DOI: 10.5061/dryad.j6q573nkz
title: Data from: The spotted parrotfish genome provides evolutionary insight into the ecological adaptation of a keystone dietary specialist

description: With over 600 valid species, the wrasses (family Labridae) are among the
 largest and most successful of the marine teleosts. They feature
 prominently on coral reefs where they are known not only for their
 impressive diversity in colouration and form, but also in their functional
 specialization and ability to occupy a wide variety of trophic guilds.
 Among the wrasses, the parrotfishes (tribe Scarini) display some one of
 the most dramatic examples of trophic specialization. Using
 abrasion-resistant biomineralized teeth, parrotfishes are able to
 mechanically extract protein-rich micro-photoautotrophs growing in and
 amongst reef carbonate material, a dietary niche that is inaccessible to
 most other teleost fishes. This ability to exploit an otherwise untapped
 trophic resource is thought to have played a role in the diversification
 and evolutionary success of the parrotfishes. In order to better
 understand the key evolutionary innovations leading to the success of
 these dietary specialists, we sequenced and analysed the genome of a
 representative species, the spotted parrotfish (Cetoscarus ocellatus). We
 find significant expansion, selection, and duplication within several
 detoxification gene families and a novel poly-glutamine expansion in the
 enamel protein ameloblastin, and we consider their evolutionary
 implications. Our genome provides a useful resource for comparative
 genomic studies investigating the evolutionary history of this highly
 specialized teleostean radiation.
description: The spotted parrotfish genomes (<em>Cetoscarus
 ocellatus</em>) was sequenced and assembled to investigate the
 evolution of this coral reef fish group, and to provide genomic resources
 for studies on the Scarini. This genome was assembled using a combination
 of long-read, linked-read, and Hi-C data (the raw seqeunce data are
 avalable on the SRA database under BioProject accession PRJNA1081164).
 Assembly methods are outlined in the associated manuscript. Briefly, an
 initial de novo assembly of the PacBio long-read data was performed using
 Canu v.2.1.1 with default settings and an estimated genome size of 1.4 Gb
 (based on published labrid genomes). TELL-seq linked reads were used to
 scaffold the draft de novo long-read assembly and improve its contiguity
 using Long Ranger basic v2.2.2, ARCS v1.2, and LINKS v1.8.7. Finally, Hi-C
 reads were aligned to the ARCS/LINKS-scaffolded draft assembly. The genome
 was annotated using FGENESH++.
description: # The spotted parrotfish genome provides evolutionary insight into the
 ecological adaptation of a keystone dietary specialist --- This dataset
 contains the Cetoscarus ocellatus genome assembly, and the accompanying
 annotation files. Assembly and annotation methods can be found in the
 associated manuscript. ## Description of the data and file structure The
 filename below is a FASTA file containing the assembled genome scaffolds:
 * `PF_genome-assembly_final.fa` The filename below is an annotation file
 corresponding to the genome assembly, in a standard GFF3 format: *
 `PF_annotation-run1_species_fgenesh.gff3` The filenames below are FASTA
 files for the annotated genes, extracted from the genome assembly,
 presented as coding sequences (CDS) (cds), mRNA sequences, and protein
 sequences respectively: * `PF_annotation-run1_species_fgenesh_cds.fa` *
 `PF_annotation-run1_species_fgenesh_mrna.fa` *
 `PF_annotation-run1_species_fgenesh_proteins.fa` The filename below is a
 FASTA file for the assembled genome: *
 'PF_genome-assembly_final.fa' The annotation files were produced
 using FGENESH++ v7.2.2. The tab-delimited 'General Feature
 Format' annotation files (i.e. the 'gff3' files) represent
 a standard file format for genome assemblies; they contains information
 for every feature in the associated reference genome. The contig/scaffold
 sequence names in the gff3 files correspond to the sequence names in the
 associated genome assembly files. The protein, mRNA and CDS fasta files
 are based on the annotations detailed in the gff3 files. ## Sharing/Access
 information All sequence data that were utilised to generate these three
 genomes are available on NCBI under BioProject PRJNA1081164