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Our data suggest that the recombination rate in the Nasonia genome varies by at least two orders of magnitude and that adjacent genome regions tend to have similar rates (Figure 1).
Plasmids may be integrated into the genome and thereby the plasmid sequences can be present in the assemblies surrounded by two different sequence environments (plasmid only sequences or adjacent genome parts), making the integration site a low coverage region.
Alternatively, differences between allele frequencies might be due to differential selection pressures on the loci themselves or on the adjacent genome regions of the single copy markers.
One class of transformants contained single or tandem copies of linear DNA stably inserted in the genome, and the insertion events were often accompanied by deletions in the integrated DNA vectors and adjacent genome sequences.
Two adjacent genome maps would be joined together if the junction a) was within 50 kb apart, b) contained at most 5 labels, c) contained, or was within 50 kb from, a fragile site, and d) also contained no more than 5 unaligned end labels.
Phylogeny analysis of the melon NBS-LRR gene cluster in the refined sequence and comparison with its syntenic counterparts in other cucurbit species allow us to conclude that new resistance genes have essentially been produced by sequence duplication in adjacent genome locations since the divergence of cucurbits from other close families, and through speciation processes within the family.
Similar(53)
In this file, sequences that are not adjacent in the reference genome are reported; these are defined as "junctions", consisting of a "left arm" reference sequence, a breakpoint with an optional transition sequence (a stretch of sequence that is not contained in the reference genome) and a "right arm" reference sequence at a non-adjacent genome location.
Every element of matrix equals 1 if two genes are adjacent in genome in given directions; otherwise, it is equal to 0. Such an approach allows us to promptly analyze large datasets.
Two genes i and j are said to be adjacent in genome G if i is immediately followed by j and can be represented by an edge (2 i, 2 j-1).
This interference would have to be dealt with, for instance by using adjacent sub-genome specific SNPs to make the assays sub-genome specific.
The microarray data were analyzed with the objective of identifying differentially methylated regions between tumor and adjacent normal genomes.
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