1887

Abstract

The genome sequence of subsp. W23 has been determined. The sequence strongly suggests that W23 is a direct descendant of ATCC 6633. W23 shares a 3.6 Mb core genome with the intensively studied model organism subsp. 168, and gene order within this core has been strongly conserved. Additionally, the W23 genome has 157 accessory (that is, non-core) genome segments that are not found in 168, while the 168 genome has 141 segments not found in W23. The distribution of sequences similar to these accessory segments among other genomes of the species complex shows that those sequences having entered into the phylogeny of the complex more recently tend to be larger and more AT-rich than those having entered earlier. A simple model can account for these observations, in which parasitic or symbiotic DNAs are transferred into the genome and then are reduced in size and modified in base composition during speciation.

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2011-07-01
2019-10-17
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Comparison of the I restriction map predicted by analysis of the W23 sequence with that observed by optical mapping. Both restriction maps were generated by the MapSolver 3.1 software. The expected resolution for optical maps is 2 kb; fragments smaller than 2 kb may be lost from the immobilized DNA and therefore may be missing from the assembled map. [PDF](225 kb) Maximum-likelihood bootstrapped tree for the species complex. Sequences and genomes analysed are as in Fig. 3 of the main paper. The bootstrapped ( =100) tree was produced by PhyML 3.0 as described in Methods. [PDF](117 kb) Distribution and conservation of W23-like accessory segments among genomes from the species complex Column A: name assigned to segment. Sequences sharing the same numerical prefix lie adjacent within the same locus, but showed separate distribution patterns within the phylogeny. Columns B–D: start and end positions in the W23 genome sequence and segment length. Column E: coding potential within the segment, based on BLASTP analysis of predicted products. Column F: phylogenetic distribution of the segment, with reference to Table 1 in the manuscript. Column G: percentage G+C content. Columns H–AN: Search results for the segment in each species complex genome. 'Coverage' refers to the portion of the segment that has a significant homologue in the target genome; 'identity' refers to the DNA sequence identity, as measured by BLASTN, shared by the similar portions of the segment and the target genome; 'locus similarity' refers to the existence of similar flanking sequences to the segment, both in W23 and in the target genome (minimum contiguous 200 nt similarity within 2 kb of the segment); 'partial' locus similarity means that similarity was found only on one side of the segment, while 'yes' indicates that similarity was found on both sides of the segment. Segments that are present in the target genome with at least 60% coverage and partial locus similarity are shaded in blue. Segments present in the genome at a different locus are shaded in green. Abbreviations for the genomes are the same as those in Fig. 3 of the main paper. [Excel file](106 kb) Distribution and conservation of 168-like accessory among genomes from the species complex As in Table S1, except that the 168 genome was used in place of W23. The phylogenetic distribution (column F) refers to Table 2 in the main paper. [Excel file](108 kb)

PDF

Comparison of the I restriction map predicted by analysis of the W23 sequence with that observed by optical mapping. Both restriction maps were generated by the MapSolver 3.1 software. The expected resolution for optical maps is 2 kb; fragments smaller than 2 kb may be lost from the immobilized DNA and therefore may be missing from the assembled map. [PDF](225 kb) Maximum-likelihood bootstrapped tree for the species complex. Sequences and genomes analysed are as in Fig. 3 of the main paper. The bootstrapped ( =100) tree was produced by PhyML 3.0 as described in Methods. [PDF](117 kb) Distribution and conservation of W23-like accessory segments among genomes from the species complex Column A: name assigned to segment. Sequences sharing the same numerical prefix lie adjacent within the same locus, but showed separate distribution patterns within the phylogeny. Columns B–D: start and end positions in the W23 genome sequence and segment length. Column E: coding potential within the segment, based on BLASTP analysis of predicted products. Column F: phylogenetic distribution of the segment, with reference to Table 1 in the manuscript. Column G: percentage G+C content. Columns H–AN: Search results for the segment in each species complex genome. 'Coverage' refers to the portion of the segment that has a significant homologue in the target genome; 'identity' refers to the DNA sequence identity, as measured by BLASTN, shared by the similar portions of the segment and the target genome; 'locus similarity' refers to the existence of similar flanking sequences to the segment, both in W23 and in the target genome (minimum contiguous 200 nt similarity within 2 kb of the segment); 'partial' locus similarity means that similarity was found only on one side of the segment, while 'yes' indicates that similarity was found on both sides of the segment. Segments that are present in the target genome with at least 60% coverage and partial locus similarity are shaded in blue. Segments present in the genome at a different locus are shaded in green. Abbreviations for the genomes are the same as those in Fig. 3 of the main paper. [Excel file](106 kb) Distribution and conservation of 168-like accessory among genomes from the species complex As in Table S1, except that the 168 genome was used in place of W23. The phylogenetic distribution (column F) refers to Table 2 in the main paper. [Excel file](108 kb)

