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

BMC Research Notes

Data Note

Theerapong Krajaejun¹  Preecha Patumcharoenpol²  Sithichoke Tangphatsornruang³  Tassanee Lohnoo⁴  Wanta Yingyong⁴  Thidarat Rujirawat⁴  Weerayuth Kittichotirat⁵ 

[1]Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand

[2]Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, Thailand

[3]National Omics Center, National Science and Technology Development Agency, 12120, Pathum Thani, Thailand

[4]Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand

[5]Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand

关键词: Pythium insidiosum;    Pythiosis;    Draft genome;    Next-generation sequencing;   

DOI  :  10.1186/s13104-023-06532-7

 received in 2022-10-01, accepted in 2023-09-22,  发布年份 2023

来源: Springer

【 摘 要 】

ObjectivesPythium 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 descriptiongDNA 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; N50: 229.9 Kb; L50: 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.

【 授权许可】

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© BioMed Central Ltd., part of Springer Nature 2023