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Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes
Characterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copA. In this study, a local BLASTN method using a copA database built in this study was developed to recover full-length pu...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4541151/ https://www.ncbi.nlm.nih.gov/pubmed/26286020 http://dx.doi.org/10.1038/srep13258 |
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author | Li, Xiaofang Zhu, Yong-Guan Shaban, Babak Bruxner, Timothy J. C. Bond, Philip L. Huang, Longbin |
author_facet | Li, Xiaofang Zhu, Yong-Guan Shaban, Babak Bruxner, Timothy J. C. Bond, Philip L. Huang, Longbin |
author_sort | Li, Xiaofang |
collection | PubMed |
description | Characterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copA. In this study, a local BLASTN method using a copA database built in this study was developed to recover full-length putative copA sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning CopA using conserved metal-binding motifs, inferred by evolutionary trace analysis of CopA sequences from known Cu resistant microorganisms. In total, 99 putative copA sequences were recovered from the tailings metagenome, out of which 70 were found with high potential to be functioning in Cu resistance. Phylogenetic analysis of selected copA sequences detected in the tailings metagenome showed that topology of the copA phylogeny is largely congruent with that of the 16S-based phylogeny of the tailings microbial community obtained in our previous study, indicating that the development of copA diversity in the tailings might be mainly through vertical descent with few lateral gene transfer events. The method established here can be used to explore copA (and potentially other metal resistance genes) diversity in any metagenome and has the potential to exhaust the full-length gene sequences for downstream analyses. |
format | Online Article Text |
id | pubmed-4541151 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-45411512015-08-31 Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes Li, Xiaofang Zhu, Yong-Guan Shaban, Babak Bruxner, Timothy J. C. Bond, Philip L. Huang, Longbin Sci Rep Article Characterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copA. In this study, a local BLASTN method using a copA database built in this study was developed to recover full-length putative copA sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning CopA using conserved metal-binding motifs, inferred by evolutionary trace analysis of CopA sequences from known Cu resistant microorganisms. In total, 99 putative copA sequences were recovered from the tailings metagenome, out of which 70 were found with high potential to be functioning in Cu resistance. Phylogenetic analysis of selected copA sequences detected in the tailings metagenome showed that topology of the copA phylogeny is largely congruent with that of the 16S-based phylogeny of the tailings microbial community obtained in our previous study, indicating that the development of copA diversity in the tailings might be mainly through vertical descent with few lateral gene transfer events. The method established here can be used to explore copA (and potentially other metal resistance genes) diversity in any metagenome and has the potential to exhaust the full-length gene sequences for downstream analyses. Nature Publishing Group 2015-08-19 /pmc/articles/PMC4541151/ /pubmed/26286020 http://dx.doi.org/10.1038/srep13258 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Li, Xiaofang Zhu, Yong-Guan Shaban, Babak Bruxner, Timothy J. C. Bond, Philip L. Huang, Longbin Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes |
title | Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes |
title_full | Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes |
title_fullStr | Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes |
title_full_unstemmed | Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes |
title_short | Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes |
title_sort | assessing the genetic diversity of cu resistance in mine tailings through high-throughput recovery of full-length copa genes |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4541151/ https://www.ncbi.nlm.nih.gov/pubmed/26286020 http://dx.doi.org/10.1038/srep13258 |
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