Comparative analysis of the silk gland transcriptomes between the domestic and wild silkworms

Structure elucidation, proliferation effect on macrophage and its mechanism of a new heteropolysaccharide from Lactarius deliciosus Gray

A new heteropolysaccharide was isolated from the fruiting bodies of Lactarius deliciosus Gray which had a molecular weight of 16kDa and was mainly composed of the galactose and glucose. Structural elucidation results indicated that Lactarius deliciosus Gray polysaccharide (LDG-B) had a backbone of (1,6)-linked d-galactose and (1, 2, 6)-linked d-galactose which branches were mainly composed of 4-linked d-glucose and 6-linked d-galactose residue. Cell cycle test results showed that LDG-B could promote the proliferation of B cells and macrophage cells by affecting G0/G1 phase, S phases and G2/M phases. The analysis of transcriptomes sequence of macrophages showed a total of 1839 genes were identified as DEGs, and approximately 708 genes were up-regulated, whereas 1131 genes were down-regulated in LDG-B group. KEGG pathway enrichment analysis showed that the MAPK, JAK-STAT and NF-κB signaling pathways are significantly enriched for DEGs in LDG-B group. Analysis of transcriptome resources enabled us to examine gene expression profiles, verify differential gene expression, and select candidate signaling pathways as the mechanisms of the immunomodulatory activity of LDG-B.

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/.

Comparative analysis of macrophage transcriptomes reveals a key mechanism of the immunomodulatory activity of Tricholoma matsutake polysaccharide

In the present study, we performed a proliferation assay, phagocytosis assay and cell cycle analysis of macrophages and sequenced the transcriptomes of control group macrophages and TMP-A group macrophages using Illumina sequencing technology to identify differentially expressed genes (DEGs) and determine the molecular mechanisms associated with differences in the immunomodulatory activity of TMP-A in macrophages. The results showed that TMP-A exhibits strong proliferation activity and phagocytosis activity in RAW264.7 cells in vitro and could also promote the proliferation of macrophage cells by abolishing cell-cycle arrest in the G0/G1 phase and promoting the cell cycle in the G2/M phase, which may induce cell division. A total of 12,616,096 and 11,798,839 bp paired-end reads were obtained for the control group and TMP-A group, respectively, and they corresponded to a total size of 12.5 G bp and 11.7 G bp, respectively, after the low-quality reads and adapter sequences were removed. Approximately 79.8% of the total number of genes (10,191) were expressed (RPKM ≥1), and more than 1,372 genes were highly expressed (RPKM >60) in the TMP-A group. A total of 1,043 unigenes were identified as DEGs, and approximately 486 genes were upregulated, whereas 557 genes were down-regulated, which might have contributed to the proliferation activity and phagocytosis activity of TMP-A in the RAW264.7 cells in vitro. A Gene Ontology (GO) enrichment analysis generated 13,042 assignments to cellular components, 13,094 assignments to biological processes, and 13,135 assignments to molecular functions. A KEGG pathway enrichment analysis showed that the MAPK and NF-κB signaling pathways are significantly enriched for DEGs between the two cell groups. Based on the experimental data, we believe that the significant antitumor activities of TMP-A in vivo involve the MAPK and NF-κB signaling pathways because the two signaling pathways intersect.

Comparative Analysis of Transcriptomes among Bombyx mori Strains and Sexes Reveals the Genes Regulating Melanic Morph and the Related Phenotypes

As a source of insect polymorphism, melanism plays an important role in ecological adaption and usually endows advantageous phenotypic-effects on insects. However, due to the mechanistic diversity, there are knowledge gaps in the molecular mechanisms underlying melanism and the related phenotypes. In silk moths, a recessive melanic mutant (sex-controlled melanism, sml) strain exhibits extended adult longevity. We took a transcriptome approach to perform a comparative analysis between this sml strain and a wild-type strain (Dazao). Our analysis resulted in the identification of 59 unique differentially expressed genes in the melanic mutant. Two key genes (laccase2 and yellow) involved in melanin formation were significantly up-regulated in melanic individuals. The laccase2 B-type isoform (BGIBMGA006746) was found to likely participate in the silkworm cuticular melanism process at late pupal stage. Moreover, we discovered 22 cuticular protein encoding genes with the possible function in melanin transport and/or maintenance. Based on our findings, we presume that the longer survival of the melanic sml male moths might be associated with the enhanced antioxidant defense systems and a reduction in the insulin/IGF-1 signaling pathway (IIS). These findings will facilitate the understanding of the molecular basis underlying melanism and the derived phenotypic-effects.

