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High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460

Overview of attention for article published in Standards in Genomic Sciences, July 2017
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Title
High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460
Published in
Standards in Genomic Sciences, July 2017
DOI 10.1186/s40793-017-0258-y
Pubmed ID
Authors

Vera Y. Matrosova, Elena K. Gaidamakova, Kira S. Makarova, Olga Grichenko, Polina Klimenkova, Robert P. Volpe, Rok Tkavc, Gözen Ertem, Isabel H. Conze, Evelyne Brambilla, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, TBK Reddy, Chris Daum, Nicole Shapiro, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke, Hajnalka Daligault, Karen Davenport, Tracy Erkkila, Lynne A. Goodwin, Wei Gu, Christine Munk, Hazuki Teshima, Yan Xu, Patrick Chain, Michael Woolbert, Nina Gunde-Cimerman, Yuri I. Wolf, Tine Grebenc, Cene Gostinčar, Michael J. Daly

Abstract

The genetic platforms of Deinococcus species remain the only systems in which massive ionizing radiation (IR)-induced genome damage can be investigated in vivo at exposures commensurate with cellular survival. We report the whole genome sequence of the extremely IR-resistant rod-shaped bacterium Deinococcus ficus KS 0460 and its phenotypic characterization. Deinococcus ficus KS 0460 has been studied since 1987, first under the name Deinobacter grandis, then Deinococcus grandis. The D. ficus KS 0460 genome consists of a 4.019 Mbp sequence (69.7% GC content and 3894 predicted genes) divided into six genome partitions, five of which are confirmed to be circular. Circularity was determined manually by mate pair linkage. Approximately 76% of the predicted proteins contained identifiable Pfam domains and 72% were assigned to COGs. Of all D. ficus KS 0460 proteins, 79% and 70% had homologues in Deinococcus radiodurans ATCC BAA-816 and Deinococcus geothermalis DSM 11300, respectively. The most striking differences between D. ficus KS 0460 and D. radiodurans BAA-816 identified by the comparison of the KEGG pathways were as follows: (i) D. ficus lacks nine enzymes of purine degradation present in D. radiodurans, and (ii) D. ficus contains eight enzymes involved in nitrogen metabolism, including nitrate and nitrite reductases, that D. radiodurans lacks. Moreover, genes previously considered to be important to IR resistance are missing in D. ficus KS 0460, namely, for the Mn-transporter nramp, and proteins DdrF, DdrJ and DdrK, all of which are also missing in Deinococcus deserti. Otherwise, D. ficus KS 0460 exemplifies the Deinococcus lineage.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 19 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 19 100%

Demographic breakdown

Readers by professional status Count As %
Student > Bachelor 4 21%
Researcher 4 21%
Other 3 16%
Student > Ph. D. Student 2 11%
Student > Master 1 5%
Other 3 16%
Unknown 2 11%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 7 37%
Agricultural and Biological Sciences 3 16%
Chemistry 2 11%
Immunology and Microbiology 2 11%
Earth and Planetary Sciences 1 5%
Other 1 5%
Unknown 3 16%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 05 August 2017.
All research outputs
#10,261,953
of 11,566,328 outputs
Outputs from Standards in Genomic Sciences
#423
of 494 outputs
Outputs of similar age
#224,209
of 265,319 outputs
Outputs of similar age from Standards in Genomic Sciences
#7
of 7 outputs
Altmetric has tracked 11,566,328 research outputs across all sources so far. This one is in the 1st percentile – i.e., 1% of other outputs scored the same or lower than it.
So far Altmetric has tracked 494 research outputs from this source. They receive a mean Attention Score of 2.4. This one is in the 1st percentile – i.e., 1% of its peers scored the same or lower than it.
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