Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes.

ABSTRACT: Microbial genomes encompass a sizable fraction of poorly characterized, narrowly spread fast-evolving genes. Using sensitive methods for sequences comparison and protein structure prediction, we performed a detailed comparative analysis of clusters of such genes, which we denote "dark matter islands", in archaeal genomes. The dark matter islands comprise up to 20% of archaeal genomes and show remarkable heterogeneity and diversity. Nevertheless, three classes of entities are common in these genomic loci: (a) integrated viral genomes and other mobile elements; (b) defense systems, and (c) secretory and other membrane-associated systems. The dark matter islands in the genome of thermophiles and mesophiles show similar general trends of gene content, but thermophiles are substantially enriche

SUBMITTER: Makarova KS 

PROVIDER: S-EPMC4158269 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature