Open preprint reviews by Donald Fordsyke

The CRISPR Spacer Space Is Dominated By Sequences From The Species-Specific Mobilome

Sergey A. Shmakov, Vassilii Sitnik, Kira S. Makarova, Yuri I. Wolf, Konstantin V. Severinov, Eugene Koonin

THE VIRUS-VIRUS ARMS RACE

The authors mention the virus-host arms race, but not the virus-virus (in common host) arms race (1). Thus, they seek to "improve our understanding of the evolution of the CRISPR spacer space and the virus-host arms race." There was a similar omission in a study of phage-host relationships in mycobacteria (2), upon which I have commented (3).

Apart from this, the slopes of regression plots of phage GC% against host GC% (Figs. 3, 4) indicate relative AT-enrichment in phage. The authors acknowledge our study (4), where we note differences in the pressures on individual codon positions between phage and bacteria. However, it is deemed that "GC-content … of microbial genomes, … and the cognate viral genomes show a nearly perfect correlation and are almost identical" (1).

This would not be expected from previous arguments (3) and is supported by the observations that "in most cases, there was indeed considerable AT-bias in phages," relative to hosts, although there are cases where "phage genomes had the same composition as the host" (1). The predicted high variance between phages that affect a common host (3), may be reflected in the scatter of points for phages in Fig. 3.

1. Shmakov SA, Sitnik V, Makarova KS, Wolf YI, Severinov KV, Koonin EV (2017) The CRISPR spacer space is dominated by sequences from the species-specific mobilome. BioRxiv preprint (doi: http://dx.doi.org/10.1101/1... ).

2. Esposito LA, Gupta S, Streiter F, Prasad A, Dennehy JJ (2016). Evolutionary interpretations of mycobacteriophage biodiversity and host-range through the analysis of codon usage bias. Microbiol Genom 2(10):e000079. <pmid:28348827>

3. Forsdyke DR (2016) Elusive preferred hosts or nucleic acid level selection? arXiv Preprint (https://arxiv.org/abs/1612.... ).


4. Mortimer JR, Forsdyke DR (2003) Comparison of responses by bacteriophage and bacteria to pressures on the base composition of open reading frames. Appl Bioinformatics 2:47-62. <pmid:15130833> (see 2003 paper )

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