PDF

Comparison of the I restriction map predicted by analysis of the W23 sequence with that observed by optical mapping. Both restriction maps were generated by the MapSolver 3.1 software. The expected resolution for optical maps is 2 kb; fragments smaller than 2 kb may be lost from the immobilized DNA and therefore may be missing from the assembled map. [PDF](225 kb) Maximum-likelihood bootstrapped tree for the species complex. Sequences and genomes analysed are as in Fig. 3 of the main paper. The bootstrapped ( =100) tree was produced by PhyML 3.0 as described in Methods. [PDF](117 kb) Distribution and conservation of W23-like accessory segments among genomes from the species complex Column A: name assigned to segment. Sequences sharing the same numerical prefix lie adjacent within the same locus, but showed separate distribution patterns within the phylogeny. Columns B–D: start and end positions in the W23 genome sequence and segment length. Column E: coding potential within the segment, based on BLASTP analysis of predicted products. Column F: phylogenetic distribution of the segment, with reference to Table 1 in the manuscript. Column G: percentage G+C content. Columns H–AN: Search results for the segment in each species complex genome. 'Coverage' refers to the portion of the segment that has a significant homologue in the target genome; 'identity' refers to the DNA sequence identity, as measured by BLASTN, shared by the similar portions of the segment and the target genome; 'locus similarity' refers to the existence of similar flanking sequences to the segment, both in W23 and in the target genome (minimum contiguous 200 nt similarity within 2 kb of the segment); 'partial' locus similarity means that similarity was found only on one side of the segment, while 'yes' indicates that similarity was found on both sides of the segment. Segments that are present in the target genome with at least 60% coverage and partial locus similarity are shaded in blue. Segments present in the genome at a different locus are shaded in green. Abbreviations for the genomes are the same as those in Fig. 3 of the main paper. [Excel file](106 kb) Distribution and conservation of 168-like accessory among genomes from the species complex As in Table S1, except that the 168 genome was used in place of W23. The phylogenetic distribution (column F) refers to Table 2 in the main paper. [Excel file](108 kb)

EXCEL

Comparison of the I restriction map predicted by analysis of the W23 sequence with that observed by optical mapping. Both restriction maps were generated by the MapSolver 3.1 software. The expected resolution for optical maps is 2 kb; fragments smaller than 2 kb may be lost from the immobilized DNA and therefore may be missing from the assembled map. [PDF](225 kb) Maximum-likelihood bootstrapped tree for the species complex. Sequences and genomes analysed are as in Fig. 3 of the main paper. The bootstrapped ( =100) tree was produced by PhyML 3.0 as described in Methods. [PDF](117 kb) Distribution and conservation of W23-like accessory segments among genomes from the species complex Column A: name assigned to segment. Sequences sharing the same numerical prefix lie adjacent within the same locus, but showed separate distribution patterns within the phylogeny. Columns B–D: start and end positions in the W23 genome sequence and segment length. Column E: coding potential within the segment, based on BLASTP analysis of predicted products. Column F: phylogenetic distribution of the segment, with reference to Table 1 in the manuscript. Column G: percentage G+C content. Columns H–AN: Search results for the segment in each species complex genome. 'Coverage' refers to the portion of the segment that has a significant homologue in the target genome; 'identity' refers to the DNA sequence identity, as measured by BLASTN, shared by the similar portions of the segment and the target genome; 'locus similarity' refers to the existence of similar flanking sequences to the segment, both in W23 and in the target genome (minimum contiguous 200 nt similarity within 2 kb of the segment); 'partial' locus similarity means that similarity was found only on one side of the segment, while 'yes' indicates that similarity was found on both sides of the segment. Segments that are present in the target genome with at least 60% coverage and partial locus similarity are shaded in blue. Segments present in the genome at a different locus are shaded in green. Abbreviations for the genomes are the same as those in Fig. 3 of the main paper. [Excel file](106 kb) Distribution and conservation of 168-like accessory among genomes from the species complex As in Table S1, except that the 168 genome was used in place of W23. The phylogenetic distribution (column F) refers to Table 2 in the main paper. [Excel file](108 kb)

EXCEL
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