Abstract
The use of low coverage genomes in comparative evolutionary analyses skews estimates of gene gains and losses.
Highlights
Given the availability of full genome sequences, mapping gene gains, duplications, and losses during evolution should theoretically be straightforward
In the context of investigating correlations between genome and phenotype evolution, describing the evolution of genome content should theoretically be straightforward given the increasing number of available sequenced genomes and of large-scale expression studies, accompanied by a constantly growing number of software and databases for better integration and exploitation of this wealth of data. This endeavor of mapping gene gains and losses suffers from the lack of explicit phylogenetic criteria in analytical tools, and the overemphasis, in genome sequencing programs, on detecting conserved genome features
The first problem relates to the fact that many of the methods and databases available for identifying duplication events and assessing orthology relationships of
Summary
Given the availability of full genome sequences, mapping gene gains, duplications, and losses during evolution should theoretically be straightforward. In the context of investigating correlations between genome and phenotype evolution, describing the evolution of genome content (in terms of protein-coding genes) should theoretically be straightforward given the increasing number of available sequenced genomes and of large-scale expression studies, accompanied by a constantly growing number of software and databases for better integration and exploitation of this wealth of data. This endeavor of mapping gene gains (including duplication events) and losses suffers from the lack of explicit phylogenetic criteria in analytical tools, and the overemphasis, in genome sequencing programs, on detecting conserved genome features. Prominent databases like ENSEMBL [14], which generates and maintains automatic annotation of selected eukaryotic genomes, included 25 mammalian and 5 teleost fish genomes, but only one bird, one amphibian, and no reptile in its version 49 (Figure 1)
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