The phylogenetic scope is correlated with the levels of genomic sequence divergence, defined in this context as the average number of nucleotide changes affecting neutral sites.
To test this hypothesis, we grouped transcripts on the basis of the local level of genomic sequence similarity with the expectation that transcripts located in regions with very high sequence similarity between C57BL/6J and NOD/ShiLtJ were less likely to be differentially expressed between two strains.
The high level of genomic sequence conservation over evolutionary time from fish to human, as in the case of NLSLH, and the presence of partial cDNA and EST sequences from rodents and human, as in the case of CBCP, were strongly suggestive that the predictions are correct.
We identified a similar level of genomic sequence diversity, but by using an unbiased population approach, we have shown phylogenetically significant neutral variation.
We focused on six known imprinted genes in mouse that also had a high level of genomic sequence conservation in eutherians, namely MEST[ 8, 30], COPG2[ 31], HTR2A[ 32], L3MBTL[ 33], IMPACT[ 34, 35] and PLAGL1[ 36].
This approach is straightforward if the interrogated CpGs are not polymorphic at the level of a genomic sequence.
Relationship between the level of repetitiveness in genomic sequence and genome size has been investigated by making use of complete prokaryotic and eukaryotic genomes, but relevant studies have been rarely made in virus genomes.
"It took a number of years and over $3 billion to sequence one person's genomic information back in 2000," says Amanda Cashin of Illumina, the leading producer of genomic sequencing instruments.
At the level of moderate length genomic sequences (typically hundreds of kilobases), recombination rates correlate with G+C content, gene density, frequencies of simple repeats and transposable elements, and a number of different sequence motifs (e.g., Jensen-Seaman et al. 2004; Meunier and Duret 2004; Groenen et al. 2009).
Following this approach, inventories of sequences bound to CENP-A have been reported for several species to define, at least at the level of consensus sequences, the genomic content of centromeres in those genomes [ 11, 20, 24, 31- 33].
