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Title: Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production

Cyanobacteria have the potential to produce bulk and fine chemicals and members belonging to Nostoc sp. have received particular attention due to their relatively fast growth rate and the relative ease with which they can be harvested. Nostoc punctiforme is an aerobic, motile, Gram-negative, filamentous cyanobacterium that has been studied intensively to enhance our understanding of microbial carbon and nitrogen fixation. The genome of the type strain N. punctiforme ATCC 29133 was sequenced in 2001 and the scientific community has used these genome data extensively since then. Advances in bioinformatics tools for sequence annotation and the importance of this organism prompted us to resequence and reanalyze its genome and to make both, the initial and improved annotation, available to the scientific community. The new draft genome has a total size of 9.1 Mbp and consists of 65 contiguous pieces of DNA with a GC content of 41.38% and 7664 protein-coding genes. Furthermore, the resequenced genome is slightly (5152 bp) larger and contains 987 more genes with functional prediction when compared to the previously published version. We deposited the annotation of both genomes in the Department of Energy’s IMG database to facilitate easy genome exploration by the scientific community without themore » need of in-depth bioinformatics skills. We expect that an facilitated access and ability to search the N. punctiforme ATCC 29133 for genes of interest will significantly facilitate metabolic engineering and genome prospecting efforts and ultimately the synthesis of biofuels and natural products from this keystone organism and closely related cyanobacteria.« less
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [2] ;  [2] ;  [2] ;  [2] ;  [1] ; ORCiD logo [5]
  1. Univ. of California, Davis, CA (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. ZeaChem, Boardman, OR (United States)
  4. Washington State Univ., Pullman, WA (United States)
  5. Univ. of California, Davis, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Published Article
Journal Name:
AMB Express
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 2191-0855
Publisher:
Springer
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)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Nostoc punctiforme; cyanobacteria; carbon cycle; nitrogen cycle; natural product synthesis; single molecule real-time sequencing
OSTI Identifier:
1344020
Alternate Identifier(s):
OSTI ID: 1379933

Moraes, Luis E., Blow, Matthew J., Hawley, Erik R., Piao, Hailan, Kuo, Rita, Chiniquy, Jennifer, Shapiro, Nicole, Woyke, Tanja, Fadel, James G., and Hess, Matthias. Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production. United States: N. p., Web. doi:10.1186/s13568-017-0338-9.
Moraes, Luis E., Blow, Matthew J., Hawley, Erik R., Piao, Hailan, Kuo, Rita, Chiniquy, Jennifer, Shapiro, Nicole, Woyke, Tanja, Fadel, James G., & Hess, Matthias. Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production. United States. doi:10.1186/s13568-017-0338-9.
Moraes, Luis E., Blow, Matthew J., Hawley, Erik R., Piao, Hailan, Kuo, Rita, Chiniquy, Jennifer, Shapiro, Nicole, Woyke, Tanja, Fadel, James G., and Hess, Matthias. 2017. "Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production". United States. doi:10.1186/s13568-017-0338-9.
@article{osti_1344020,
title = {Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production},
author = {Moraes, Luis E. and Blow, Matthew J. and Hawley, Erik R. and Piao, Hailan and Kuo, Rita and Chiniquy, Jennifer and Shapiro, Nicole and Woyke, Tanja and Fadel, James G. and Hess, Matthias},
abstractNote = {Cyanobacteria have the potential to produce bulk and fine chemicals and members belonging to Nostoc sp. have received particular attention due to their relatively fast growth rate and the relative ease with which they can be harvested. Nostoc punctiforme is an aerobic, motile, Gram-negative, filamentous cyanobacterium that has been studied intensively to enhance our understanding of microbial carbon and nitrogen fixation. The genome of the type strain N. punctiforme ATCC 29133 was sequenced in 2001 and the scientific community has used these genome data extensively since then. Advances in bioinformatics tools for sequence annotation and the importance of this organism prompted us to resequence and reanalyze its genome and to make both, the initial and improved annotation, available to the scientific community. The new draft genome has a total size of 9.1 Mbp and consists of 65 contiguous pieces of DNA with a GC content of 41.38% and 7664 protein-coding genes. Furthermore, the resequenced genome is slightly (5152 bp) larger and contains 987 more genes with functional prediction when compared to the previously published version. We deposited the annotation of both genomes in the Department of Energy’s IMG database to facilitate easy genome exploration by the scientific community without the need of in-depth bioinformatics skills. We expect that an facilitated access and ability to search the N. punctiforme ATCC 29133 for genes of interest will significantly facilitate metabolic engineering and genome prospecting efforts and ultimately the synthesis of biofuels and natural products from this keystone organism and closely related cyanobacteria.},
doi = {10.1186/s13568-017-0338-9},
journal = {AMB Express},
number = ,
volume = 7,
place = {United States},
year = {2017},
month = {2}
}

Works referenced in this record:

Real-Time DNA Sequencing from Single Polymerase Molecules
journal, January 2009