Genesis, effects and fates of repeats in prokaryotic genomes

Abstract

DNA repeats are causes and consequences of genome plasticity. Repeats are created by intrachromosomal recombination or horizontal transfer. They are targeted by recombination processes leading to amplifications, deletions and rearrangements of genetic material. The identification and analysis of repeats in nearly 700 genomes of bacteria and archaea is facilitated by the existence of sequence data and adequate bioinformatic tools. These have revealed the immense diversity of repeats in genomes, from those created by selfish elements to the ones used for protection against selfish elements, from those arising from transient gene amplifications to the ones leading to stable duplications. Experimental works have shown that some repeats do not carry any adaptive value, while others allow functional diversification and increased expression. All repeats carry some potential to disorganize and destabilize genomes. Because recombination and selection for repeats vary between genomes, the number and types of repeats are also quite diverse and in line with ecological variables, such as host-dependent associations or population sizes, and with genetic variables, such as the recombination machinery. From an evolutionary point of view, repeats represent both opportunities and problems. We describe how repeats are created and how they can be found in genomes. We then focus on the functional and genomic consequences of repeats that dictate their fate.

Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist

“…Non-coding elements within IGSs may play important roles in fundamental cellular processes. We searched the Blochmannia genomes for long palindromic sequences, which may impact control of transcription or mRNA stabilization [30]. We identified 20 large (›30 bp) palindromes in B. floridanus , 10 in B. vafer and 6 in B. pennsylvanicus ; all but two were located at least partially in IGSs.…”

Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle

“…The distribution of repeats around a genome can give insights into the mechanism by which they propagate [i.e., DNA replication slippage for tandem and transposition/recombination for distributed repeats, respectively (58,61,62)]. Here, we compared the distribution of putative transposase genes and insertion sequences in the IMS101 genome to the top 10 intergenic regions containing the most abundant repeats identified in our pipeline (Table S1).…”

“…The intergenic regions of the IMS101 genome contain numerous DNA repeats, ranging from very small noncoding elements [e.g., highly interspersed palindromic sequences (35,57) or other repeating sequences (58,59)] to larger, gene-encoding insertion sequences (e.g., ref. 60).…”

Mushrooms: Morphological complexity in the fungi

“…The picture that has emerged is of a highly dynamic genome where chromosomal regions frequently duplicate, and those rare duplications that facilitate adaptation are retained (8), with a bias toward subtelomeric regions. It is a generality that can be extended to the bacteria, where genomes can be sorted into stable regions, with genes coding for core activities, and dynamic regions, where selfish elements and genes responsible for local adaptation are more likely to be found (9,10).…”