Chromosome-scale thraustochytrid genome assembly

We used long-read sequencing to produce a telomere-to-telomere genome assembly for the osmoheterotrophic stramenopile protist Aurantiochytrium limacinum MYA-1381. Its ~62 Mb genome is mainly organized in 26 linear chromosomes with a novel configuration: subtelomeric rDNAs are interspersed with long repeated sequence elements denoted as LOng REpeated - TElomere And Rdna Spacers (LORE-TEARS). These repeats may play a role in chromosome end maintenance. A putative circular mirusvirus genome is present at a high copy number (called circular element 1; CE1). The presence of another mirusvirus genome at the end of chromosome 15 in superposition between two complete sets of rRNA and LORE-TEAR elements suggests a dynamic process at the chromosome ends., For Nanopore sequencing, Aurantiochytrium ATCC MYA-1381 and two putative crtIBY knockout mutants (designated KO32 and KO33; (Rius et al. 2023)) were cultured for three days in 50 ml ATCC 790 By+ medium. Genomic DNA was extracted as described in the manuscript. The precipitated DNA was left to dissolve in water by spontaneous diffusion for 48+ hours at room temperature to avoid shearing and subsequently purified using QIAGEN Genomic-tip 20/G. Agarose gel electrophoresis (1%) was used to visually assess and confirm the integrity of high molecular weight (20+ Kb) DNA. DNA quality was evaluated using a NanoPhotometer P360 (Implen) to measure A260/280 (~1.8) and A260/230 (2.0-2.2) ratios. The quantity of DNA was calculated using a Qubit 2.0 Fluorometer (ThermoFisher Scientific) with the dsDNA broad range assay kit.
A multiplexed Nanopore (MinION, Oxford Nanopore Technologies) sequencing library was prepared using the Oxford Nanopore Technology (ONT) ligation sequencing kit (SQK-LSK109) and t...,