Genome and transcriptome sequencing for Macquarie perch and golden perch
For Macquarie perch, we used fin, tail bone and muscle tissues of MP_SCH12: a 2-month-old hatchery-produced juvenile of unknown sex of Yarra River origin, born in November 2012. For golden perch genome, we used fin tissue collected non-lethally from adult GOP001 of unknown sex (aged as 3+ years based on size), captured in the Broken River, Victoria, in May 2017. For both species, DNA samples were preserved in ethanol and kept at -20°C.
DNA was extracted using Qiagen DNeasy Blood & Tissue kits. For Illumina sequencing, 100 ng of gDNA was fragmented to 350 bp using QSonica, processed with a NEB Ultra Illumina Library Preparation Kit and sequenced on a Novaseq6000 at the Deakin Genomics Centre using 2 × 151 bp run configuration (Appendix A). To obtain long-read data, 1 µg of gDNA was fragmented to 8 kb using a Covaris G-Tube and processed with a LSK108 library preparation kit according to the manufacturer’s instructions (Oxford Nanopore, UK). The library was subsequently sequenced on a Nanopore R9.4 flowcell. Base-calling of the Nanopore signal used Albacore v2.0.1 (Oxford Nanopore, UK).
To facilitate genome annotations, we performed mRNA sequencing for both species. We used adult female Macquarie perch MP_527, captured November 2017 from Lake Dartmouth. Samples from liver, ovary, brain, kidney and muscle were collected. We used adult golden perch GPTT01 (aged as 3 years by otolith analysis), sexed in the field as putatively male, captured in the Ovens River, Victoria, in April 2018. Samples of brain, gills, heart, gonads, kidney, liver and cheek muscle were collected.
Immediately after fish were humanely killed, RNA samples were collected and preserved in DNA/RNA Shield (Zymo Research) and stored at -80°C (Macquarie perch) or -20°C (golden perch). Total RNA was extracted from individual tissue samples using Quick-RNA Kits (Zymo Research), quantified using a TapeStation (Agilent) and 440 ng pooled per tissue. This was enriched for mRNA via poly-T beads using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB). The enriched mRNA was processed using Universal Plus mRNA-Seq Library Preparation Kits and sequenced on an Illumina NovaSeq6000.