10.5061/DRYAD.NV1SV
Marcionetti, Anna
University of Lausanne
Swiss Institute of Bioinformatics
Rossier, Victor
University of Lausanne
Swiss Institute of Bioinformatics
Bertrand, Joris A.M.
University of Lausanne
Litsios, Glenn
University of Lausanne
Swiss Institute of Bioinformatics
Salamin, Nicolas
University of Lausanne
Swiss Institute of Bioinformatics
Bertrand, Joris A. M.
University of Lausanne
Swiss Institute of Bioinformatics
Data from: First draft genome of an iconic clownfish species (Amphiprion
frenatus)
Dryad
dataset
2018
Amphiprioninae
Indo-Pacific
Pomacentridae
Amphiprion frenatus
2018-02-07T21:01:46Z
2018-02-07T21:01:46Z
en
https://doi.org/10.1111/1755-0998.12772
1028918292 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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