This clade contains the halophilic extremophiles, none
of which were represented as genome sequences on GenBank. Aliivibrio logei, formerly Vibrio logei and Photobacterium logei, is the predominant light-organ symbiont Temozolomide chemical structure of squids in the genus Sepiola. This species was chosen for genome sequencing as a next step in the attempt to complete sequencing of all bioluminescent species of Vibrio and Photobacterium. Results and discussion 19–taxon dataset Results Table 1 contains the taxon details (strain names and numbers) and the GenBank accession numbers for the 19 taxa included in this dataset. Those taxa for which only one strain is included will be referred to by only their species name. Those taxa for which more than one strain is included will be referred to by species selleck kinase inhibitor + strain name, abbreviated in most cases for the sake of brevity. The full names are listed in Table 1. For the large chromosome, 306 locally collinear segments of DNA (locally collinear blocks; LCBs) were found common to all taxa. For the small
chromosome, 37 LCBs were found common to all taxa. The lengths of the alignments were, for the large chromosome, 3,644,395 bp and for the small chromosome, 426,592 bp. The lengths of individual LCB alignments for each chromosome are given in Additional file 1: Table S1 and Additional file 2: Table S2. It is striking that the small chromosome yielded so few LCBs. Even though it is the smaller chromosome, as a percentage, much less of this genome was able to be homologized. For example, for V. cholerae 0395, 140,579 bp out of 1,108,250 bp (12.7%) of the small chromosome was homologized. In contrast, 1,904,555 bp out of 3,024,069 (63%)
of the large chromosome of V. cholerae was homologized. These measurements were made when gaps were removed from the alignments. Cediranib (AZD2171) In comparison to , 1,525,080 bp out of 4,969,803 bp (30.7%) of Shewanella oneidensis was able to be selleck chemicals llc homologized using Mauve. Figure 1 shows the large chromosome LCBs plotted in circular form showing their arrangement in CGView. Each circle represents a genome in the analysis, and each colored block, an LCB. LCBs of the same color are putatively homologous. The orientation of taxa is based on the phylogenetic relationships presented below. Figure 2 shows the circular orientation of LCBs for the small chromosome. The individual genome circles have been rotated to maximize the visual similarity or orientation. Table 1 Vibrionaceae taxon table: 19-taxon dataset Taxon name Taxon # Genbank accession numbers Large chromosome Small chromosome Aliivibrio fischeri ES114 14 NC_006840.2, NC_006841.2 2,897,536 1,330,333 Aliivibrio fischeri MJ11 15 NC_011184.1, NC_011186.1 2,905,029 1,418,848 Photobacterium profundum SS9 17 NC_006370.1, NC_006371.1 4,085,304 2,237,943 Aliivibrio salmonicida LFI1238 16 NC_011312.1, NC_011313.