Additional file 5: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Additional file 2 of Environmentally-driven gene content convergence and the Bacillus phylogeny

Ismael L. Hernández-González (5816516)
Gabriel Moreno-Hagelsieb (578)
Gabriela Olmedo-Álvarez (5784455)

October 2018

Supplementary Table S2. General information about the organisms used in this study. (TXT 5 kb

Additional file 16 of Pan-genome and phylogeny of Bacillus cereus sensu lato

Adam L. Bazinet (388401)

August 2017

BCSL_498 maximum likelihood phylogenetic analysis results, color-coded by species. Phylogram depicti...

Additional file 4: of Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities

Teresa Mohr (3502610)
Habibu Aliyu (5495321)
Raphael KĂźchlin (5495318)
Michaela Zwick (5495324)
Don Cowan (2605876)
Anke Neumann (15638)
Pieter de Maayer (6059294)

December 2018

SNPs occurring in the CODH-NiFe group 4a locus genes of the compared P. thermoglucosidasius strains....

Additional file 7: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Table S5. List of 1718 single-copy core genes shared by 14 lineage P strains. (XLSX 97 kb)

Additional file 4: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Table S2. Genetic characteristics of strains in the current research. (XLSX 15 kb

Additional file 1: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Table S1. The features of prophage, genomic islands, secondary metabolite clusters and CRISPR in MDJ...

Additional file 8: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Figure S3. A: Neighbor-joining phylogenetic tree of 47 Bacillus genome. B: NJ tree of the 14 lineage...

Additional file 3: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Figure S2. Comparative analysis of biosynthetic gene clusters for secondary metabolism from MDJK30 a...

Additional file 6: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Table S4. Table S4. Average Nucleotide Identity (ANI) (%) based on whole-genome alignments. ANI valu...

Additional file 9: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Figure S4. Comparison of GC content between gene clusters of Fengycin, Bacitracin and Paralichenicid...

Additional file 2: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Figure S1. A: Biosynthetic gene clusters and predicted structures for NRPS in MDJK30. B: Other biosy...

Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du
Jinjin Ma
Zhiqiu Yin
Kai Liu
Gan Yao
Wenfeng Xu
Lingchao Fan
Binghai Du
Yanqin Ding
Chengqiang Wang

April 2019

Abstract Background Members of the genus Bacillus are important plant growth-promoting rhizobacteria...

Additional file 1: of In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

Ghofran Othoum (5258480)
Salim Bougouffa (529649)
Rozaimi Razali (553806)
Ameerah Bokhari (5258474)
Soha Alamoudi (5258477)
AndrĂŠ Antunes (5258483)
Xin Gao (14001)
Robert Hoehndorf (38206)
Stefan Arold (487269)
Takashi Gojobori (2581)
Heribert Hirt (30710)
Ivan Mijakovic (27922)
Vladimir Bajic (3479747)
Feras Lafi (3404420)
Magbubah Essack (419839)

May 2018

Table S1. Basic statistics relating to the PacBio SMRT sequencing that was done for B. paralichenifo...

Additional file 5 of Environmentally-driven gene content convergence and the Bacillus phylogeny

Ismael L. Hernández-González (5816516)
Gabriel Moreno-Hagelsieb (578)
Gabriela Olmedo-Álvarez (5784455)

October 2018

Table S3. List of putative adaptive COGs in the B. subtilis and B. cereus groups. (TXT 16 kb

Additional file 1: of Draft genome sequences of three fungal-interactive Paraburkholderia terrae strains, BS007, BS110 and BS437

Pratama, Akbar Adjie
Haq, Irshad Ul
Nazir, Rashid
Chaib De Mares, Maryam
van Elsas, Jan Dirk
Van Elsas lab

December 2017

Table S1 Sequencing statistics analysis of Paraburkholderia terrae BS007, BS110, and BS437. Table S2...

Additional file 2 of Environmentally-driven gene content convergence and the Bacillus phylogeny

Ismael L. Hernández-González (5816516)
Gabriel Moreno-Hagelsieb (578)
Gabriela Olmedo-Álvarez (5784455)

October 2018

Supplementary Table S2. General information about the organisms used in this study. (TXT 5 kb

Additional file 16 of Pan-genome and phylogeny of Bacillus cereus sensu lato

Adam L. Bazinet (388401)

August 2017

BCSL_498 maximum likelihood phylogenetic analysis results, color-coded by species. Phylogram depicti...

