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Lotmaria passim strain 422 isolate BRL genome sequencing and assembly

dataset
posted on 2024-02-06, 23:48 authored by USDA-ARS
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.

Funding

National Institute of Food and Agriculture, 2020-67013-31861

National Institute of Food and Agriculture, 2022-67012-37482

National Science Foundation, DEB-2225083

National Science Foundation, DGE-2236417

Eva Crane Trust, ECTA_20201204

History

Data contact name

BioProject Curation Staff

Publisher

National Center for Biotechnology Information

Temporal Extent Start Date

2023-12-13

Theme

  • Non-geospatial

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

Biological Sciences; biotechnology; genetics

Pending citation

  • No

Public Access Level

  • Public

Accession Number

PRJNA1052050

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