Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Small RNA Profile of Silkworm Hemolymph Using Deep Sequencing

ABSTRACT: Human utilization of the mulberry-silkworm interaction started at least 5,000 years ago and greatly influenced world history through the Silk Road. Complementing the silkworm genome sequence, here we describe the genome of a mulberry species (Morus notabilis C. K. Schneider). In the 330 Mb genome assembly of M. notabilis, we identified 128 Mb of repetitive sequences and 29,338 genes, 60.8% of which were supported by transcriptome sequencing. Mulberry gene sequences appear to evolve ~3 times faster than other Rosales, perhaps facilitating its spread to Europe, Africa, and America. It is among few eudicots but several Rosales not preserving genome duplications in more than 100 million years – however neopolyploid series in mulberry and several others suggest that new duplications may confer benefits. Strikingly, five predicted mulberry miRNAs were found in the hemolymph and silkglands of silkworm, suggesting profound molecular level interactions that promise to expand knowledge of plant-herbivore relationship which constitute key elements of most terrestrial habitats. In addition, we investigated the characters of hemolymph small RNA.

ORGANISM(S): Bombyx mori

PROVIDER: GSE48168 | GEO | 2013/09/12

SECONDARY ACCESSION(S): PRJNA209084

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The Small RNA Profile of Silkworm Hemolymph Using Deep Sequencing

Project description:Human utilization of the mulberry-silkworm interaction started at least 5,000 years ago and greatly influenced world history through the Silk Road. Complementing the silkworm genome sequence, here we describe the genome of a mulberry species (Morus notabilis C. K. Schneider). In the 330 Mb genome assembly of M. notabilis, we identified 128 Mb of repetitive sequences and 29,338 genes, 60.8% of which were supported by transcriptome sequencing. Mulberry gene sequences appear to evolve ~3 times faster than other Rosales, perhaps facilitating its spread to Europe, Africa, and America. It is among few eudicots but several Rosales not preserving genome duplications in more than 100 million years – however neopolyploid series in mulberry and several others suggest that new duplications may confer benefits. Strikingly, five predicted mulberry miRNAs were found in the hemolymph and silkglands of silkworm, suggesting profound molecular level interactions that promise to expand knowledge of plant-herbivore relationship which constitute key elements of most terrestrial habitats. In addition, we investigated the characters of hemolymph small RNA. small mRNA profiles of silkworm hemolymph in the fifth instar day-5 silkworm were generated by deep sequencing, in twice, using Illumina Hiseq 2000.

2013-09-12 | E-GEOD-48168 | biostudies-arrayexpress

SWATH-based quantitative proteomics reveals the mechanism of enhanced Bombyx mori nucleopolyhedrovirus-resistance in silkworm reared on UV-B treated mulberry leaves

Project description:Bombyx mori nucleopolyhedrovirus (BmNPV) is one of the most acute infectious diseases in silkworm, which has caused great economic loss in sericulture. Previous study showed that the content of components in mulberry leaves, particularly for moracin N, was increased after UV-B irradiation. In this study, the BmNPV resistance of silkworms reared on UV-B treated and moracin N spreaded mulberry leaves was improved. To uncover the mechanism of enhanced BmNPV resistance, silkworm midguts from UV-B treated mulberry leaves (BUM) and moracin N (BNM) groups were analyzed by SWATH-based proteomic technique. Of note, the abundance of ribosomal proteins in BUM and BNM groups was significantly changed to maintain the synthesis of total protein levels and cell survival. While, cytochrome c oxidase subunit II, calcium ATPase and programmed cell death 4 involved in apoptotic process were up-regulated in BNM group. Expressions of lipase-1, serine protease precursor, Rab1 protein, and histone genes were increased significantly in BNM group. These results suggest that moracin N might be the main active components in UV-B treated mulberry leaves to affect the BmNPV-resistance of silkworm, which could promote apoptotic cell death, enhance the organism immunity, and regulate the intercellular environment of cells in silkworm. It also presents an innovative process to reduce the mortality rate of silkworm infected with BmNPV.