Comparative transcriptome analysis of Bombyx mori spinnerets and Filippi's glands suggests their role in silk fiber formation

The spinneret is located at the end of silk glands in the silkworm, Bombyx mori. The Filippi's gland (FG), which communicates with the silk gland, is considered an accessory to the latter. Although these two organs have been known for centuries, only their morphology has been studied. Their gene expression profiles and physiological roles are still unknown. Aided by next-generation sequencing, we profiled more than 11000 transcripts from the spinneret and FG of silkworm larvae on day 3 of the fifth instar (L5D3) and wandering stage (W1) in this study. A total of 59 ion-transporting protein genes and 106 cuticle protein genes were identified in the spinneret. To analyze the dynamic changes in the expression of spinneret genes, differential expression analysis was performed, and 1452 differentially expressed genes (DEGs) were identified in spinneret tissue harvested on L5D3 and W1 of the silkworm larvae. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of the DEGs revealed that the spinneret had active ion-transporting, chitin binding, and energy metabolism processes at W1. Based on these data, we hypothesized that the role of the spinneret is to provide a favorable physiological environment for the silk fiber formation. Furthermore, differential expression analysis and GO enrichment of the DEGs in the FG suggested a possible role of this gland in transporting small solutes such as ions, sugars and amino acids to the silk gland. Our findings pave a way for further functional explanation of the spinneret and FG.

Transcriptomic Analysis of the Anterior Silk Gland in the Domestic Silkworm (Bombyx mori) - Insight into the Mechanism of Silk Formation and Spinning

Silk proteins are synthesized in the middle and posterior silk glands of silkworms, then transit into the anterior of the silk gland, where the silk fibers are produced, stored and processed. The mechanism of formation and spinning of the silk fibers has not been fully elucidated, and transcriptome analyses specific to the anterior silk gland have not been reported. In the present study, we explored gene expression profiles in five regions of silk gland samples using the RNA-Seq method. As a result, there were 959,979,570 raw reads obtained, of which 583,068,172 reads were mapped to the silkworm genome. A total of 7419 genes were found to be expressed in terms of reads per kilobase of exon model per million mapped reads ≥ 5 in at least one sample. The gene numbers and expression levels of the expressed genes differed between these regions. The differentially expressed genes were analyzed, and 282 genes were detected as up-regulated in the anterior silk gland, compared with the other parts. Functions of these genes were addressed using the gene ontology and Kyoto Encyclopedia of Genes and Genomes databases, and seven key pathways were enriched. It suggested that the ion transportation, energy metabolism, protease inhibitors and cuticle proteins played essential roles in the process of silk formation and spinning in the anterior silk gland. In addition, 210 genes were found differently expressed between males and females, which should help to elucidate the mechanism of the quality difference in silk fibers from male and female silkworms.

Deep sequencing analysis of transcriptomes in Aspergillus flavus in response to resveratrol

Background

Resveratrol has been reported as a natural phytoalexin that inhibits infection or the growth of certain fungi including Aspergillus flavus. Our previous research revealed that aflatoxin production in A. flavus was reduced in medium with resveratrol. To understand the molecular mechanism of the A. flavus response to resveratrol treatment, the high-throughput paired-end RNA-Seq was applied to analyze the transcriptomic profiles of A. flavus.

Results

In total, 366 and 87 genes of A. flavus were significantly up- and down- regulated, respectively, when the fungus was treated with resveratrol. Gene Ontology (GO) functional enrichment analysis revealed that 48 significantly differentially expressed genes were involved in 6 different terms. Most genes in the aflatoxin biosynthetic pathway genes cluster (#54) did not show a significant change when A. flavus was treated with resveratrol, but 23 of the 30 genes in the #54 cluster were down-regulated. The transcription of aflA and aflB was significantly suppressed under resveratrol treatment, resulting in an insufficient amount of the starter unit hexanoate for aflatoxin biosynthesis. In addition, resveratrol significantly increased the activity of antioxidative enzymes that destroy radicals, leading to decreased aflatoxin production. Moreover, stuA, fluG, flbC, and others genes involved in mycelial and conidial development were down-regulated, which disrupted the cell’s orderly differentiation and blocked conidia formation and mycelia development. The transcripts of laeA and veA were slightly inhibited by resveratrol, which may partly decrease aflatoxin production and depress conidia formation.

Conclusions

Resveratrol can affect the expression of A. flavus genes that are related to developmental and secondary metabolic processes, resulting in decreased aflatoxin production and conidia formation and could also cause abnormal mycelia development. These results provide insight into the transcriptome of A. flavus in response to resveratrol and a new clew for further study in regulation of aflatoxin biosynthesis in A. flavus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0513-6) contains supplementary material, which is available to authorized users.