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We indeed found some genomic regions of high silencing activity containing two or more consecutive genes that are involved in such processes (Fig. 1).
Two or more consecutive genes were regarded as part of an operon, if they fulfilled the following criteria: (a) they are expressed and transcribed in same direction, and (b) the intergenic region was identified as a single expressed transcript that overlapped the genes in both directions.
We identified 10 S. pealeana loci with three or more consecutive genes that have a very high probability of being linked to cold tolerance (Supplementary Table 4S).
We found many instances of two or more consecutive genes in H. sp. NRC-1 that may be similarly linked in the four newly sequenced halophiles (Table 2).
Clearly, if an LCB is sufficiently large, it is likely to contain one or more consecutive genes with related functions in addition to their regulatory regions.
In order to detect instances of two or more consecutive genes in H. sp. NRC-1 that may be similarly linked in the four newly sequenced halophiles, all sequence reads were compared to the H. sp. NRC-1 genome as a reference sequence.
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Only segments with three or more consecutive syntenic genes were considered in order to avoid annotation errors or the inclusion of pseudogenes and retrotransposed genes.
We then determined the groups of four or more consecutive FADA-selected genes that were all either over- or underexpressed in tumoral samples and simultaneously colocalized within a distance of 4 Mb, or less.
In the context of this study, a genomic island (GI) was broadly defined as any stretch of five or more consecutive protein coding genes that: 1) are not present in the other members of the genus, and 2) show a divergent %GC content compared to the core genome.
Furthermore, 64 consecutive genes, encompassing more than half of the genome, feature the same polarity.
- The presence of one or more consecutive DNA large spirals of approximately 16 genes on the nucleoid surface.
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