2017-06-01 | PXD006136 | Pride

RNA-seqencing of Jojoba seed tissues, seed developmental stages, and other tissues

Project description:Seeds of the desert shrub, jojoba (Simmondsia chinensis) are an abundant, renewable source of liquid wax-esters, which are valued additives in cosmetic products and industrial lubricants. Jojoba is relegated to its own taxonomic family, and there is little genetic information available to elucidate its phylogeny. Here we report the high-quality, 887 Mb, genome of jojoba assembled into 26 chromosomes with 23,490 protein-coding genes. The jojoba genome has only the whole-genome triplication (γ) shared among eudicots, and no recent duplications. These genomic resources coupled with extensive transcriptome, proteome and lipidome data helped to define heterogeneous pathways and machinery for lipid synthesis and storage, provided missing evolutionary history information for this taxonomically-segregated dioecious plant species, and will support efforts to improve the agronomic properties of jojoba

2020-03-11 | GSE130603 | GEO

Performance of Immunochip 1.0 with hemolymph samples collected at 3 and 48 hours from Vibrio-challenged mussels

2011-04-12 | GSE23535 | GEO

Antimicrobial potential of a ponericin-like peptide isolated from Bombyx mori L. hemolymph in response to Pseudomonas aeruginosa infection

Project description:The main effectors in innate immune system of B. mori L. are antimicrobial peptides (AMPs). We imunizied B. mori with varied inoculum size of Pseudomonas aeruginosa ATCC 25668 cells to relate the importance of inoculum size towards AMP production. There is a sharp change in λmax from 278 nm to 285 nm (bathochromic shift) in the hemolymph of immunized silkworm incubated for 24 h. FTIR study of the hemolymph extracted from the immunized B. mori showed peak at 1550 cm-1 indicates the presence of α-helical peptides in the hemolymph.The peptide fraction was obtained through methanol, acetic acid and water mixture (90:1:9) extraction, followed by peptide purification using RP-HPLC. The fraction exhibiting antibacterial property was collected and characterized further using MALDI-TOF mass spectrometry. A linear -helical peptide with flexible termini (LLKELWTKMKGAGKAVLGKIKGLL -Bm-Frac6), corresponding to a previously described peptide from ant venom and denominated ponericin-L1. This peptide showed antibacterial activity against P. aeruginosa. Moreover, MTT assay and hemolytic study revealed that the Bm-Frac6 (B. mori ponericin-L1) is non-toxic toward mammalian healthy cells. Finally, our study shows that silkworm larvae challenged with P. aeruginosa also induced modification in physiological processes, leading to significant morpho-anatomical changes.

2022-06-23 | PXD032794 | Pride

Unravelling the cellular and humoral immune responses of Antheraea pernyi hemolymph to Antheraea pernyi nucleopolyhedrovirus infection

Project description:Purpose: With the advent of next generation sequencing technologies, several researches have been focused on the molecular mechanism underlying the innate immunity of insects based on the changes of gene expression profiles in hemolymph. The goal of this study is to detect the differences in transcript levels in A. pernyi hemolymph in response to ApNPV. Methods:The A. pernyi hemolymph infected by ApNPV and normal samples were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000. The high-quality reads were obtained by removing the reads that contained adaptor contamination, low quality bases and undetermined bases.The transcriptome were de novo assembly. Results:We constructed six cDNA libraries using RNA samples from the hemolymph in ApNPV-infected and non-infected A. pernyi larvae with three replicates for each group. A total of 50459962, 49797542, 54402474 and 56342454, 56036432, 55471402 raw reads in ApNPV-infected and control groups were generated. After filtering, 48009732, 47241848, 51319586 and 53555764, 53364108, 53077540 clean reads were obtained. All short-read sequences were assembled into 49966 transcripts and 37498 unigenes. Conclusions: The transcriptome sequences were de novo assembled. The differentially expressed genes (DEGs) including both up- and down-regulated genes were obtained. We focused on the innate immunity related DEGs, and screened numerous of DEGs involved in cellular and humoral immune related pathways via bioinformatic analysis. The results of this study lay the foundation for a better understanding of the molecular mechanisms of cellular and humoral immunity of A. pernyi.

