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Comparative Genome Analysis of a Novel Alkaliphilic Actinobacterial Species Nesterenkonia haasae

Shuang Wang

Shuang Wang

  • Heilongjiang Academy of Black Soil Conservation and UtilizationBeijing, People’s Republic of China
  • State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of SciencesBeijing, People’s Republic of China
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Wang, Shuang
, 
Lei Sun

Lei Sun

Heilongjiang Academy of Black Soil Conservation and UtilizationBeijing, People’s Republic of China
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Sun, Lei
, 
Manik Prabhu Narsing Rao

Manik Prabhu Narsing Rao

State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, People’s Republic of China
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Narsing Rao, Manik Prabhu
, 
Bao‑zhu Fang

Bao‑zhu Fang

  • State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of SciencesBeijing, People’s Republic of China
  • State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, People’s Republic of China
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Fang, Bao‑zhu
 and 
Wen‑jun Li

Wen‑jun Li

  • State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of SciencesBeijing, People’s Republic of China
  • State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, People’s Republic of China
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Li, Wen‑jun
  
Sep 24, 2022
Comparative Genome Analysis of a Novel Alkaliphilic Actinobacterial Species Nesterenkonia haasae's Cover Image
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Article Category: Original Paper
Published Online: Sep 24, 2022
Page range: 453 - 461
Received: May 03, 2022
Accepted: Jul 31, 2022
DOI: https://doi.org/10.33073/pjm-2022-040
Keywords
© 2022 Shuang Wang at al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Fig. 1

Graphical circular map of the genomes showing the presence and absence of the gene. The important genes were highlighted.
Graphical circular map of the genomes showing the presence and absence of the gene. The important genes were highlighted.

Fig. 2

Functional annotation of Nesterenkonia haasae using RAST server.
Functional annotation of Nesterenkonia haasae using RAST server.

Fig. 3

Pangenome analysis of Nesterenkonia members.
Pangenome analysis of Nesterenkonia members.

Fig. 4

Phylogenomic tree based on 71 bacterial single-copy genes showing the position of Nesterenkonia members. Bootstrap values (expressed as percentages of 1,000 replications) greater than 50% are shown at branch points. Bar, 0.05 represents substitution per nucleotide position. Arthrobacter pigmenti was used as an out-group.
Phylogenomic tree based on 71 bacterial single-copy genes showing the position of Nesterenkonia members. Bootstrap values (expressed as percentages of 1,000 replications) greater than 50% are shown at branch points. Bar, 0.05 represents substitution per nucleotide position. Arthrobacter pigmenti was used as an out-group.

antiSMASH results of Nesterenkonia members_

Nesterenkonia members Most similar known cluster Similarity
N. alba Ectoine 75%
N. alkaliphila Kocurin 88%
Ectoine 75%
T3pks 3%
Redox-cofactor 100%
Livipeptin 66%
N. aurantiaca Terpenes 28%
Ectoine 50%
N. haasae Chejuenolide A/Chejuenolide B 7%
Terpenes 28%
Foxicins A-D 4%
Ectoine 75%
N. halotolerans Terpenes 28%
Tetronasin 3%
Ectoine 50%
N. jeotgali Terpenes 28%
Ectoine 50%
N. lacusekhoensis Glycopeptidolipid 20%
Terpenes 21%
Ectoine 75%
N. lute Terpenes 28%
Ectoine 75%
N. massiliensis Ectoine 50%
Terpenes 28%
N. muleiensis Ectoine 75%
Terpenes 50%
N. natronophila Ectoine 75%
Terpenes 28%
N. pannonica Ectoine 50%
Terpenes 21%
N. populi Salinichelins 23%
Ectoine 75%
Terpenes 50%
N. salmonea Terpenes 28%
Tetronasin 3%
Ectoine 75%
N. sandarakina Pentalenolactone 15%
Ectoine 50%
Ishigamide 11%
Terpenes 28%
N. sedimenti Ectoine 75%
Lankacidin C 13%
N. sphaerica Terpenes 50%
Ectoine 50%
N. xinjiangensis Terpenes 28%
Pentostatine/Vidarabine 9%
Ectoine 75%
Desferrioxamin B 60%

Genome attributes of present study Nesterenkonia members_

Nesterenkonia members (accession numbers) Genome completeness (%) Genome contamination (%) Genome size (bp) Genomic DNA G + C (%) rRNAs tRNAs
“stercoripullorum” Candidatus Nesterenkonia (DXGD00000000) 84.3 3.7 2,634,134 65.8 0 34
N. alba (ATXP00000000)  98.3 0 2,591,866 63.7 6 49
N. alkaliphile (BMFX00000000)   98.8 1.4 3,397,286 64.7 5 49
N. aurantiaca (SOAN00000000)  99.1 0 2,947,649 67.5 3 48
N. cremea (BMIS00000000)   99.5 0.8 3,083,451 66.8 5 50
N. haasae (VFIE00000000)   99.1 1.2 3,433,063 60.8 7 48
N. halophila (WIAX00000000)   75.9 0.07 2,188,008 71.7 4 31
N. halotolerans (JADBEE000000000)   99.1 1.2 2,966,101 66.2 6 47
N. jeotgali (JACJIH000000000)   98.5 3.2 3,002,985 67.4 6 50
N. lacusekhoensis (JAGINX000000000) 100 0.9 2,742,649 66.6 6 55
N. lutea (JADBED000000000)   99.5 0.07 2,958,123 66.7 6 47
N. massiliensis (CBLL000000000)   97.7 0.4 2,641,000 62.8 3 46
N. muleiensis (QWLD00000000)   97.7 0.8 3,676,111 63.5 2 46
N. natronophila (QYZP00000000)   98.3 0.07 2,524,489 61.8 5 47
N. pannonica (CP080575)   70.4 0.8 2,699,453 66 6 48
N. populi (VOIL00000000)   98.1 0.8 2,551,278 66.8 6 49
N. salmonea (VAVZ00000000)   99.1 0.3 3,283,675 61.1 3 51
N. sandarakina (JACCFQ000000000)  98.5 1 3,017,448 67.5 6 47
N. sedimenti (JABAHY000000000) 98.8 1.6 3,113,980 63 3 49
N. sphaerica (VAWA00000000)   99 1.4 2,791,176 64.2 5 47
N. xinjiangensis (JACCFY000000000)   99.7 0.6 3,569,370 68.8 6 49
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