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Asian arowana (Scleropages formosus), an ancient teleost belonging to the Order Osteoglossomorpha, has been a valuable ornamental fish with some varieties. However, its biological studies and breeding germplasm have been remarkably limited by the lack of a reference genome. To solve these problems, here we report high-quality genome sequences of three common varieties of Asian arowana (the golden, red and green arowana). We firstly generated a chromosome-level genome assembly of the golden arowana, on basis of the genetic linkage map constructed with the restriction site-associated DNA sequencing (RAD-seq). In addition, we obtained draft genome assemblies of the red and green varieties. Finally, we annotated 22,016, 21,256 and 21,524 protein-coding genes in the genome assemblies of golden, red and green varieties respectively. Our data were deposited in publicly accessible repositories to promote biological research and molecular breeding of Asian arowana.
Pubmed ID: 27922628 RIS Download
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Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).
View all literature mentionsSoftware that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries.
View all literature mentionsCompendium of protein fingerprints. Diagnostic fingerprint database.
View all literature mentionsA database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Users can analyze protein sequences for Pfam matches, view Pfam family annotation and alignments, see groups of related families, look at the domain organization of a protein sequence, find the domains on a PDB structure, and query Pfam by keywords. There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families that may automatically generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found. Pfam also generates higher-level groupings of related families, known as clans (collections of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM).
View all literature mentionsSoftware tool for identification and annotation of genetically mobile domains and analysis of domain architectures.
View all literature mentionsComprehensive set of protein domain families automatically generated from UniProt Knowledge Database. Automated clustering of homologous domains generated from global comparison of all available protein sequences.
View all literature mentionsSoftware for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes.
View all literature mentionsSoftware application for construction of genetic linkage maps for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, outbreeders full-sib family. Can combine (''join'') data derived from several sources into an integrated map. Further: linkage group determination, automatic phase determination for outbreeders full-sib family, several diagnostics, and map charts. Everything available in an intuitive MS-Windows user interface. (entry from Genetic Analysis Software)
View all literature mentionsTool to search translated nucleotide databases using a protein query.
View all literature mentionsWeb server for identification of complete gene structures in genomic DNA.Tool for predicting locations and exon-intron structures of genes in genomic sequences from variety of organisms. Used for prediction of complete gene structures in human genomic DNA.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds.
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