2019-01-29 | GSE125800 | GEO

Performance of Immunochip 1.0 with hemolymph samples collected at 3 and 48 hours from Vibrio-challenged mussels

Project description:We aimed to exemplify early and late transcriptional response of M. galloprovincialis to live Vibrio cells. Hemolymph was collected at 3 and 48 hours after the injection of 10 to 7 cells Vibrio splendidus LGP32 into the posterior adductor muscle. Hemolymph samples were similarly collected from paired control mussels injected with PBS-NaCl. The purified RNAs were successfully amplified, labelled and competitively hybridized to the new mussel oligoarray Immunochip 1.0. After acclimatization, groups of 40 farmed mussels from the Venice lagoon (Italy) were injected either with 10 to 7 cells of Vibrio splendidus LGP32 or with NaCl-enriched PBS. One ml of hemolymph was withdrawn at 3 h and 48 h post-injection from each control or treated mussel. Two RNA pools (N=10) per time point were composed from the treated mussels, processed and competitively hybridized in dye-swap combination (Cy3 / Cy5 aRNAs) on the same Immunochip slide against time-paired control RNA pools (N=40). Since each Immunochip array contains 4 replicates per probe, the dye-swap testing yielded a total of 16 expression values per probe per time-point.

2011-04-12 | E-GEOD-23535 | biostudies-arrayexpress

Drosophila melanogaster hemolymph gelatinase

Project description:The innate immune response of insects relies on several humoral and cellular mechanisms that require the activation of circulating proteases in the hemolymph to be functional. Here, we analyzed the gelatinase and caseinase activities of Drosophila larval hemolymph under normal and pathogenic conditions (bacterial lipopolysaccharides or endoparasitoid Leptopilina boulardi) using in gel zymography. Gelatinase activity was more intense than caseinase activity and qualitative and quantitative variations were observed between D. melanogaster strains and Drosophila species. Mass spectrometry identified a large number of serine proteases in gel bands equivalent to the major gelatinase and caseinase bands and of these, the most abundant and redundant were Tequila and members of the Jonah and Trypsin protease families. However, hemolymph from Tequila null mutant larvae showed no obvious changes in zymographic bands. Nor did we observe any significant changes in hemolymph gelatinases activity 24 h after injection of bacterial lipopolysaccharides or after oviposition by endoparasitoid wasps. These data confirmed that many serine proteases are present in Drosophila larval hemolymph but those with gelatinase and caseinase activity may not change drastically during the immune response.

2024-04-29 | PXD045527 | Pride

Improving silkworm genome annotation using a proteogenomics approach

Project description:We collected a total of 9.8 million mass spectra data generated in the laboratory from the proteomics analyses of different silkworm tissues, including the posterior silk gland 29, middle silk gland 30, ovary and testis 31, head 32, brain, prothoracic glands, subesophageal ganglion 33, hemolymph 34, fat body 35 and embryo 36,37 of domestic silkworm, and the posterior silk gland of wild silkworm 38.

2019-07-01 | PXD009672 | Pride

Improving silkworm genome annotation using a proteogenomics approach

Project description:We collected a total of 9.8 million mass spectra generated in the laboratory from the proteomics analyses of different silkworm tissues, including the posterior silk gland (PSG) 30, middle silk gland 31, ovary and testis 32, head 33, brain, prothoracic glands, subesophageal ganglion 34, hemolymph 35, fat body 36 and embryo 37,38 of domestic silkworm, and the posterior silk gland of wild silkworm 39.

2019-07-01 | PXD009697 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data