Figure 1.

Flowchart of sequence capture approach. (a) Sequence data from the Atlantic cod genome (Tørresen et al., 2017; gadMor2) combined with gene sequences of target genes and sequences from low coverage genomes of the additional codfishes are combined to generate probes. (b) Isolated DNA is multiplexed with Illumina and PacBio barcodes. (c) Raw reads for each species are used to score all probes, ensuring that no repeated sequences are present. DNA probes are used in solution on isolated DNA for all of the included species, hybridizing to the target sequences. Target sequences are then captured and sequences on the PacBio RSII sequencing platform. (d) Downstream bioinformatics includes demultiplexing of reads and trimming, making the reads ready for downstream analysis such as mapping and de novo assembly