The right-skewed distribution of the bRPD values (see Figure 2) manifests itself in the fact that only about 2,000 strains … Using bRPD as primary http://www.selleckchem.com/products/Paclitaxel(Taxol).html selection criterion and matching the GOLD database in the current version during the GEBA phase I planning period (December 2010) resulted in the following numbers. Among the total of 8,029 strains, 453 had a ��completed�� genome-sequencing project, 38 a project ��in progress��, and 766 a ��targeted�� project. Among the remaining strains lacking a genome-sequencing project registered in GOLD at the time being, 7 were Cyanobacteria, 970 were not contained in the holdings of the DSMZ, 36 had to be rejected for technical reasons, 685 were set aside as replacement strains in case any of the 1,000 targeted ones turned out to pose difficulties in sequencing.

Finally, 4,074 strains with low scores or expected technical difficulties remained that were postponed and not considered for this phase of the project. Some of the strains not available at DSMZ were selected using the same procedure for potential targeting by the ATCC, Manassas, VA. Table 3 shows the results for the 20 highest-scoring strains according to the bRPD. Apparently, strains from a considerable diversity of phyla are included in the list, and mainly from sparsely sampled phyla with accordingly high inter-species differences [32,36]. Only comparatively few strains had to be postponed or rejected because of their current unavailability or for technical reasons related to cultivation and gDNA extraction. Most of the strains that were not selected were known as targets of other genome projects (or the GEBA pilot project).

Stability of the scoring The comparison of the LTP release ��LTPs106�� with release ��LTPs102�� revealed that 7,991 of the INSDC 16S RNA accessions used in LTPs102 were still in use in the more recent dataset. The Kendall correlation between the bRPD values from both releases after restricting the dataset to the common accessions was 0.925; for uRPD, it was 0.917. Among the 1,000 accessions of the LTPs102 release with the highest bRPD score, 76 were not among the highest-scoring ones from LTPs106; if uRPD was used, this number amounted to 83. This result indicates an additional advantage of bRPD over uRPD. Suitable targets for genome sequencing within the Roseobacter clade The phylogenetic tree used for target selection within the Roseobacter clade is shown in Figure 4, whereas Supplementary Table 1 includes the scores for the species.

As expected, the scoring preferred species situated in isolated positions (e.g., Methylarcula terricola) and/or at long branches (e.g., Rubellimicrobium spp.). Eight species were selected for genome sequencing (see Supplementary Table 1 for details), among them was Roseibacterium elongatum, the one with the Brefeldin_A overall highest score.