We still believe that this provides a useful estimation of the amount of conservation of ancestral genes in each genome.
However, to get a first estimation of pseudogene conservation among strains, we examined the conservation of the pseudogenes identified in the S. cerevisiae reference strain S288C (Additional file 1, Table S1) among 7 other sequenced strains (see Methods).
Phylogenetic analysis as well as estimation of the rate of synteny conservation clearly shows that H. polymorpha, a methylotrophic yeast, is phylogenetically closer to the non-methylotrophic D. bruxellensis than to the methylotrophic species P. pastoris.
We then demonstrate the use of our approach for implementation decisions, including parcel selection under a budget constraint and the estimation of a total conservation budget necessary to meet specific conservation goals.
We agree with the Reviewer that the estimation of MVP for conservation purposes can be problematic and therefore we added some sentences to the Discussion section to point out these shortcomings.
Models for restrained strains and self-stresses estimation based on the concepts of the conservation law of chemical energy and initial strains calculation in the expansive concrete members are considered, together with their advantages and disadvantages.
Promoter region conservation was estimated using phastCon scores, based on 17 vertebrate species genome data and using the same approach as for the estimation of novel contig conservation.
Constraint can then be inferred directly by estimating the parameters of the mutation-selection model without the potentially misleading estimation of conservation with respect to a reference sequence.
Thus, the estimation of gene expression conservation requires two components: (i) a measure of gene expression similarity; and (ii) the expected value of the divergence level under neutrality.
