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

Wei Yee Wee; Xin Yi Chew; Sima Taheri; Xue Li Tan; Chee How Teo

doi:10.1007/s13205-022-03185-4

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

3 Biotech. 2022 May;12(5):123. doi: 10.1007/s13205-022-03185-4. Epub 2022 Apr 25.

Authors

Wei Yee Wee¹, Xin Yi Chew¹, Sima Taheri², Xue Li Tan², Chee How Teo²

Affiliations

¹ School of Science, Monash University Malaysia, 47500 Subang Jaya, Malaysia.
² Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603 Kuala Lumpur, Malaysia.

Abstract

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, gyr B, rpo B, and rpo D) 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.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-022-03185-4.

Keywords: 16S rRNA; GGDC; Glufosinate; MLSA; Pseudomonas sp..