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Comparative Genomics of Erwinia amylovora and Related Erwinia Species-What do We Learn?

Zhao Y, Qi M - Genes (Basel) (2011)

Bottom Line: The potential evolutionary origin of these Erwinia species is also proposed.The current understanding of the pathogen, its virulence mechanism and host specificity from genome sequencing data is summarized.Future research directions are also suggested.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801, USA. zhao888@illinois.edu.

ABSTRACT
Erwinia amylovora, the causal agent of fire blight disease of apples and pears, is one of the most important plant bacterial pathogens with worldwide economic significance. Recent reports on the complete or draft genome sequences of four species in the genus Erwinia, including E. amylovora, E. pyrifoliae, E. tasmaniensis, and E. billingiae, have provided us near complete genetic information about this pathogen and its closely-related species. This review describes in silico subtractive hybridization-based comparative genomic analyses of eight genomes currently available, and highlights what we have learned from these comparative analyses, as well as genetic and functional genomic studies. Sequence analyses reinforce the assumption that E. amylovora is a relatively homogeneous species and support the current classification scheme of E. amylovora and its related species. The potential evolutionary origin of these Erwinia species is also proposed. The current understanding of the pathogen, its virulence mechanism and host specificity from genome sequencing data is summarized. Future research directions are also suggested.

No MeSH data available.


Related in: MedlinePlus

Evolutionary relationship of Erwinia amylovora and related Erwinia species. Phylogenetic tree was constructed from concatenated sequences (2222 aa) of four housekeeping proteins (AcnB, GltA, GyrB and RpoD) using Neighbor-Joining (NJ) method. Bootstrap scores greater than 60 are given at each node. The scale bar represents 0.005 amino acids substitutions per site. E. billingiae strain Eb661 was used as an outgroup.
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f1-genes-02-00627: Evolutionary relationship of Erwinia amylovora and related Erwinia species. Phylogenetic tree was constructed from concatenated sequences (2222 aa) of four housekeeping proteins (AcnB, GltA, GyrB and RpoD) using Neighbor-Joining (NJ) method. Bootstrap scores greater than 60 are given at each node. The scale bar represents 0.005 amino acids substitutions per site. E. billingiae strain Eb661 was used as an outgroup.

Mentions: The subtractive hybridization-based mGenomeSubtractor program is used to run BLAST searches of the reference genome against one or multiple bacterial genomes as reported recently for in silico comparative genomic analyses [15,16]. Table 2 shows the numbers of specific and conserved proteins for each Erwinia genome against five others. Specific and conserved proteins are arbitrarily defined for those proteins with homology (H) value less than 0.42 and more than 0.81, respectively [15,16]. The most significant conclusion from this table is that the number of conserved proteins is around 2100, no matter which genome as reference, indicating these 2100 proteins may represent the “core” proteins of E. amylovora and related Erwinia species. In contrast, the specific proteins vary among genomes, indicating these proteins are unique ones for each genome. A phylogenetic tree reflecting their potential evolutionary relationship is thus generated using conserved housekeeping proteins (Figure 1).


Comparative Genomics of Erwinia amylovora and Related Erwinia Species-What do We Learn?

Zhao Y, Qi M - Genes (Basel) (2011)

Evolutionary relationship of Erwinia amylovora and related Erwinia species. Phylogenetic tree was constructed from concatenated sequences (2222 aa) of four housekeeping proteins (AcnB, GltA, GyrB and RpoD) using Neighbor-Joining (NJ) method. Bootstrap scores greater than 60 are given at each node. The scale bar represents 0.005 amino acids substitutions per site. E. billingiae strain Eb661 was used as an outgroup.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3927617&req=5

f1-genes-02-00627: Evolutionary relationship of Erwinia amylovora and related Erwinia species. Phylogenetic tree was constructed from concatenated sequences (2222 aa) of four housekeeping proteins (AcnB, GltA, GyrB and RpoD) using Neighbor-Joining (NJ) method. Bootstrap scores greater than 60 are given at each node. The scale bar represents 0.005 amino acids substitutions per site. E. billingiae strain Eb661 was used as an outgroup.
Mentions: The subtractive hybridization-based mGenomeSubtractor program is used to run BLAST searches of the reference genome against one or multiple bacterial genomes as reported recently for in silico comparative genomic analyses [15,16]. Table 2 shows the numbers of specific and conserved proteins for each Erwinia genome against five others. Specific and conserved proteins are arbitrarily defined for those proteins with homology (H) value less than 0.42 and more than 0.81, respectively [15,16]. The most significant conclusion from this table is that the number of conserved proteins is around 2100, no matter which genome as reference, indicating these 2100 proteins may represent the “core” proteins of E. amylovora and related Erwinia species. In contrast, the specific proteins vary among genomes, indicating these proteins are unique ones for each genome. A phylogenetic tree reflecting their potential evolutionary relationship is thus generated using conserved housekeeping proteins (Figure 1).

Bottom Line: The potential evolutionary origin of these Erwinia species is also proposed.The current understanding of the pathogen, its virulence mechanism and host specificity from genome sequencing data is summarized.Future research directions are also suggested.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801, USA. zhao888@illinois.edu.

ABSTRACT
Erwinia amylovora, the causal agent of fire blight disease of apples and pears, is one of the most important plant bacterial pathogens with worldwide economic significance. Recent reports on the complete or draft genome sequences of four species in the genus Erwinia, including E. amylovora, E. pyrifoliae, E. tasmaniensis, and E. billingiae, have provided us near complete genetic information about this pathogen and its closely-related species. This review describes in silico subtractive hybridization-based comparative genomic analyses of eight genomes currently available, and highlights what we have learned from these comparative analyses, as well as genetic and functional genomic studies. Sequence analyses reinforce the assumption that E. amylovora is a relatively homogeneous species and support the current classification scheme of E. amylovora and its related species. The potential evolutionary origin of these Erwinia species is also proposed. The current understanding of the pathogen, its virulence mechanism and host specificity from genome sequencing data is summarized. Future research directions are also suggested.

No MeSH data available.


Related in: MedlinePlus