This method allows the visualization of the ancestral relationships between elements by showing conflicting signal for whole-genome data (genome conservation, genomic content, and genetic distance data) and for core proteome data (concatenated sequences).
Overall, as the product of major differences in genome conservation, CNSs (conserved noncoding sequences) have been reported in mammals as larger (i.e., 69 to >100 bp) compared with small and highly degenerated in plants (i.e., >20 to 30 bp), (Lockton and Gaut 2005; Elgar and Vavouri 2008; Reineke et al. 2011).
We found that recombination, genomic rearrangements, and genome conservation all show evidence of network-like evolution at whole-genome scale.
We compare the whole genomes of both subspecies to get insights into genomic architecture, phylogenetic relationships, genome conservation and core virulence factors.
A phylogenetic approach was used to visualize splice variant form genesis and identify conserved splice variants (genome conservation with EST support) across the vertebrate taxa.
Additional details of genome conservation are presented in the comparative genomics paper [ 1].
We did not extend this part of the study, but all known genomic information suggested high levels of local genome conservation.
A useful tool is the genome conservation matrix, which estimates the extent of the genetic-genomic difference between one genotype and another through measurement of their divergence-conservation distance.
This will then allow us to conduct a comprehensive genomic comparison to unravel the ultimate evolutionary causes of the high genome conservation in social bees.
Despite the high level of genome conservation, it is reasonable to expect that some degree of intra-genomic recombination has occurred since these two strains R. etli and R. leguminosarum had a common ancestor.
Moreover, centromeres showed consistent localization along the same chromosome in the two cotton species (Supplementary Table 17), implying a high level of genome conservation and a relatively short time to divergence.
