Proteome sequencing and analysis of the entomopathogenic fungus Hirsutella sinensis isolated from Cordyceps sinensis
Ontology highlight
ABSTRACT:
ORGANISM(S): Ophiocordyceps Sinensis
SUBMITTER: 
Zhiqiang Liu
PROVIDER: PXD016899 | iProX | Tue Dec 24 00:00:00 GMT 2019
REPOSITORIES: iProX
Similar Datasets
Project description:Clonorchis sinensis is a zoonotic parasite causing clonorchiasis associated with human diseases such as biliary calculi, cholecystitis, liver cirrhosis, and is classified as carcinogenic to humans for cholangiocarcinoma. MicroRNAs (miRNAs) are non-coding, regulating small RNA molecules essential for the complex life cycle of parasites and involved in parasitic infections. To identify and characterize miRNAs expressed in adult C. sinensis residing chronically in the biliary tract, we developed an integrative approach combining deep sequencing, bioinformatic predictions with stem-loop real-time PCR analysis. Here we report the use of this approach to identify and clone 6 new and 62,512 conserved C. sinensis miRNAs which belong to 284 families. There is strong bias on families, family members and sequence nucleotides in C. sinensis. Uracil is the dominant nucleotide, particularly at positions 1, 14 and 22, which were located approximately at the beginning, middle and the end of conserved miRNAs. There is no significant M-bM-^@M-^\seed regionM-bM-^@M-^] at the first and ninth positions commonly found in human, animals and plants. Categorization of conserved miRNAs indicated that miRNAs of C. sinensis are still innovated and concentrated along three branches of the phylogenetic tree leading to bilaterians, insects and coelomates. There are two miRNA strategies in C. sinensis for its parasitic life: keeping a large category of miRNA families of different animals and keeping a stringent conserved seed region with high active innovation in other place of miRNA mainly in the middle and the end, which are perfect for the parasite to perform its complex life style and for host changes. The present study represents the first large scale characterization of C. sinensis miRNAs, which have implications for understanding the complex biology of this zoonotic parasite, as well as the miRNA studies of other related species such as Opisthorchis felineus and O. viverrini of human and animal health significance. Analysis of miRNA profile in parasite of C. sinensis
2010-09-03 | E-GEOD-22244 | biostudies-arrayexpress
Project description:Ophiocordyceps sinensis (Berk.) Sacc., a complex of larval carcass (sclerotium) and stroma formed by the fungus of Hirsutella sinensis infecting Hepialidae insect larvae, whose fruiting body is also the main fungal structure used for taxonomic identification. However, the induction of fruiting body is still inefficient and the high cost resulting in the large-scale artificial cultivation of this fungus has been unsuccessful in China.In this study,important factors and target genes associated with the fruiting body induction during the development of O. sinensis were identified, providing a basic molecular mechanism for facilitating the large-scale artificial cultivation of O. sinensis.
2021-06-30 | GSE160505 | GEO
Project description:Ophiocordyceps sinensis (Berk.) Sacc., a complex of larval carcass (sclerotium) and stroma formed by the fungus of Hirsutella sinensis infecting Hepialidae insect larvae, whose fruiting body is also the main fungal structure used for taxonomic identification. However, the induction of fruiting body is still inefficient and the high cost resulting in the large-scale artificial cultivation of this fungus has been unsuccessful in China.In this study,important factors and target genes associated with the fruiting body induction during the development of O. sinensis were identified, providing a basic molecular mechanism for facilitating the large-scale artificial cultivation of O. sinensis.
2021-06-30 | GSE160504 | GEO
Project description:Clonorchis sinensis is a zoonotic parasite causing clonorchiasis associated with human diseases such as biliary calculi, cholecystitis, liver cirrhosis, and is classified as carcinogenic to humans for cholangiocarcinoma. MicroRNAs (miRNAs) are non-coding, regulating small RNA molecules essential for the complex life cycle of parasites and involved in parasitic infections. To identify and characterize miRNAs expressed in adult C. sinensis residing chronically in the biliary tract, we developed an integrative approach combining deep sequencing, bioinformatic predictions with stem-loop real-time PCR analysis. Here we report the use of this approach to identify and clone 6 new and 62,512 conserved C. sinensis miRNAs which belong to 284 families. There is strong bias on families, family members and sequence nucleotides in C. sinensis. Uracil is the dominant nucleotide, particularly at positions 1, 14 and 22, which were located approximately at the beginning, middle and the end of conserved miRNAs. There is no significant “seed region” at the first and ninth positions commonly found in human, animals and plants. Categorization of conserved miRNAs indicated that miRNAs of C. sinensis are still innovated and concentrated along three branches of the phylogenetic tree leading to bilaterians, insects and coelomates. There are two miRNA strategies in C. sinensis for its parasitic life: keeping a large category of miRNA families of different animals and keeping a stringent conserved seed region with high active innovation in other place of miRNA mainly in the middle and the end, which are perfect for the parasite to perform its complex life style and for host changes. The present study represents the first large scale characterization of C. sinensis miRNAs, which have implications for understanding the complex biology of this zoonotic parasite, as well as the miRNA studies of other related species such as Opisthorchis felineus and O. viverrini of human and animal health significance.
2010-09-03 | GSE22244 | GEO
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Citrus sinensis tissues (including leaves, flowers and fruit). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features, such as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, flowers and fruit of Citrus sinensis. Total RNA was isolated using the TriReagent (Molecular Research Center) for leaves and flowers and the Guanidinium-free for fruits, and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Erik Mirkov for providing the plant material, as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.
2011-04-29 | E-GEOD-28754 | biostudies-arrayexpress
Project description:Purpose: transcriptome sequencing of Conopomorpha sinensis Methods: high-through Illumina HiSeqTM 2000 Results:66017 transcripts,35383 unigenes Conclusions:This study provided valuable transcriptome data for the litchi fruit borer, which was the first fundamental genomic basis for exploiting gene resources from the litchi fruit borer
2018-03-03 | GSE67194 | GEO
Project description: Not available
| S-EPMC7270455 | biostudies-literature
Project description:Large-scale analysis of the androgenic gland proteome in the Chinese mitten crab Eriocheir sinensis
2021-09-10 | PXD024496 | Pride
Project description:the chromatin accessibility and gene expression of muscle in E. sinensis in pre-molt (D) and post-molt (A) stages were sequenced by Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) and RNA-seq, respectively.The differntial peaks in ATAC-seq and differntial genes in RNA-seq were analzed. The data was used to analysis the differentially expressed genes (DEGs) in muscle before and after molting by combining ATAC-seq and RNA-seq
2022-07-17 | GSE206232 | GEO
Project description:the chromatin accessibility and gene expression of muscle in E. sinensis in pre-molt (D) and post-molt (A) stages were sequenced by Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) and RNA-seq, respectively.The differntial peaks in ATAC-seq and differntial genes in RNA-seq were analzed. The data was used to analysis the differentially expressed genes (DEGs) in muscle before and after molting by combining ATAC-seq and RNA-seq
2022-07-17 | GSE206231 | GEO