Ontology highlight
ABSTRACT:
PROVIDER: PRJNA594711 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10619117_1.fastq.gz | Fastqsanger.gz | |||
| SRR10619117_2.fastq.gz | Fastqsanger.gz | |||
| SRR10619118_1.fastq.gz | Fastqsanger.gz | |||
| SRR10619118_2.fastq.gz | Fastqsanger.gz | |||
| SRR10619119_1.fastq.gz | Fastqsanger.gz |
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Project description:Parasitized Chrysodeixis includens hemocyte transcriptome
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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized genetic information from organisms that lack of gene sequencing data. Sequences of transcriptomic or genomic data of C. includens are no longer available to conduct relevant and applied studies to agriculture, such as, characterize biological process, screening for resistance and identification of new target genes. In this sense, we constructed a reference transcriptome of C. includens from head and body tissues of third instar larvae and we performed and analysis of gene expression functionality of transcripts between head and body. Methods: Two replicates of pool 5 larvae (third instar) were dissected into two parts: head (enriched with neural tissue) and body (enriched with adipose and gut tissues). Paired-end libraries of head and body tissues, with an approximate average insert length of 300 bp, were sequenced on an Illumina HiSeq platform with 150 bp paired-end sequencing. Trimmed RNA-Seq reads from transcriptomes of head and body larvae were used for de novo assembly using de Bruijn graph-based assembler (Trinity). All contig sequences built on the reference transcriptome assembled were annotated using Blast2GO pipeline. For the expression analysis RNA-seq reads were mapped to the built reference transcriptome using TopHat and expression values of transcripts in FPKM (fragments per kilobase per million mapped reads) between head and body tissues were estimated on Cufflinks. Results: The assembled transcriptome from reads of head and body tissues of C. includens larvae generated a fasta file format (136.2MB) containing 102,249 transcript sequences and 60,347 “genes”. The length distribution of transcripts was between a minimum of 200bp and a maximum of 37,230bp with an average of 1,005bp. As the RNA extraction of body included enriched tissues of tegument, gut, and hemolymph of third instar larvae, the transcripts were found to be involved on transmembrane transport, proteolysis, cation transport and many types of metabolic process. These biological processes in soybean looper were related to the cellular functionality of oxidoreductase, transmembrane transporter and serine-type endopeptidase activities and many types of binding functions. In the head tissue of C. includens we found most transcripts with gene ontology related to signal transduction. This biological process could be associated with the functionality of genes related to odorant binding, signaling receptor binding, DNA binding and other types of molecular binding. As we found, we suggest that these genes expressed only in the head tissue might be involved mainly in the detection of a signal and subsequent cascade expression of biological processes. Conclusions: Our study represents the first detailed transcriptome of Chrysodeixis includens of different larvae tissues, with biologic replicates, generated by RNA-seq technology. Our results show that NGS offers a comprehensive and accurate sequencing data to species with reference genome not available. Also, RNA-seq data offer a global gene expression analysis between tissues and permit understand some biological process involved in insect physiology.
2019-09-30 | GSE121104 | GEO
Project description:Chrysodeixis includens genome and annotation from the Pest Genomics Initiative
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Project description:Chrysodeixis includens isolate:SIMRU Inbred Laboratory Colony Genome sequencing and assembly
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Project description:Neisseria meningitidis is a major cause of bacterial meningitis and septicemia worldwide. Seven new serogroup C meningococci were isolated from two provinces of China in January, 2006. Their PorA VR types were P1.20, 9. Multilocus sequence typing results indicated that they all belonged to ST-7. It is a new serogroup C N. meningitidis sequence type clone identified in China. Here we also present the results of a genomic comparison of these isolates with other 15 N. meningitidis serogroup A and B isolates, which belonged to ST-7, based on comparative genomic hybridization analysis. The data described here would be helpful to monitor the spread of this new serogroup C meningococci sequence type clone in China and worldwide. Keywords: comparative genomic hybridization To compare the genome compositions of these menC ST-7 isolates with those of menC ST-4821 isolates, menA ST-7 isolates and menB ST-7 isolates, we performed comparative genomic hybridization (CGH) analysis among 17 N. meningitidis isolates (including two newly identified menC ST-7 isolates) using an updated version of the whole-genome microarray of N. meningitidis serogroup C isolate 053442 .
2007-10-10 | E-GEOD-7331 | biostudies-arrayexpress