Lotmaria passim strain:422 | isolate:BRL Genome sequencing, principal assembly
A chromosome-level diploid genome assembly for the honey bee parasite Lotmaria passim, with a complete maxicircle sequence and 31 minicircle sequences. The initial contigs were assembled from 115x-per-haplotig PacBio HiFi reads by Hifiasm. Chromosome-level haplotigs were retained by purge_dups and scaffolded by YaHS, and confirmed by Hi-C-Pro. Maxicircle contigs were identified and maxicircle reads were extracted and reassembled by Hifiasm. Minicircle reads were iteratively identified starting by profile HMMs built from Leptomonas pyrrhocoris minicircles. Complete minicircle sequences were realigned at their homologous conservative regions and duplicated sequences were removed by building phylogenetic trees using iqtrees. See Methods section of publication for full procedures.