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Flatfish exon-capture

Citation

Atta, Calder (2021), Flatfish exon-capture, Dryad, Dataset, https://doi.org/10.5061/dryad.d51c5b036

Abstract

This dataset contains alignments used to study phylogenetic relationships of flatfishes based on exon-capture data. The samples in this dataset represent 89 species: 86 flatfishes and 3 outgroup Carangidae. 57 samples were extracted and assembled from tissues collected for this project, while 39 were sourced from previously assembled data that were prepared as part of the FishLife project. For this study we targeted 4,434 markers developed by Jiang et al. (2019) for capture efficiency in ray-finned fishes (Actinopterygii). Library preparation followed the protocol from Li et al. (2013) involving a double capture method used to increase concentrations of hybridized DNA. Raw reads were assembled into loci using the Assexon bioinformatics pipeline (Yuan et al. 2020). Assembled exons were aligned on amino acids using MAFFT (Katoh et al., 2002), then translated back to codon-based alignment using a custom perl script mafft_aln.pl, and poorly aligned markers were removed. These aligned data represent the unfiltered dataset in the associated study, which was further processed into subsets based on missing data, clocklikeness, nucleotide composition, and evolutionary rate.

Methods

For 57 samples processed for the study: DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA). RNA baits and gene-capture reagents were supplied by the Arbor Biosciences myBaits Hybridization Capture Kit. Target-capture hybridizations were done according to the myBaits Manual v.4.01 specifications, with baits diluted down as to use only 0.5μL per capture. Sequencing was performed by the University of Delaware Sequencing and Genotyping Center on two lanes of Illumina HiSeq 2500 System using paired-end 150 bp reads. The Assexon pipeline used to assemble reads into loci used the following dependencies: TrimGalore (Krüger 2012), String Graph Assembler (Simpson and Durbin 2012), Exonerate (Slater and Birney, 2005), MAFFT (Katoh et al., 2002).

Funding

National Oceanic and Atmospheric Administration, Award: NA15OAR4320063

William W. and Dorothy T. Gilbert Ichthyology Research Fund

National Science Foundation, Award: DEB-1932759

National Science Foundation, Award: DEB-1929248

National Science Foundation, Award: DEB-2015404