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Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum.

Hossain MJ, Ran C, Liu K, Ryu CM, Rasmussen-Ivey CR, Williams MA, Hassan MK, Choi SK, Jeong H, Newman M, Kloepper JW, Liles MR - Front Plant Sci (2015)

Bottom Line: Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and colonization of roots and/or leaves, including 73 genes uniquely associated with subsp. plantarum strains that have predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization.Although B. amyloliquefaciens subsp. plantarum strains contain gene clusters that encode many different secondary metabolites, only polyketide biosynthetic clusters that encode difficidin and macrolactin are conserved within this subspecies.This study defines genomic features of PGPR strains and links them with biocontrol activity and with host colonization.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Auburn University Auburn, AL, USA.

ABSTRACT
To understand the growth-promoting and disease-inhibiting activities of plant growth-promoting rhizobacteria (PGPR) strains, the genomes of 12 Bacillus subtilis group strains with PGPR activity were sequenced and analyzed. These B. subtilis strains exhibited high genomic diversity, whereas the genomes of B. amyloliquefaciens strains (a member of the B. subtilis group) are highly conserved. A pairwise BLASTp matrix revealed that gene family similarity among Bacillus genomes ranges from 32 to 90%, with 2839 genes within the core genome of B. amyloliquefaciens subsp. plantarum. Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and colonization of roots and/or leaves, including 73 genes uniquely associated with subsp. plantarum strains that have predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization. Although B. amyloliquefaciens subsp. plantarum strains contain gene clusters that encode many different secondary metabolites, only polyketide biosynthetic clusters that encode difficidin and macrolactin are conserved within this subspecies. To evaluate their role in plant pathogen biocontrol, genes involved in secondary metabolite biosynthesis were deleted in a B. amyloliquefaciens subsp. plantarum strain, revealing that difficidin expression is critical in reducing the severity of disease, caused by Xanthomonas axonopodis pv. vesicatoria in tomato plants. This study defines genomic features of PGPR strains and links them with biocontrol activity and with host colonization.

No MeSH data available.


Related in: MedlinePlus

The distribution of different subsystem categories of four different core genomes specific to genus Bacillus (n = 81), B. subtilis subgroup (n = 53), species B. amyloliquefaciens (n = 32) and subsp. plantarum (n = 28). (A) The total counts for genes within different subsystem categories for each of the core genomes. (B) The % relative abundance of the genes within different subsystem categories for each of the core genomes. (C) Represents the change in % relative abundance of subsystem categories as the number of genomes is reduced after inclusion of additional genomes for core genome prediction. (D) Categories of functions encoded by the 73 B. amyloliquefaciens subsp. plantarum-specific genes present in the B. amyloliquefaciens subsp. plantarum core genome but absent in the B. amyloliquefaciens species-level core genome. The number beside each subgroup of the pie figure represents the number of genes encoding the function.
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Figure 2: The distribution of different subsystem categories of four different core genomes specific to genus Bacillus (n = 81), B. subtilis subgroup (n = 53), species B. amyloliquefaciens (n = 32) and subsp. plantarum (n = 28). (A) The total counts for genes within different subsystem categories for each of the core genomes. (B) The % relative abundance of the genes within different subsystem categories for each of the core genomes. (C) Represents the change in % relative abundance of subsystem categories as the number of genomes is reduced after inclusion of additional genomes for core genome prediction. (D) Categories of functions encoded by the 73 B. amyloliquefaciens subsp. plantarum-specific genes present in the B. amyloliquefaciens subsp. plantarum core genome but absent in the B. amyloliquefaciens species-level core genome. The number beside each subgroup of the pie figure represents the number of genes encoding the function.

Mentions: Analysis of genome sequence alignment using progressive Mauve determined that the core genome of 13 PGPR Bacillus spp. strains contains 1,407,980 bp of genomic DNA which encode 1454 ORFs (data not shown). Comparison of core genome sequences of the genus Bacillus, subgroup B. subtilis, species B. amyloliquefaciens, and subspecies plantarum demonstrated that as the number of genomes increases, the number of different subsystems within each respective core genome decreases (Figures 2A–C). The highest numbers of subsystems in each of the core genome categories, except for the genus Bacillus core genome, was devoted to carbohydrate metabolism. These findings suggest that strains from the genus Bacillus use diverse carbon sources. In addition, the core genome for the genus Bacillus has more subsystems devoted to RNA, DNA, and protein metabolism compared to carbohydrate metabolism (Figures 2A–C).


Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum.

