Searching the Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
The eyestalks of crustaceans play an essential role in controlling a variety of physiological functions by converting light into hormonal signals. To obtain a more complete description of eyestalk biology in the commercially important Chinese mitten crab (Eriocheir sinensis), we conducted comparative transcriptome analysis of eyestalks during the day and at night using high-throughput sequencing on an Illumina HiSeq 4000 platform. We obtained 47,092 unigenes-including 4771 differentially expressed genes (DEGs)-from eyestalks during the day and at night. We found that 4269 DEGs were upregulated during the day and 502 DEGs were upregulated at night. We identified five DEGs that may contribute to molting, including molt-inhibiting hormone, cuticle, catalase, aquaporin, and ubiquitin-conjugating enzyme; hence, similar to other crustaceans, Eriocheir sinensis may molt at night. We further identified eight DEGs related to behavior regulation, including three glutamate dehydrogenase genes that were upregulated during the day. Thus, changes in the eyestalks may partially compensate for daily changes in illumination in the Chinese mitten crab's normal environment. Our present study is the first genome-wide transcriptome analysis of the eyestalks of Eriocheir sinensis during the day and at night. Our findings provide a valuable insight into the molecular basis of circadian cycle regulation in crustaceans.
Pubmed ID: 30716437
Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.
Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level.
View all literature mentionsAn ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher''''s Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
View all literature mentionsIntegrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
View all literature mentionsSoftware for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
View all literature mentions