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We also found pervasive and strong positive correlations between the coding density of a genome and the average number of genes in operons (fig. 1 G– I).
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Analysis of the eleven completely sequenced contigs showed that the coding density varies significantly between contigs.
The choice of the sliding window size could also influence the characterization of the genomic configuration, which was clearly demonstrated in the case of comparing the coding density of essential genes between the quasi-core and non-core regions.
The coding density was found to be very high, with a mean distance between genes of only 118 base pairs.
The high percentage of genic spacers likely reflects the coding density of the genomes (∼87%).
The N. limnia genome has a coding density of 1.16 protein coding genes per kb of sequence data, which is slightly higher than the coding density for N. maritimus (1.09) or C. symbiosum A (0.99) [Table 2].
Thus, the coding density of the genome is quite high.
The coding density is 84.9%, identical to strain NRRL 23338.
This is higher than the coding density for strain 26695 (1,576 genes and 90.2% coding density), for strain J99 (1,489 genes and 90.2% coding density) and for strain P12 (1,568 genes and 89.7% coding density).
The GC content and the coding density are in range with other rhizobia and soil bacteria.
However, we did note a weak but consistent correlation (Pearson's r = 0.37) between axis protein enrichment and the local coding density of the genome.
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