Abstract
A substantial fraction of archaeal genes, from ∼30% to as much as 80%, encode ‘hypothetical' proteins or genomic ‘dark matter'. Archaeal genomes typically contain a higher fraction of dark matter compared with bacterial genomes, primarily, because isolation and cultivation of most archaea in the laboratory, and accordingly, experimental characterization of archaeal genes, are difficult. In the present study, we present quantitative characteristics of the archaeal genomic dark matter and discuss comparative genomic approaches for functional prediction for ‘hypothetical' proteins. We propose a list of top priority candidates for experimental characterization with a broad distribution among archaea and those that are characteristic of poorly studied major archaeal groups such as Thaumarchaea, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) and Asgard.
Highlights
The drop of sequencing costs over the last decade has led to a dramatic increase in the influx of new genomes into public databases
Metagenomics has yielded more than 10 major new archaeal groups including most of the lineages in the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) superphylum that include, mostly, unculturable archaea with small genomes, many if not most of them, symbionts or parasites of other archaea
The quality of the annotation depends on the quality of the computational analyses themselves and on the speed and completeness of the integration of new experimental data on protein functions integrated into annotation pipelines
Summary
A substantial fraction of archaeal genes, from ∼30% to as much as 80%, encode ‘hypothetical’ proteins or genomic ‘dark matter’. Archaeal genomes typically contain a higher fraction of dark matter compared with bacterial genomes, primarily, because isolation and cultivation of most archaea in the laboratory, and experimental characterization of archaeal genes, are difficult. We present quantitative characteristics of the archaeal genomic dark matter and discuss comparative genomic approaches for functional prediction for ‘hypothetical’ proteins. We propose a list of top priority candidates for experimental characterization with a broad distribution among archaea and those that are characteristic of poorly studied major archaeal groups such as Thaumarchaea, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) and Asgard
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