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Front. Microbiol. | doi: 10.3389/fmicb.2019.00033

Whole genome sequencing and comparative genomics analyses of Pandoraea sp. XY-2, a new species capable of biodegrade tetracycline

Xueling Wu1, Xiaoyan Wu1, Li Shen1,  Jiaokun Li1,  Runlan Yu1, Yuandong Liu1, Guanzhou Qiu1 and  Weimin Zeng1*
  • 1School of Resource Processing and Bioengineering, Central South University, China

Few bacteria are resistant to tetracycline and can even biodegrade tetracycline in the environment. In this study, we isolated a bacterium Pandoraea sp. XY-2, which could biodegrade 74% tetracycline at pH 7.0 and 30°C within 6 days. Thereafter, we determined the whole genome sequence of Pandoraea sp. XY-2 genome is a single circular chromosome of 5.06 Mb in size. Genomic annotation showed that two AA6 family members-encoding genes and nine glutathione S-transferase (GSTs)-encoding genes could be relevant to tetracycline biodegradation. In addition, the average nucleotide identities (ANI) analysis between the genomes of Pandoraea sp. XY-2 and other Pandoraea spp. revealed that Pandoraea sp. XY-2 belongs to a new species. Moreover, comparative genome analysis of 36 Pandoraea strains identified the pan and specific genes, numerous single nucleotide polymorphisms (SNPs), insertions, and deletion variations (InDels) and different syntenial relationships in the genome of Pandoraea sp. XY-2. Finally, the evolution and the origin analysis of genes related to tetracycline resistance revealed that the six tetA(48) genes and two specific genes tetG and tetR in Pandoraea sp. XY-2 were acquired by horizontal gene transfer (HGT) events from sources related to Paraburkholderia, Burkholderia, Caballeronia, Salmonella, Vibrio, Proteobacteria, Pseudomonas, Acinetobacter, Flavimaricola and some unidentified sources. As a new spicies, Pandoraea sp. XY-2 will be an excellent resource for the bioremediation of tetracycline-contaminated environment.

Keywords: Pandoraea sp. XY-2, tetracycline biodegradation, Genome sequencing, Comparative genomic, Tetracycline Resistance

Received: 25 Oct 2018; Accepted: 10 Jan 2019.

Edited by:

Rakesh Sharma, Institute of Genomics and Integrative Biology (CSIR), India

Reviewed by:

Vasvi Chaudhry, University of Tübingen, Germany
Kelle C. Freel, University of Hawaii at Manoa, United States  

Copyright: © 2019 Wu, Wu, Shen, Li, Yu, Liu, Qiu and Zeng. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Weimin Zeng, School of Resource Processing and Bioengineering, Central South University, Changsha, Hunan Province, China, zengweimin1024@126.com