FishDB: an integrated functional genomics database for fishes
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FishDB: an integrated functional genomics database for fishes Liandong Yang1, Zetan Xu2, Honghui Zeng1, Ning Sun1,3, Baosheng Wu3,4, Cheng Wang1,3, Jing Bo3,4, Lin Li1,3, Yang Dong2 and Shunping He1,4,5*
Abstract Background: Hundreds of genomes and transcriptomes of fish species have been sequenced in recent years. However, fish scholarship currently lacks a comprehensive, integrated, and up-to-date collection of fish genomic data. Results: Here we present FishDB, the first database for fish multi-level omics data, available online at http://fishdb. ihb.ac.cn. The database contains 233 fish genomes, 201 fish transcriptomes, 5841 fish mitochondrial genomes, 88 fish gene sets, 16,239 miRNAs of 65 fishes, 1,330,692 piRNAs and 4852 lncRNAs of Danio rerio, 59,040 Mb untranslated regions (UTR) of 230 fishes, and 31,918 Mb coding sequences (CDS) of 230 fishes. Among these, we newly generated a total of 11 fish genomes and 53 fish transcriptomes. Conclusions: This release contains over 410,721.67 Mb sequences and provides search functionality, a BLAST server, JBrowse, and PrimerServer modules. Keywords: Fish, Genome, Transcriptome, Evolution, Adaptation
Background Fish are the largest group of vertebrates, covering over one-half of the world’s living vertebrates [1]. Considering the vast diversity of species and morphology, fish have received intense attention from scholars and the public, as they are important to both scientific research and aquaculture. The availability of fish genomes and transcriptomes will provide valuable resources for ichthyological research. However, fish scholarship currently lacks a comprehensive, integrated, up-to-date collection of fish omics data. Currently, at least 222 fish genomes have been sequenced and deposited in public databases, including the NCBI genome database [2], Ensembl [3], UCSC [4], * Correspondence: [email protected] 1 State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China 4 Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China Full list of author information is available at the end of the article
SalmoBase [5], GCGD [6], and cBARBEL [7]. Because the cost of whole-genome sequencing has decreased, many whole-genome sequencing projects on fish have been performed in recent years, usually by small research groups with technical support from private companies. Although the genomes are often required to be submitted to the NCBI genome database before publication, the database is not scheduled to be updated frequently in the future. More importantly, many more genomes have already been sequenced, but the necessary studies take time to publish, leaving many genomes unavailable to the research community. In this way, ichthyological research has been severely hampered for lack of a comprehensive, integrated, and up-to-date collection of fish omics database. Here, we generated FishDB (http://fishdb.ihb.ac.cn), which is intended to meet the
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