Hossain MJ, Ran C, Liu K, Ryu CM, Rasmussen-Ivey CR, Williams MA, Hassan MK, Choi SK, Jeong H, Newman M, Kloepper JW, Liles MR - Front Plant Sci (2015)

The distribution of different subsystem categories of four different core genomes specific to genus Bacillus (n = 81), B. subtilis subgroup (n = 53), species B. amyloliquefaciens (n = 32) and subsp. plantarum (n = 28). (A) The total counts for genes within different subsystem categories for each of the core genomes. (B) The % relative abundance of the genes within different subsystem categories for each of the core genomes. (C) Represents the change in % relative abundance of subsystem categories as the number of genomes is reduced after inclusion of additional genomes for core genome prediction. (D) Categories of functions encoded by the 73 B. amyloliquefaciens subsp. plantarum-specific genes present in the B. amyloliquefaciens subsp. plantarum core genome but absent in the B. amyloliquefaciens species-level core genome. The number beside each subgroup of the pie figure represents the number of genes encoding the function.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4538294&req=5

Figure 2: The distribution of different subsystem categories of four different core genomes specific to genus Bacillus (n = 81), B. subtilis subgroup (n = 53), species B. amyloliquefaciens (n = 32) and subsp. plantarum (n = 28). (A) The total counts for genes within different subsystem categories for each of the core genomes. (B) The % relative abundance of the genes within different subsystem categories for each of the core genomes. (C) Represents the change in % relative abundance of subsystem categories as the number of genomes is reduced after inclusion of additional genomes for core genome prediction. (D) Categories of functions encoded by the 73 B. amyloliquefaciens subsp. plantarum-specific genes present in the B. amyloliquefaciens subsp. plantarum core genome but absent in the B. amyloliquefaciens species-level core genome. The number beside each subgroup of the pie figure represents the number of genes encoding the function.
Mentions: Analysis of genome sequence alignment using progressive Mauve determined that the core genome of 13 PGPR Bacillus spp. strains contains 1,407,980 bp of genomic DNA which encode 1454 ORFs (data not shown). Comparison of core genome sequences of the genus Bacillus, subgroup B. subtilis, species B. amyloliquefaciens, and subspecies plantarum demonstrated that as the number of genomes increases, the number of different subsystems within each respective core genome decreases (Figures 2A–C). The highest numbers of subsystems in each of the core genome categories, except for the genus Bacillus core genome, was devoted to carbohydrate metabolism. These findings suggest that strains from the genus Bacillus use diverse carbon sources. In addition, the core genome for the genus Bacillus has more subsystems devoted to RNA, DNA, and protein metabolism compared to carbohydrate metabolism (Figures 2A–C).

Bottom Line: Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and colonization of roots and/or leaves, including 73 genes uniquely associated with subsp. plantarum strains that have predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization.Although B. amyloliquefaciens subsp. plantarum strains contain gene clusters that encode many different secondary metabolites, only polyketide biosynthetic clusters that encode difficidin and macrolactin are conserved within this subspecies.This study defines genomic features of PGPR strains and links them with biocontrol activity and with host colonization.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Auburn University Auburn, AL, USA.

ABSTRACT
To understand the growth-promoting and disease-inhibiting activities of plant growth-promoting rhizobacteria (PGPR) strains, the genomes of 12 Bacillus subtilis group strains with PGPR activity were sequenced and analyzed. These B. subtilis strains exhibited high genomic diversity, whereas the genomes of B. amyloliquefaciens strains (a member of the B. subtilis group) are highly conserved. A pairwise BLASTp matrix revealed that gene family similarity among Bacillus genomes ranges from 32 to 90%, with 2839 genes within the core genome of B. amyloliquefaciens subsp. plantarum. Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and colonization of roots and/or leaves, including 73 genes uniquely associated with subsp. plantarum strains that have predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization. Although B. amyloliquefaciens subsp. plantarum strains contain gene clusters that encode many different secondary metabolites, only polyketide biosynthetic clusters that encode difficidin and macrolactin are conserved within this subspecies. To evaluate their role in plant pathogen biocontrol, genes involved in secondary metabolite biosynthesis were deleted in a B. amyloliquefaciens subsp. plantarum strain, revealing that difficidin expression is critical in reducing the severity of disease, caused by Xanthomonas axonopodis pv. vesicatoria in tomato plants. This study defines genomic features of PGPR strains and links them with biocontrol activity and with host colonization.

No MeSH data available.


Related in: MedlinePlus