Additional file 4: of Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities

Teresa Mohr (3502610)
Habibu Aliyu (5495321)
Raphael KĂźchlin (5495318)
Michaela Zwick (5495324)
Don Cowan (2605876)
Anke Neumann (15638)
Pieter de Maayer (6059294)

December 2018

SNPs occurring in the CODH-NiFe group 4a locus genes of the compared P. thermoglucosidasius strains....

Additional file 7: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Table S5. List of 1718 single-copy core genes shared by 14 lineage P strains. (XLSX 97 kb)

Additional file 4: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Table S2. Genetic characteristics of strains in the current research. (XLSX 15 kb

Additional file 1: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Table S1. The features of prophage, genomic islands, secondary metabolite clusters and CRISPR in MDJ...

Additional file 8: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Figure S3. A: Neighbor-joining phylogenetic tree of 47 Bacillus genome. B: NJ tree of the 14 lineage...

Additional file 3: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Figure S2. Comparative analysis of biosynthetic gene clusters for secondary metabolism from MDJK30 a...

Additional file 6: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Table S4. Table S4. Average Nucleotide Identity (ANI) (%) based on whole-genome alignments. ANI valu...

Additional file 9: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Figure S4. Comparison of GC content between gene clusters of Fengycin, Bacitracin and Paralichenicid...

Additional file 2: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du (4889518)
Jinjin Ma (3937364)
Zhiqiu Yin (4374091)
Kai Liu (159026)
Gan Yao (6582068)
Wenfeng Xu (311895)
Lingchao Fan (6582071)
Binghai Du (6582074)
Yanqin Ding (219852)
Chengqiang Wang (6582077)

April 2019

Figure S1. A: Biosynthetic gene clusters and predicted structures for NRPS in MDJK30. B: Other biosy...

Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Yuhui Du
Jinjin Ma
Zhiqiu Yin
Kai Liu
Gan Yao
Wenfeng Xu
Lingchao Fan
Binghai Du
Yanqin Ding
Chengqiang Wang

April 2019

Abstract Background Members of the genus Bacillus are important plant growth-promoting rhizobacteria...

Additional file 1: of In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

Ghofran Othoum (5258480)
Salim Bougouffa (529649)
Rozaimi Razali (553806)
Ameerah Bokhari (5258474)
Soha Alamoudi (5258477)
AndrĂŠ Antunes (5258483)
Xin Gao (14001)
Robert Hoehndorf (38206)
Stefan Arold (487269)
Takashi Gojobori (2581)
Heribert Hirt (30710)
Ivan Mijakovic (27922)
Vladimir Bajic (3479747)
Feras Lafi (3404420)
Magbubah Essack (419839)

May 2018

Table S1. Basic statistics relating to the PacBio SMRT sequencing that was done for B. paralichenifo...

Additional file 5 of Environmentally-driven gene content convergence and the Bacillus phylogeny

Ismael L. Hernández-González (5816516)
Gabriel Moreno-Hagelsieb (578)
Gabriela Olmedo-Álvarez (5784455)

October 2018

Table S3. List of putative adaptive COGs in the B. subtilis and B. cereus groups. (TXT 16 kb

Additional file 1: of Draft genome sequences of three fungal-interactive Paraburkholderia terrae strains, BS007, BS110 and BS437

Pratama, Akbar Adjie
Haq, Irshad Ul
Nazir, Rashid
Chaib De Mares, Maryam
van Elsas, Jan Dirk
Van Elsas lab

December 2017

Table S1 Sequencing statistics analysis of Paraburkholderia terrae BS007, BS110, and BS437. Table S2...

Additional file 2 of Environmentally-driven gene content convergence and the Bacillus phylogeny

Ismael L. Hernández-González (5816516)
Gabriel Moreno-Hagelsieb (578)
Gabriela Olmedo-Álvarez (5784455)

October 2018

Supplementary Table S2. General information about the organisms used in this study. (TXT 5 kb

Additional file 16 of Pan-genome and phylogeny of Bacillus cereus sensu lato

Adam L. Bazinet (388401)

August 2017

BCSL_498 maximum likelihood phylogenetic analysis results, color-coded by species. Phylogram depicti...

Additional file 4: of Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities

Teresa Mohr (3502610)
Habibu Aliyu (5495321)
Raphael KĂźchlin (5495318)
Michaela Zwick (5495324)
Don Cowan (2605876)
Anke Neumann (15638)
Pieter de Maayer (6059294)

December 2018

SNPs occurring in the CODH-NiFe group 4a locus genes of the compared P. thermoglucosidasius strains....

Additional file 5: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Abstract

Extracted data

Additional file 5: of Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Abstract

Extracted data

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