk with superior properties that may be useful for wider applications. Further utilization of such silks is hampered by the non-domestication status or limited culturing population of wild silkworms. To date there is insufficient basic genomic or transcriptomic data on these organisms or their silk production.

RESULTS

We sequenced and compared the transcriptomes of silk glands of six Saturniidae wild silkmoth species through next-generation sequencing technology, identifying 37758 ~ 51734 silkmoth unigenes, at least 36.3% of which are annotated with an e-value less than 10(-5). Sequence analyses of these unigenes identified a batch of genes specific to Saturniidae that are enriched in growth and development. Analyses of silk proteins including fibroin and sericin indicate intra-genus conservation and inter-genus diversification of silk protein features among the wild silkmoths, e.g., isoelectric points, hydrophilicity profile and amino acid composition in motifs of silk H-fibroin. Interestingly, we identified p25 in two of the silkmoths, which were previously predicted to be absent in Saturniidae. There are rapid evolutionary changes in sericin proteins, which might account for the highly heterogeneity of sericin in Saturniidae silkmoths. Within the six sikmoths, both colored-cocoon silkmoth specific transcripts and differentially expressed genes between the colored-cocoon and non-colored-cocoon silkmoths are significantly enriched in catalytic activity, especially transferase activity, suggesting potentially viable targets for future gene mining or genetic manipulation.

CONCLUSIONS

Our results characterize novel and potentially valuable gene resources of saturniid silkmoths that may facilitate future genetic improvement and modification of mulberry silkworms. Our results suggest that the disparate features of silk--coloration, retention, strength, etc. --are likely not only due to silk proteins, but also to the environment of silk assembly, and more specifically, that stable silk coloration exhibited by some Saturniidae silkmoths may be attributable to active catalytic progress in pigmentation.

Multidimensional approaches for studying plant defence against insects: from ecology to omics and synthetic biology

The biggest challenge for modern biology is to integrate multidisciplinary approaches towards understanding the organizational and functional complexity of biological systems at different hierarchies, starting from the subcellular molecular mechanisms (microscopic) to the functional interactions of ecological communities (macroscopic). The plant-insect interaction is a good model for this purpose with the availability of an enormous amount of information at the molecular and the ecosystem levels. Changing global climatic conditions are abruptly resetting plant-insect interactions. Integration of discretely located heterogeneous information from the ecosystem to genes and pathways will be an advantage to understand the complexity of plant-insect interactions. This review will present the recent developments in omics-based high-throughput experimental approaches, with particular emphasis on studying plant defence responses against insect attack. The review highlights the importance of using integrative systems approaches to study plant-insect interactions from the macroscopic to the microscopic level. We analyse the current efforts in generating, integrating and modelling multiomics data to understand plant-insect interaction at a systems level. As a future prospect, we highlight the growing interest in utilizing the synthetic biology platform for engineering insect-resistant plants.

Determination of the proteins encoded by BmBDV VD1-ORF4 and their interacting proteins in BmBDV-infected midguts

Bombyx mori bidensovirus (BmBDV) VD1-ORF4 consists of 3,318 nucleotides, which codes for a predicted protein with molecular weight of about 127 kDa. However, the authentic proteins encoded by VD1-ORF4 in silkworm midguts infected with BmBDV and their interacting proteins are still unclear. In this study, Western blot analysis revealed that a 127-kDa protein was confirmed to be translated from the VD1-ORF4 transcript using polyclonal antibodies and monoclonal antibodies against VD1-ORF4 deduced amino acid. Moreover, four smaller proteins with molecular weight of about 70, 60, 53, and 42 kDa were also examined in the infected midguts. Transient expression assay indicated that the expression amount of VD1-ORF4 fused with egfp was at least 30-fold lower than that of egfp gene, and immunofluorescence staining result indicated that these proteins encoded by VD1-ORF4 were located in both the cytoplasm and nucleus. Co-immunoprecipitation result showed that Aminopeptidase and Heat shock protein 90 can be captured by these proteins encoded by VD1-ORF4. In conclusion, multiple proteins were produced from the transcripts of VD1-ORF4 gene by an uncertain expression strategy, which may play important roles in viral replication and assembly.

KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella

Background

The diamondback moth (DBM), Plutella xylostella, is one of the most harmful insect pests for crucifer crops worldwide. DBM has rapidly evolved high resistance to most conventional insecticides such as pyrethroids, organophosphates, fipronil, spinosad, Bacillus thuringiensis, and diamides. Therefore, it is important to develop genomic and transcriptomic DBM resources for analysis of genes related to insecticide resistance, both to clarify the mechanism of resistance of DBM and to facilitate the development of insecticides with a novel mode of action for more effective and environmentally less harmful insecticide rotation. To contribute to this goal, we developed KONAGAbase, a genomic and transcriptomic database for DBM (KONAGA is the Japanese word for DBM).

