Abstract
BackgroundThe reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions.ResultsWe use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses.ConclusionsWe show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics.
Highlights
The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions
We explore the difficulty in establishing synteny blocks for three genomes based on the pairwise output of SYNMAP, as a preliminary to a stepwise decrease in resolution in the calculation of the median estimate of the ancestor. (The median is a reconstructed genome that minimizes the sum of some distance measure from itself to three or more given genomes.)
Comparing the three genomic (DCJ) distances with evolutionary time in the fully resolved analysis, reveals that coffee is much more conservative than Rhazya
Summary
The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions. Setting the level of resolution involves a trade-off between trying to decipher precise genomic details on one hand and being overwhelmed by noise at higher resolutions due to both mutational processes and methodological difficulties, on the other. Despite some successes, notably with the ancient “boreoeutherian” mammalian genome [3], in most cases, a nucleotide by nucleotide reconstruction of even the coding region of an ancestral gene contains a large amount of uncertainty, while non-coding DNA reconstruction is much more refractory. A telling aspect in the widely-used synteny block identifier SYNMAP [12, 13] is the default requirement that at least five pairs of orthologous genes in two genomes or five pairs of paralogous genes in a single genome, in close succession, are necessary before we have confidence that the two apparently homologous segments containing these genes are genuinely contemporaneous descendants of the same ancestral genomic fragment
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