DOI: 10.5061/dryad.nv1sv
title: Data from: First draft genome of an iconic clownfish species (Amphiprion frenatus)

description: Clownfishes (or anemonefishes) form an iconic group of coral reef fishes,
 principally known for their mutualistic interaction with sea anemones.
 They are characterized by particular life-history traits, such as a
 complex social structure and mating system involving sequential
 hermaphroditism, coupled with an exceptionally long lifespan.
 Additionally, clownfishes are considered to be one of the rare group to
 have experienced an adaptive radiation in the marine environment. Here, we
 assembled and annotated the first genome of a clownfish species, the
 tomato clownfish (Amphiprion frenatus). We obtained a total of 17,801
 assembled scaffolds, containing a total of 26,917 genes. The completeness
 of the assembly and annotation was satisfying, with 96.5% of the
 Actinopterygii BUSCOs (benchmarking universal Single-Copy Orthologs) being
 retrieved in A. frenatus assembly. The quality of the resulting assembly
 is comparable to other bony fish assemblies. This resource is valuable for
 the advancing of studies of the particular life-history traits of
 clownfishes, as well as being useful for population genetic studies and
 the development of new phylogenetic markers. It will also open the way to
 comparative genomics. Indeed, future genomic comparison among closely
 related fishes may provide means to identify genes related to the unique
 adaptations to different sea anemone hosts, as well as better characterize
 the genomic signatures of an adaptive radiation.
description: Genome assembly of
 Amphiprion frenatusGenome assembly of A.
 frenatus in fasta format. The genome was obtained with a combination of
 high-coverage Illumina short paired-end reads (350 bo insertion size),
 Illumina mate-pairs (3 kb insertion sizes) and low-coverage long Pacbio
 reads. For more information, please refer to the
 publication.Amphiprion_frenatus_GenomeAssembly.fastaStructural genome annotation of Amphiprion frenatusStructural genome annotation of Amphiprion frenatus genome, in gff3 format. Structural annotation was obtained with a combination of ab initio and RNAseq-data based approaches. Final gene models were obtained with MAKER2. For more information, please refer to the publication.afrenatus.all_contigs.onlystandardFiltered.gff3Amphiprion frenatus protein sequences and annotationPredicted protein sequences from Amphiprion frenatus genome assembly, in fasta format. Each protein is annotated with the best blast hit with SwissProt database. For more information, please refer to the publication.afrenatus.proteins.uniprot.faAmphiprion frenatus CDS sequences and annotationPredicted coding sequences (CDS) sequences from Amphiprion frenatus genome assembly, in fasta format. Each CDS is annotated with the best blast hit with SwissProt database. For more information, please refer to the publication.afrenatus.transcripts.uniprot.faMitochondrial genome Amphiprion frenatusThe mitochondrial genome of Amphiprion frenatus, in fasta format. The mitochondrial genome was obtained by assembling short Illumina reads with MITObim. For further information, please refer to the publication.Afrenatus_Mitochondrial_Consensus.fastaMitochondrial genome annotation Amphiprion frenatusMitochondrial genome annotation for Amphiprion frenatus, in csv format. MitoAnnotator and MitoFish were used to obtain the mitochondrial genome annotation. For more information, please refer to the publicationMitochondrial_genome_annotation.csv