Description

KONAGAbase provides (1) transcriptomic sequences of 37,340 ESTs/mRNAs and 147,370 RNA-seq contigs which were clustered and assembled into 84,570 unigenes (30,695 contigs, 50,548 pseudo singletons, and 3,327 singletons); and (2) genomic sequences of 88,530 WGS contigs with 246,244 degenerate contigs and 106,455 singletons from which 6,310 de novo identified repeat sequences and 34,890 predicted gene-coding sequences were extracted. The unigenes and predicted gene-coding sequences were clustered and 32,800 representative sequences were extracted as a comprehensive putative gene set. These sequences were annotated with BLAST descriptions, Gene Ontology (GO) terms, and Pfam descriptions, respectively. KONAGAbase contains rich graphical user interface (GUI)-based web interfaces for easy and efficient searching, browsing, and downloading sequences and annotation data. Five useful search interfaces consisting of BLAST search, keyword search, BLAST result-based search, GO tree-based search, and genome browser are provided. KONAGAbase is publicly available from our website (http://dbm.dna.affrc.go.jp/px/) through standard web browsers.

Conclusions

KONAGAbase provides DBM comprehensive transcriptomic and draft genomic sequences with useful annotation information with easy-to-use web interfaces, which helps researchers to efficiently search for target sequences such as insect resistance-related genes. KONAGAbase will be continuously updated and additional genomic/transcriptomic resources and analysis tools will be provided for further efficient analysis of the mechanism of insecticide resistance and the development of effective insecticides with a novel mode of action for DBM.

Molecular cloning and characterization of two 12 kDa FK506-binding protein genes in the Chinese oak silkworm, Antheraea pernyi

Two 12 kDa FK506-binding protein (FKBP12) genes were isolated and characterized from Chinese oak silkworm Antheraea pernyi , an important agricultural and edible insect, designated ApFKBP12 A and B, respectively. Both ApFKBP12 A and B contained 108 amino acids with 82% sequence identity. Phylogenetic analysis showed that FKBP12 B sequences of A. pernyi, Bombyx mori , and Danaus plexippus were clearly separated from FKBP12 A sequences of these three species, suggesting that insect FKBP12 A and B may have been evolving independently. RT-PCR analyses revealed that two ApFKBP12 genes were expressed during the four developmental stages and in all tested tissues, and that the mRNA expression level of the ApFKBP12 A gene was significantly higher than that of the ApFKBP12 B gene. After heat shock treatment, expressions of the two FKBP12 genes were up-regulated, but at different time points. The results suggested that each paralogue of the FKBP12 genes may play a distinct functional role in the development of A. pernyi.

Identification of a cuticle protein with unique repeated motifs in the silkworm, Bombyx mori

The insect cuticle is non-cellular matrix secreted from a monolayer of epidermal cells. After abrasion of the larval cuticle of the silkworm, Bombyx mori, a protein with molecular mass of 135 kDa is newly detected in the cuticle. Mass spectrometric analysis of the tryptic fragments from this protein revealed that the 135-kDa protein is encoded by the Cb10 gene. In the predicted amino acid sequence of Cb10, three repeated motifs with [YxGGFGGppG(L/V)L] sequence are found in the C-terminal region. In addition to the repeated motifs, Cb10 has seventeen CxxxxC motifs randomly distributed throughout the polypeptide chain and serine rich region at the N-terminal region. The Cb10 gene is strongly expressed in epidermal cells after pupal ecdysis, and its expression in the larval epidermal cells is induced not only by cuticular abrasion, but also by bacterial infection. These expression patterns suggest some specific roles of this protein in pupal cuticle formation and defense reactions.

Characterization of cDNAs encoding serine proteases and their transcriptional responses to Cry1Ab protoxin in the gut of Ostrinia nubilalis larvae

