Whole genome sequencing and phylogenomic analyses of a novel glufosinate-tolerant Pseudomonas species

Wee, Wei Yee and Chew, Xin Yi and Taheri, Sima and Li Tan, Xue and Teo, Chee How (2022) Whole genome sequencing and phylogenomic analyses of a novel glufosinate-tolerant Pseudomonas species. 3 Biotech, 12 (5). ISSN 2190-572X, DOI https://doi.org/10.1007/s13205-022-03185-4.

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A novel glufosinate-tolerant Pseudomonas sp. LA21, was isolated from soil samples of an oil palm plantation with a long history of glufosinate application. The genome of Pseudomonas sp. LA21 was sequenced with 150 bp paired-end conducted using Illumina sequencing technology. De novo genome assembly was performed using SPAdes, ABySS, and Velvet assemblers. Phylogenetic analysis using 16S rRNA gene sequence showed that Pseudomonas sp. LA21 was closely related to Pseudomonas nitroreducens ATCC 33634. Multilocus sequence analysis (MLSA) based on four bacterial housekeeping genes (16S rRNA, gyrB, rpoB, and rpoD) was conducted together with 138 reference genomes of Pseudomonas species. The phylogenetic tree derived from MLSA analysis using concatenated 16S rRNA-gryB-rpoD-rpoB sequences grouped Pseudomonas sp. LA21 under Pseudomonas aeruginosa group and Pseudomonas nitroreducens subgroup. Detailed phylogenomic analysis using average nucleotide identity (ANI) and genome-to-genome distance calculator (GGDC) approaches showed that Pseudomonas sp. LA21 could be classified as a novel Pseudomonas species.

Item Type: Article
Funders: Universiti Malaya [Grant No: BKP078-2016], Universiti Malaya [Grant No: RU006-2017]
Uncontrolled Keywords: Pseudomonas sp; Glufosinate; 16S rRNA; MLSA; GGDC
Subjects: S Agriculture > S Agriculture (General)
Divisions: Deputy Vice Chancellor (Research & Innovation) Office > Centre for Research in Biotechnology for Agriculture
Depositing User: Ms. Juhaida Abd Rahim
Date Deposited: 06 Oct 2023 07:34
Last Modified: 06 Oct 2023 07:34
URI: http://eprints.um.edu.my/id/eprint/42859

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