Limits...
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

A typical phylogenetic tree using orthologous genes with a single linkage cluster. A gene product (BJ6T39800: recombinase) from USDA6T was selected based on an ortholog cluster corresponding to the phylogenetic pattern of ITS sequences in Bradyrhizobiaceae. Orthologs from USDA110 and other Bradyrhizobium sp. members (BTAi1 and ORS278) were analyzed using the neighbor-joining method, and the resulting phylogenetic tree is depicted. An ortholog from M. loti MAFF303099 was used as the outgroup for this tree.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3927601&req=5

f2-genes-02-00763: A typical phylogenetic tree using orthologous genes with a single linkage cluster. A gene product (BJ6T39800: recombinase) from USDA6T was selected based on an ortholog cluster corresponding to the phylogenetic pattern of ITS sequences in Bradyrhizobiaceae. Orthologs from USDA110 and other Bradyrhizobium sp. members (BTAi1 and ORS278) were analyzed using the neighbor-joining method, and the resulting phylogenetic tree is depicted. An ortholog from M. loti MAFF303099 was used as the outgroup for this tree.

Mentions: In order to evaluate conservation of the genes in the genome of USDA6T, we carried out ortholog cluster analysis using information on genes predicted in USDA6T and USDA110 as well as in Bradyrhizobium sp. BTAi1, Bradyrhizobium sp. ORS278, and Mesorhizobium loti MAFF303099 [8,20]. The data from this analysis were assessed by focusing on orthologous clusters showing single linkages among the five bacterial strains. As a result, 705 groups were extracted as acceptable orthologous clusters from the grouping data, and 682 of these exhibited patterns corresponding to the phylogenetic tree generated using 16S rRNA genes or ITS sequences from Bradyrhizobiaceae members (Figure 2) [15]. This result shows that many of the protein-encoding genes that maintained a single orthologous relationship within Bradyrhizobiaceae members had evolved at a similar pace.


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)

A typical phylogenetic tree using orthologous genes with a single linkage cluster. A gene product (BJ6T39800: recombinase) from USDA6T was selected based on an ortholog cluster corresponding to the phylogenetic pattern of ITS sequences in Bradyrhizobiaceae. Orthologs from USDA110 and other Bradyrhizobium sp. members (BTAi1 and ORS278) were analyzed using the neighbor-joining method, and the resulting phylogenetic tree is depicted. An ortholog from M. loti MAFF303099 was used as the outgroup for this tree.
© Copyright Policy
Related In: Results  -  Collection

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

f2-genes-02-00763: A typical phylogenetic tree using orthologous genes with a single linkage cluster. A gene product (BJ6T39800: recombinase) from USDA6T was selected based on an ortholog cluster corresponding to the phylogenetic pattern of ITS sequences in Bradyrhizobiaceae. Orthologs from USDA110 and other Bradyrhizobium sp. members (BTAi1 and ORS278) were analyzed using the neighbor-joining method, and the resulting phylogenetic tree is depicted. An ortholog from M. loti MAFF303099 was used as the outgroup for this tree.
Mentions: In order to evaluate conservation of the genes in the genome of USDA6T, we carried out ortholog cluster analysis using information on genes predicted in USDA6T and USDA110 as well as in Bradyrhizobium sp. BTAi1, Bradyrhizobium sp. ORS278, and Mesorhizobium loti MAFF303099 [8,20]. The data from this analysis were assessed by focusing on orthologous clusters showing single linkages among the five bacterial strains. As a result, 705 groups were extracted as acceptable orthologous clusters from the grouping data, and 682 of these exhibited patterns corresponding to the phylogenetic tree generated using 16S rRNA genes or ITS sequences from Bradyrhizobiaceae members (Figure 2) [15]. This result shows that many of the protein-encoding genes that maintained a single orthologous relationship within Bradyrhizobiaceae members had evolved at a similar pace.

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