Serine proteases, such as trypsin and chymotrypsin, are the primary digestive enzymes in lepidopteran larvae, and are also involved in Bacillus thuringiensis (Bt) protoxin activation and protoxin/toxin degradation. We isolated and sequenced 34 cDNAs putatively encoding trypsins, chymotrypsins and their homologs from the European corn borer (Ostrinia nubilalis) larval gut. Our analyses of the cDNA-deduced amino acid sequences indicated that 12 were putative trypsins, 12 were putative chymotrypsins, and the remaining 10 were trypsin and chymotrypsin homologs that lack one or more conserved residues of typical trypsins and chymotrypsins. Reverse transcription PCR analysis indicated that all genes were highly expressed in gut tissues, but one group of phylogenetically-related trypsin genes, OnTry-G2, was highly expressed in larval foregut and midgut, whereas another group, OnTry-G3, was highly expressed in the midgut and hindgut. Real-time quantitative PCR analysis indicated that several trypsin genes (OnTry5 and OnTry6) were significantly up-regulated in the gut of third-instar larvae after feeding on Cry1Ab protoxin from 2 to 24 h, whereas one trypsin (OnTry2) was down-regulated at all time points. Four chymotrypsin and chymotrypsin homolog genes (OnCTP2, OnCTP5, OnCTP12 and OnCTP13) were up-regulated at least 2-fold in the gut of the larvae after feeding on Cry1Ab protoxin for 24 h. Our data represent the first in-depth study of gut transcripts encoding expanded families of protease genes in O. nubilalis larvae and demonstrate differential expression of protease genes that may be related to Cry1Ab intoxication and/or resistance.

Genetic analysis of scattered populations of the Indian eri silkworm, Samia cynthia ricini Donovan: Differentiation of subpopulations

Deforestation and exploitation has led to the fragmentation of habitats and scattering of populations of the economically important eri silkworm, Samia cynthia ricini, in north-east India. Genetic analysis of 15 eri populations, using ISSR markers, showed 98% inter-population, and 23% to 58% intra-population polymorphism. Nei's genetic distance between populations increased significantly with altitude (R(2) = 0.71) and geographic distance (R(2) = 0.78). On the dendrogram, the lower and upper Assam populations were clustered separately, with intermediate grouping of those from Barpathar and Chuchuyimlang, consistent with geographical distribution. The Nei's gene diversity index was 0.350 in total populations and 0.121 in subpopulations. The genetic differentiation estimate (Gst) was 0.276 among scattered populations. Neutrality tests showed deviation of 118 loci from Hardy-Weinberg equilibrium. The number of loci that deviated from neutrality increased with altitude (R(2) = 0.63). Test of linkage disequilibrium showed greater contribution of variance among eri subpopulations to total variance. D('2)IS exceeded D('2)ST, showed significant contribution of random genetic drift to the increase in variance of disequilibrium in subpopulations. In the Lakhimpur population, the peripheral part was separated from the core by a genetic distance of 0.260. Patchy habitats promoted low genetic variability, high linkage disequilibrium and colonization by new subpopulations. Increased gene flow and habitat-area expansion are required to maintain higher genetic variability and conservation of the original S. c. ricini gene pool.

A BTB domain-containing gene is upregulated by immune challenge

20-Hydroxyecdysone (20E) is an important hormone that regulates the development of insects. Although previous evidence revealed that 20E promotes innate immunity in insects, the mechanism involved is still unclear. In this study, the HaBBP gene from Helicoverpa armigera is cloned, which contains BTB (broad-complex, tramtrack, and bric-a-brac), a BACK (BTB and carboxyl-terminus kelch repeats), and PHR (PAM, highwire, and RPM) domains. RT-PCR analysis of HaBBP and western blot analysis of HaBBP show that the mRNA and protein level are higher in the fat body and hemocytes during the molting and metamorphic stages compared with the feeding stage. HaBBP was upregulated by 20E in hemocytes. Knockdown of the 20E receptor EcR-B1 and the heterodimeric partner ultraspiracle protein USP1 in an epidermal cell line (HaEpi) blocked the transcription of HaBBP. HaBBP is distributed in granulocytes and plasmatocytes. Immune stimulation by Escherichia coli caused the upregulation of HaBBP in both hemocytes and fat body. Thus, HaBBP is regulated by the 20E signaling pathway, and is likely involved in the insect innate immunity.

Samia cynthia versus Bombyx mori: comparative gene mapping between a species with a low-number karyotype and the model species of Lepidoptera

We performed gene-based comparative FISH mapping between a wild silkmoth, Samia cynthia ssp. with a low number of chromosomes (2n=25-28) and the model species, Bombyx mori (2n=56), in order to identify the genomic components that make up the chromosomes in a low-number karyotype. Mapping of 64 fosmid probes containing orthologs of B. mori genes revealed that the homologues of either two or four B. mori chromosomes constitute the S. c. ricini (Vietnam population, 2n=27♀/28♂, Z0/ZZ) autosomes. Where tested, even the gene order was conserved between S. c. ricini and B. mori. This was also true for the originally autosomal parts of the neo-sex chromosomes in S. c. walkeri (Sapporo population, 2n=26♀/26♂, neo-Wneo-Z/neo-Zneo-Z) and S. cynthia subsp. indet. (Nagano population, 2n=25♀/26♂, neo-WZ₁Z₂/Z₁Z₁Z₂Z₂). The results are evidence for an internal stability of lepidopteran chromosomes even when all autosomes had undergone fusion processes to form a low-number karyotype.

