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Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T.

Kaneko T, Maita H, Hirakawa H, Uchiike N, Minamisawa K, Watanabe A, Sato S - Genes (Basel) (2011)

Bottom Line: A significantly high level of sequence conservation was detected in three regions on each genome.An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements.The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Engineering, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan. tkaneko@cc.kyoto-su.ac.jp.

ABSTRACT
The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.

No MeSH data available.


Related in: MedlinePlus

Comparative genomic analysis among three strains: USDA6T, USDA110, and BTAi1. The total non-redundant number of deduced proteins from the three strains is 13,837. The number of proteins per genome is given inside the circles representing the bacterial strains. The overlapping sections indicate shared numbers of proteins. The proportion of the entire protein number is shown in parenthesis.
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f5-genes-02-00763: Comparative genomic analysis among three strains: USDA6T, USDA110, and BTAi1. The total non-redundant number of deduced proteins from the three strains is 13,837. The number of proteins per genome is given inside the circles representing the bacterial strains. The overlapping sections indicate shared numbers of proteins. The proportion of the entire protein number is shown in parenthesis.

Mentions: We subsequently performed comparative analysis by comparing genetic data from Bradyrhizobium sp. BTAi1 with that from the two B. japonicum strains in order to identify the genetic characteristics that are commonly shared by two B. japonicum strains. Bradyrhizobium sp. BTAi1 possesses the ability to form nodules on stems of Aeschynomene spp., and to perform nitrogen fixation in nodules, but BTAi1 has neither symbiosis islands nor symbiotic plasmids [25]. A comparison of the gene constitutions of these strains revealed 4,105 genes commonly conserved in all three strains. This is 29.7% of the combined non-redundant set of genes (13,837) (Figure 5). This group is anticipated to contain the essential genes that are indispensable to support bacterial cellular life, in addition to genes involved in nitrogen fixation and interactions with the host. The number of genes conserved between USDA6T and USDA110 is 2,094 (15.1%). This is significantly larger than 307 (2.2%) between USDA6T and BTAi1 and 320 (2.3%) between USDA110 and BTAi1. These may indicate that many of genes conserved between USDA6T and USDA110 can become the significant candidates in charge of functions involved in soybean symbiosis.


Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T.

Kaneko T, Maita H, Hirakawa H, Uchiike N, Minamisawa K, Watanabe A, Sato S - Genes (Basel) (2011)

Comparative genomic analysis among three strains: USDA6T, USDA110, and BTAi1. The total non-redundant number of deduced proteins from the three strains is 13,837. The number of proteins per genome is given inside the circles representing the bacterial strains. The overlapping sections indicate shared numbers of proteins. The proportion of the entire protein number is shown in parenthesis.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3927601&req=5

f5-genes-02-00763: Comparative genomic analysis among three strains: USDA6T, USDA110, and BTAi1. The total non-redundant number of deduced proteins from the three strains is 13,837. The number of proteins per genome is given inside the circles representing the bacterial strains. The overlapping sections indicate shared numbers of proteins. The proportion of the entire protein number is shown in parenthesis.
Mentions: We subsequently performed comparative analysis by comparing genetic data from Bradyrhizobium sp. BTAi1 with that from the two B. japonicum strains in order to identify the genetic characteristics that are commonly shared by two B. japonicum strains. Bradyrhizobium sp. BTAi1 possesses the ability to form nodules on stems of Aeschynomene spp., and to perform nitrogen fixation in nodules, but BTAi1 has neither symbiosis islands nor symbiotic plasmids [25]. A comparison of the gene constitutions of these strains revealed 4,105 genes commonly conserved in all three strains. This is 29.7% of the combined non-redundant set of genes (13,837) (Figure 5). This group is anticipated to contain the essential genes that are indispensable to support bacterial cellular life, in addition to genes involved in nitrogen fixation and interactions with the host. The number of genes conserved between USDA6T and USDA110 is 2,094 (15.1%). This is significantly larger than 307 (2.2%) between USDA6T and BTAi1 and 320 (2.3%) between USDA110 and BTAi1. These may indicate that many of genes conserved between USDA6T and USDA110 can become the significant candidates in charge of functions involved in soybean symbiosis.

Bottom Line: A significantly high level of sequence conservation was detected in three regions on each genome.An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements.The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Engineering, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan. tkaneko@cc.kyoto-su.ac.jp.

ABSTRACT
The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.

No MeSH data available.


Related in: MedlinePlus