Long-read sequencing analysis of fish rearing water
This project aims to recover complete fish mitochondrial genomes from aquarium (rearing) water using long-read sequencing. We developed a workflow to isolate high-molecular-weight (HMW) DNA from the rearing water of Carassius auratus and Oryzias latipes, and to assemble full-length mitogenomes from Oxford Nanopore MinION reads. The dataset comprises (i) PCR-free eDNA from rearing water, (ii) long-range PCR datasets targeting whole mitogenomes, and (iii) benchmarking tissue datasets: ONT long-reads and Illumina NextSeq 1000 short-reads from muscle of C. auratus and O. latipes. These data enable comparisons between water-derived and tissue-derived sequences and between long- and short-read approaches. The workflows provide a non-invasive route to individual- and population-level mitochondrial analyses from eDNA and are readily applicable to other species and settings.