Horizontal gene transfer in silkworm, Bombyx mori

BACKGROUND

The domesticated silkworm, Bombyx mori, is the model insect for the order Lepidoptera, has economically important values, and has gained some representative behavioral characteristics compared to its wild ancestor. The genome of B. mori has been fully sequenced while function analysis of BmChi-h and BmSuc1 genes revealed that horizontal gene transfer (HGT) maybe bestow a clear selective advantage to B. mori. However, the role of HGT in the evolutionary history of B. mori is largely unexplored. In this study, we compare the whole genome of B. mori with those of 382 prokaryotic and eukaryotic species to investigate the potential HGTs.

RESULTS

Ten candidate HGT events were defined in B. mori by comprehensive sequence analysis using Maximum Likelihood and Bayesian method combining with EST checking. Phylogenetic analysis of the candidate HGT genes suggested that one HGT was plant-to- B. mori transfer while nine were bacteria-to- B. mori transfer. Furthermore, functional analysis based on expression, coexpression and related literature searching revealed that several HGT candidate genes have added important characters, such as resistance to pathogen, to B. mori.

CONCLUSIONS

Results from this study clearly demonstrated that HGTs play an important role in the evolution of B. mori although the number of HGT events in B. mori is in general smaller than those of microbes and other insects. In particular, interdomain HGTs in B. mori may give rise to functional, persistent, and possibly evolutionarily significant new genes.

Forest habitat conservation in Africa using commercially important insects

African forests, which host some of the world's richest biodiversity, are rapidly diminishing. The loss of flora and fauna includes economically and socially important insects. Honey bees and silk moths, grouped under commercial insects, are the source for insect-based enterprises that provide income to forest-edge communities to manage the ecosystem. However, to date, research output does not adequately quantify the impact of such enterprises on buffering forest ecosystems and communities from climate change effects. Although diseases/pests of honey bees and silk moths in Africa have risen to epidemic levels, there is a dearth of practical research that can be utilized in developing effective control mechanisms that support the proliferation of these commercial insects as pollinators of agricultural and forest ecosystems. This review highlights the critical role of commercial insects within the environmental complexity of African forest ecosystems, in modern agroindustry, and with respect to its potential contribution to poverty alleviation and pollination services. It identifies significant research gaps that exist in understanding how insects can be utilized as ecosystem health indicators and nurtured as integral tools for important socioeconomic and industrial gains.

Drosophila intersex orthologue in the silkworm, Bombyx mori and related species

Intersex (ix), a gene required for female sexual development in Drosophila, acts in concert with doublesex (dsx) at the end of the sex determination pathway. In the present study a homologue of ix was identified in Bombyx mori. Expression analysis of this gene by RT-PCR and RNase protection assay revealed a diagnostic alternative splice form present only in testis, whereas the most common splice form was found to express in all other tissues from early embryonic developmental stages. The present study provides evidence for the presence of an alternative splice form of ix in three species of silkmoths examined. Taken together with the results of an earlier study on ix in piralid moth, Maruca vitrata (Cavaliere et al. 2009), the present study suggests that the testis-specific splice form may be a characteristic feature of lepidopterans. Though ix lacks a conserved splicing pattern it appears to have retained its functional conservation in terminal sexual differentiation. We speculate that the presence of an additional splice form, perhaps encoding non-functional protein only in testis, may prevent the feminizing effects exerted by the functional IX protein.

cDNA cloning and expression pattern of two enolase genes from the Chinese oak silkworm, Antheraea pernyi

