scholarly journals Genome Evolution at the Genus Level: Comparison of Three Complete Genomes of Hyperthermophilic Archaea

2001 ◽  
Vol 11 (6) ◽  
pp. 981-993 ◽  
Author(s):  
O. Lecompte
Keyword(s):  
Genome Evolution ◽  
Hyperthermophilic Archaea ◽  
Genus Level ◽  
Complete Genomes

scholarly journals Genome Evolution at the Genus Level: Comparison of Three Complete Genomes of Hyperthermophilic Archaea

2001 ◽  
Vol 11 (6) ◽  
pp. 981-993
Author(s):  
Odile Lecompte ◽  
Raymond Ripp ◽  
Valérie Puzos-Barbe ◽  
Simone Duprat ◽  
Roland Heilig ◽  
...  
Keyword(s):  
Pyrococcus Furiosus ◽  
Hyperthermophilic Archaea ◽  
Trna Genes ◽  
Distance Ratio ◽  
Genomic Plasticity ◽  
Relative Contribution ◽  
Complete Genomes ◽  
Replication Terminus ◽  
Living Organisms ◽  
High Level

We have compared three complete genomes of closely related hyperthermophilic species of Archaea belonging to thePyrococcus genus: Pyrococcus abyssi, Pyrococcus horikoshii, and Pyrococcus furiosus. At the genomic level, the comparison reveals a differential conservation among four regions of the Pyrococcus chromosomes correlated with the location of genetic elements mediating DNA reorganization. This discloses the relative contribution of the major mechanisms that promote genomic plasticity in these Archaea, namely rearrangements linked to the replication terminus, insertion sequence-mediated recombinations, and DNA integration within tRNA genes. The combination of these mechanisms leads to a high level of genomic plasticity in these hyperthermophilic Archaea, at least comparable to the plasticity observed between closely related bacteria. At the proteomic level, the comparison of the threePyrococcus species sheds light on specific selection pressures acting both on their coding capacities and evolutionary rates. Indeed, thanks to two independent methods, the “reciprocal best hits“ approach and a new distance ratio analysis, we detect the false orthology relationships within the Pyrococcus lineage. This reveals a high amount of differential gains and losses of genes since the divergence of the three closely related species. The resulting polymorphism is probably linked to an adaptation of these free-living organisms to differential environmental constraints. As a corollary, we delineate the set of orthologous genes shared by the three species, that is, the genes that may characterize the Pyrococcus genus. In this conserved core, the amino acid substitution rate is equal between P. abyssi and P. horikoshii for most of their shared proteins, even for fast-evolving ones. In contrast, strong discrepancies exist among the substitution rates observed in P. furiosus relative to the two other species, which is in disagreement with the molecular clock hypothesis.

scholarly journals Virus-borne mini-CRISPR arrays are involved in interviral conflicts

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Sofia Medvedeva ◽  
Ying Liu ◽  
Eugene V. Koonin ◽  
Konstantin Severinov ◽  
David Prangishvili ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Deep Sequencing ◽  
Temporal Dynamics ◽  
Sampling Site ◽  
Virus Genome ◽  
Hyperthermophilic Archaea ◽  
Archaeal Virus ◽  
Distinct Mechanism ◽  
Archaeal Viruses ◽  
Virus Strains

AbstractCRISPR-Cas immunity is at the forefront of antivirus defense in bacteria and archaea and specifically targets viruses carrying protospacers matching the spacers catalogued in the CRISPR arrays. Here, we perform deep sequencing of the CRISPRome—all spacers contained in a microbiome—associated with hyperthermophilic archaea of the order Sulfolobales recovered directly from an environmental sample and from enrichment cultures established in the laboratory. The 25 million CRISPR spacers sequenced from a single sampling site dwarf the diversity of spacers from all available Sulfolobales isolates and display complex temporal dynamics. Comparison of closely related virus strains shows that CRISPR targeting drives virus genome evolution. Furthermore, we show that some archaeal viruses carry mini-CRISPR arrays with 1–2 spacers and preceded by leader sequences but devoid of cas genes. Closely related viruses present in the same population carry spacers against each other. Targeting by these virus-borne spacers represents a distinct mechanism of heterotypic superinfection exclusion and appears to promote archaeal virus speciation.

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