Abstract
The vast majority of environmental bacteria and archaea remain uncultivated, yet their genome sequences are rapidly becoming available through single cell sequencing technologies. Reconstructing metabolism is one common way to make use of genome sequences of ecologically important bacteria, but molecular evolutionary analysis is another approach that, while currently underused, can reveal important insights into the function of these uncultivated microbes in nature. Because genome sequences from single cells are often incomplete, metabolic reconstruction based on genome content can be compromised. However, this problem does not necessarily impede the use of phylogenomic and population genomic approaches that are based on patterns of polymorphisms and substitutions at nucleotide and amino acid sites. These approaches explore how various evolutionary forces act to assemble genetic diversity within and between lineages. In this mini-review, I present examples illustrating the benefits of analyzing single cell genomes using evolutionary approaches.
Highlights
Haiwei Luo *Because genome sequences from single cells are often incomplete, metabolic reconstruction based on genome content can be compromised
Single cell genome sequencing technology has been widely used to unravel the metabolism of uncultivated microbes in the past 5 years, and this trend is expected to continue in that 99% of the environmental microbes remain uncultivated
It is important to note that there is a considerable difference in genomic G+C content between this largely uncultivated lineage (37% in both genomes) and all cultured ones (60 ± 4%), and evolutionary models of nucleotide substitution that do not take into account the base for the possible effect of biased nucleotide content on the measurement of dR and dC, leading to equivocal interpretations of the pattern derived from the analyses of genomes displaying considerable variability in G+C content
Summary
Because genome sequences from single cells are often incomplete, metabolic reconstruction based on genome content can be compromised This problem does not necessarily impede the use of phylogenomic and population genomic approaches that are based on patterns of polymorphisms and substitutions at nucleotide and amino acid sites. These approaches explore how various evolutionary forces act to assemble genetic diversity within and between lineages. In this mini-review, I present examples illustrating the benefits of analyzing single cell genomes using evolutionary approaches
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