PacBio long read-assembled draft genome of Pythium insidiosum strain Pi-S isolated from a Thai patient with pythiosis

Journal article

Authors/Editors

WEERAYUTH KITTICHOTIRAT

Strategic Research Themes

Other (Strategic Research Themes)

Publication Details

Author list: Krajaejun, Theerapong; Patumcharoenpol, Preecha; Rujirawat, Thidarat; Kittichotirat, Weerayuth;
Tangphatsornruang, Sithichoke; Lohnoo, Tassanee; Yingyong, Wanta

Publisher: BioMed Central

Publication year: 2023

Volume number: 16

Issue number: 1

ISSN: 17560500

eISSN: 1756-0500

URL: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85174153044&doi=10.1186%2fs13104-023-06532-7&partnerID=40&md5=6ea1089c0d5b231c7874a3dc76a2d794

Languages: English-Great Britain (EN-GB)

View on publisher site

Abstract

Objectives: Pythium insidiosum is the causative agent of pythiosis, a difficult-to-treat condition, in humans and animals worldwide. Biological information about this filamentous microorganism is sparse. Genomes of several P. insidiosum strains were sequenced using the Illumina short-read NGS platform, producing incomplete genome sequence data. PacBio long-read platform was employed to obtain a better-quality genome of Pythium insidiosum. The obtained genome data could promote basic research on the pathogen’s biology and pathogenicity. Data description: gDNA sample was extracted from the P. insidiosum strain Pi-S for whole-genome sequencing by PacBio long-read NGS platform. Raw reads were assembled using CANU (v2.1), polished using ARROW (SMRT link version 5.0.1), aligned with the original raw PacBio reads using pbmm2 (v1.2.1), consensus sequence checked using ARROW, and gene predicted using Funannotate pipeline (v1.7.4). The genome completion was assessed using BUSCO (v4.0.2). As a result, 840 contigs (maximum length: 1.3 Mb; N 50: 229.9 Kb; L 50: 70) were obtained. Sequence assembly showed a genome size of 66.7 Mb (178x coverage; 57.2% G-C content) that contained 20,375 ORFs. A BUSCO-based assessment revealed 85.5% genome completion. All assembled contig sequences have been deposited in the NCBI database under the accession numbers BBXB02000001 - BBXB02000840. © 2023, BioMed Central Ltd., part of Springer Nature.

Keywords

Draft genome