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Title: High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413

Abstract

We report that Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A survey of symbionts of P. rigida in Uruguay demonstrated that this species is nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this host. Currently, the only other sequenced isolate to fix with this host is Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was selected for sequencing on the basis of its environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the GEBA-RNB project. Here we describe the features of Burkholderia sp. strain UYPR1.413, together with sequence and annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in 336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only encoding genes.

Authors:
 [1];  [2];  [1];  [3];  [4];  [4];  [5];  [4];  [4];  [4];  [1];  [6];  [1]
  1. Murdoch Univ., Western Australia (Australia)
  2. Biological Research Inst. Clemente Estable, Montevideo (Uruguay)
  3. BARC-West USDA ARS, Beltsville, MD (United States)
  4. DOE Joint Genome Inst., Walnut Creek, CA (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. DOE Joint Genome Inst., Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1256920
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344; AC02-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Root-nodule bacteria; Nitrogen fixation; Rhizobia; Betaproteobacteria; GEBA-RNB

Citation Formats

De Meyer, Sofie E., Fabiano, Elena, Tian, Rui, Van Berkum, Peter, Seshadri, Rekha, Reddy, T. B. K., Markowitz, Victor, Ivanova, Natalia, Pati, Amrita, Woyke, Tanja, Howieson, John, Kyrpides, Nikos, and Reeve, Wayne. High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413. United States: N. p., 2015. Web. doi:10.1186/s40793-015-0018-9.
De Meyer, Sofie E., Fabiano, Elena, Tian, Rui, Van Berkum, Peter, Seshadri, Rekha, Reddy, T. B. K., Markowitz, Victor, Ivanova, Natalia, Pati, Amrita, Woyke, Tanja, Howieson, John, Kyrpides, Nikos, & Reeve, Wayne. High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413. United States. doi:10.1186/s40793-015-0018-9.
De Meyer, Sofie E., Fabiano, Elena, Tian, Rui, Van Berkum, Peter, Seshadri, Rekha, Reddy, T. B. K., Markowitz, Victor, Ivanova, Natalia, Pati, Amrita, Woyke, Tanja, Howieson, John, Kyrpides, Nikos, and Reeve, Wayne. Thu . "High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413". United States. doi:10.1186/s40793-015-0018-9. https://www.osti.gov/servlets/purl/1256920.
@article{osti_1256920,
title = {High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413},
author = {De Meyer, Sofie E. and Fabiano, Elena and Tian, Rui and Van Berkum, Peter and Seshadri, Rekha and Reddy, T. B. K. and Markowitz, Victor and Ivanova, Natalia and Pati, Amrita and Woyke, Tanja and Howieson, John and Kyrpides, Nikos and Reeve, Wayne},
abstractNote = {We report that Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A survey of symbionts of P. rigida in Uruguay demonstrated that this species is nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this host. Currently, the only other sequenced isolate to fix with this host is Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was selected for sequencing on the basis of its environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the GEBA-RNB project. Here we describe the features of Burkholderia sp. strain UYPR1.413, together with sequence and annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in 336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only encoding genes.},
doi = {10.1186/s40793-015-0018-9},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 10,
place = {United States},
year = {2015},
month = {6}
}

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