- 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..
- ihb.ac.cn.
- Among these, we newly generated a total of 11 fish genomes and 53 fish transcriptomes..
- Fish are the largest group of vertebrates, covering over one-half of the world’s living vertebrates [1].
- The availability of fish genomes and tran- scriptomes will provide valuable resources for ichthyo- logical 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 se- quenced and deposited in public databases, including the NCBI genome database [2], Ensembl [3], UCSC [4],.
- In this way, ich- thyological research has been severely hampered for lack of a comprehensive, integrated, and up-to-date collec- tion of fish omics database..
- Here, we generated FishDB (http://fishdb.ihb.ac.cn), which is intended to meet the needs of the fish scholar- ship community.
- 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.
- its fish genomes and most of its fish transcriptomes from public databases.
- We also included a total of 11 fish ge- nomes and 53 fish transcriptomes collected by our group, which have not been accessible previously..
- Here, we generated a total of 11 fish genomes and 53 fish transcriptomes for the first time..
- Most of the fish genomes were obtained from the gen- ome database in NCBI [2], Ensembl [3], UCSC [4], EFish, SalmoBase [5], GCGD [6], and cBARBEL [7].
- We also assembled 11 new ge- nomes of comparable quality to those of the other fishes (Supplementary Data S2).
- All individual fish were eutha- nized, which was approved by the Institutional Animal Care and Use Committee of Institute of Hydrobiology, Chinese Academy of Sciences (Approval ID:.
- When the fish died, their muscle tissue was collected for sequencing.
- This generated a total of 233 fish genomes (Table 2).
- Among them, we obtained annotation files of genes for a total of 88 fish genomes (Supplementary Data S3) (Fig.
- Assembled fish transcriptomes were downloaded from the NCBI TSA (Transcriptome Shotgun Assemblies) database (Supplementary Data S4).
- We generated a total of 53 new transcriptomes sampled from tissues including muscle, brain, liver, kidney, and heart, which were then assembled using Trinity [8] with default parameters (Supplementary Data S5).
- We further collected a total of 49,406 raw RNA-seq from NCBI SRA (Sequence Read Archive) database (Supplementary Data S6)..
- A total of 2726 complete mtDNA sequences from 2726 fish species were obtained.
- We further downloaded a total of 8094 complete mtDNA sequences from 3121 fish species (Supplementary Data S7)..
- In total, the miRNAs from 65 fish were stored in FishDB (Supplementary Data S9)..
- For piRNA and long noncoding RNA (lncRNA), a total of 1,330,692 piRNAs and 4852 lncRNAs of Danio rerio Table 1 Summary of the data content of FishDB.
- Table 2 The distribution of fish genome resource.
- FishDB 303 91 http://fishdb.ihb.ac.cn.
- c Page of ortholog in fish genomes.
- We also predicted CDS and UTR using TransDecoder from tran- scriptome sequences, producing CDS and UTR se- quences for a total of 230 fish.
- In addition, we obtained CDS and UTR sequences from 48 fish genomes pre- dicted by Ensembl.
- Collectively, CDS and UTR se- quences from a total of 230 fish species were collected in FishDB (Supplementary Data S10)..
- The JBrowse module enables users to visualize the 88 fish genomes [17], which is a related browser to the con- ventional CGI-based genome browser (GBrowse).
- Three main tracks, including CDS, mRNA, and exon, are integrated for all fish genomes.
- We have built the Fish Genome Database (FishDB), which provides a central portal for genomics, tran- scriptomics, genetics, and evolutionary biology of fish..
- FishDB stores various sequences, including genomes, transcriptomes, mitochondrial genomes, ESTs, ortho- logs, noncoding RNAs, UTRs, and CDSs of fish species..
- FishDB will be continuously updated when new genome, transcriptome, and genetic datasets of fish be- come available, and more enhanced functionality will be possible in the future to generate a more valuable re- source for promoting comparative genomics, transcrip- tomes, and evolutionary biology studies..
- Additional file 1 : Supplementary Data S1.
- The fish genomes downloaded from public databases in FishDB..
- Additional file 2 : Supplementary Data S2.
- The fish genomes newly generated from our lab in FishDB..
- Additional file 3 : Supplementary Data S3.
- The fish gene sets in FishDB..
- Additional file 4 : Supplementary Data S4.
- The fish transcriptomes downloaded from Transcriptome Shotgun Assembly (TSA) in FishDB..
- Additional file 5 : Supplementary Data S5.
- The fish transcriptomes newly generated from our lab in FishDB..
- Additional file 6 : Supplementary Data S6.
- The RNA-seq data sets of fish transcriptomes downloaded from Sequence Read Archive (SRA) in FishDB..
- Additional file 7 : Supplementary Data S7.
- The fish mitochondrial genomes obtained from MitoFish and NCBI in FishDB..
- Additional file 8 : Supplementary Data S8.
- Additional file 9 : Supplementary Data S9.
- The fish miRNAs in FishDB..
- Additional file 10 : Supplementary Data S10.
- The UTRs and CDSs of fishes in FishDB..
- This research was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB31000000) and the National Natural Science Foundation of China (31972866).
- This research was supported by the Wuhan Branch, Supercomputing Center, Chinese Academy of Sciences, China..
- FishDB can be accessed at http://fishdb.ihb.ac.cn.
- All data used in this study are available from Supplementary Data S1, S3, S4, S6, S7, and S8..
- All this study was submitted to and approved by the Institutional Animal Care and Use Committee of Institute of Hydrobiology, Chinese Academy of Sciences (Approval ID: Y21304501)..
- 3 University of Chinese Academy of Sciences, Beijing 100049, China.
- 5 Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China..
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