In this study, two enolase genes were isolated and characterized from the Chinese oak silkworm, Antheraea perny, which were designated as enolase I and II, respectively. The enolase I cDNA sequence was 1712 bp with an open reading frame (ORF) of 1302 bp encoding 433 amino acids. The enolase II cDNA sequence was 1549 bp with an ORF of 1296 bp encoding 431 amino acids. The amino acid sequences of the two genes share several conserved features/sites of enolase. Antheraea pernyi enolase I shows 93%-97% sequence identity to enolases of lepidopterans available to date, 75%-82% identity to enolases of other invertebrates, 60%-72% identity to enolases of other organisms including vertebrates, plants, and fungi. Antheraea pernyi enolase II shows 84% identity to Bombyx mori enolase II, but 60% identity to A. pernyi enolase I. In the phylogenetic tree, enolase II sequences from A. pernyi and B. mori were clearly separated from the majority of enolase sequences of higher organisms including A. pernyi and B. mori enolase I sequences. By sequence comparisons and phylogenetic analysis, we suggest that enolase II from A. pernyi and B. mori may be a new member of the enolase superfamily. Antheraea pernyi enolase I mRNA was found in all tested tissues whereas enolase II mRNA was expressed specifically in the spermaries and ovaries, suggesting that the product of enolase II gene may be related to reproduction. The transcript abundance of A. pernyi enolase I gene was significantly down-regulated after cold shock and significantly up-regulated after heat shock, suggesting that A. pernyi enolase I gene may be inducible by temperature stress.

Analysis of Transcripts Expressed in One-Day-Old Larvae and Fifth Instar Silk Glands of Tasar Silkworm, Antheraea mylitta

Antheraea mylitta is one of the wild nonmulberry silkworms, which produces tasar silk. An EST project has been undertaken to understand the gene expression profile of A. mylitta silk gland. Two cDNA libraries, one from the whole bodies of one-day-old larvae and the other from the silkglands of fifth instar larvae, were constructed and sequenced. A total of 2476 good-quality ESTs (1239 clones) were obtained and grouped into 648 clusters containing 390 contigs and 258 singletons to represent 467 potential unigenes. Forty-five sequences contained putative coding region, and represented potentially novel genes. Among the 648 clusters, 241 were categorized according to Gene Ontology hierarchy and showed presence of several silk and immune-related genes. The A. mylitta ESTs have been organized into a freely available online database “AmyBASE”. These data provide an initial insight into the A. mylitta transcriptome and help to understand the molecular mechanism of silk protein production in a Lepidopteran species.

An integrated database for the enhanced identification of silkworm gene resources

The National Academy of Agricultural Science (NAAS) has developed a web-based database to provide characterization information in silkworm. The silkworm database has four major function menus: variety searching, characterization viewing, general information and photo gallery. It provides 321 silkworm varieties characterization information for six different regions namely, Korean, Japanese, Chinese, European, Tropical and non-classified group. Additionally, the database provides 1,132 photo images regarding life cycle of various silkworm varieties. A specific characterization information table provides accession number, variety, strain and larval marking, blood color, cocoon color, cocoon shape, egg colors, remarks and image table provides photos which consist of shape and color in the different stages of larval, egg and cocoon stages.

AVAILABILITY

The database is available for free at http://www.naas.go.kr/silkworm/english/

SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology

The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). Since the draft sequence was completed and the SilkDB was first released 5 years ago, we have collaborated with other groups to make much remarkable progress on silkworm genome research, such as the completion of a new high-quality assembly of the silkworm genome sequence as well as the construction of a genome-wide microarray to survey gene expression profiles. To accommodate these new genomic data and house more comprehensive genomic information, we have reconstructed SilkDB database with new web interfaces. In the new version (v2.0) of SilkDB, we updated the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarray expression data, Expressed Sequence Tags (ESTs) and corresponding references. Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently. SilkDB is publicly available at the new URL of http://www.silkdb.org.

Construction of a full-length cDNA Library from Chinese oak silkworm pupa and identification of a KK-42-binding protein gene in relation to pupa-diapause termination

In this study we successfully constructed a full-length cDNA library from Chinese oak silkworm, Antheraea pernyi, the most well-known wild silkworm used for silk production and insect food. Total RNA was extracted from a single fresh female pupa at the diapause stage. The titer of the library was 5 × 10⁵ cfu/ml and the proportion of recombinant clones was approximately 95%. Expressed sequence tag (EST) analysis was used to characterize the library. A total of 175 clustered ESTs consisting of 24 contigs and 151 singlets were generated from 250 effective sequences. Of the 175 unigenes, 97 (55.4%) were known genes but only five from A. pernyi, 37 (21.2%) were known ESTs without function annotation, and 41 (23.4%) were novel ESTs. By EST sequencing, a gene coding KK-42-binding protein in A. pernyi (named as ApKK42-BP; GenBank accession no. FJ744151) was identified and characterized. Protein sequence analysis showed that ApKK42-BP was not a membrane protein but an extracellular protein with a signal peptide at position 1-18, and contained two putative conserved domains, abhydro_lipase and abhydrolase_1, suggesting it may be a member of lipase superfamily. Expression analysis based on number of ESTs showed that ApKK42-BP was an abundant gene in the period of diapause stage, suggesting it may also be involved in pupa-diapause termination.