Abstract
BackgroundAquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data for aquatic animals are publicly available. However, currently there is no comprehensive resource exist for the analysis, unification, and integration of these datasets. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals. This aquatic animal transcriptome map database dbATM provides de novo assembly of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome.ResultsTo improve the assembly quality, three computational tools (Trinity, Oases and SOAPdenovo-Trans) were employed to enhance individual transcriptome assembly, and CAP3 and CD-HIT-EST software were then used to merge these three assembled transcriptomes. In addition, functional annotation analysis provides valuable clues to gene characteristics, including full-length transcript coding regions, conserved domains, gene ontology and KEGG pathways. Furthermore, all aquatic animal genes are essential for comparative genomics tasks such as constructing homologous gene groups and blast databases and phylogenetic analysis.ConclusionIn conclusion, we establish a resource for non model organism aquatic animals, which is great economic and ecological importance and provide transcriptomic information including functional annotation and comparative transcriptome analysis. The database is now publically accessible through the URL http://dbATM.mbc.nctu.edu.tw/.
Highlights
Aquatic animals have great economic and ecological importance
To effectively increase the our knowledge on aquatic animal gene discovery at mRNA level, RNAseq has been applied to several important aquaculture species such as, Plecoglossus altivelis [5], Cyprinus carpio [6], Penaeus monodon [7], Hyriopsis cumingii [8], Mytilus galloprovincialis [9], and Anguilla anguilla [10]
Following systematic analysis (Fig. 2), the individual species information and comparative analysis can be accessed from dbATM
Summary
Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals. This aquatic animal transcriptome map database dbATM provides de novo assembly of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome. To investigate the genomic resource of aquatic animals, generation sequencing (NGS) approach has been adapted to uncover new genes and biological mechanisms. To effectively increase the our knowledge on aquatic animal gene discovery at mRNA level, RNAseq has been applied to several important aquaculture species such as, Plecoglossus altivelis [5], Cyprinus carpio [6], Penaeus monodon [7], Hyriopsis cumingii [8], Mytilus galloprovincialis [9], and Anguilla anguilla [10]. To gain insights into the immunogenetics and immune response system, RNA-seq has been successfully adapting to
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
