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Viral genome sequencing and targeted amplification studies have led to the important discovery that phage encode environmentally relevant genes of host origin [27], [29], [30], [32], [44], [57].
We have presented strong evidence for the significant occurrence and geographically widespread distribution of environmentally important viral genes of host origin in aquatic ecosystems.
As more viral genes of host origin are detected in environmental samples and cultured phage genomes, their evolutionary relationships with host genes should become clearer.
Quantitative analyses of viral genes of host origin performed on the viral fraction of aquatic samples confirmed the viral nature of these sequences and suggested that significant portions of aquatic viral communities behave as reservoirs of such genetic material.
The data presented here allowed us to evaluate the impact of various environmental parameters on the occurrence and geographic distribution of viral genes of host origin captured within GOS samples.
Viral genes of host origin were identified in varying abundances across all sites sampled (Fig. S1, S2, S3, S4, S5, S6, S7, S8), indicating the prevalence and widespread nature of this phenomenon in aquatic ecosystems.
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Type II retrocopies consisted of duplications of one or more coding exons derived from the parent gene that formed new genes independent of host genes.
MST markers have been developed for identifying the source of fecal pollution by targeting the 16S rRNA genes and other genes of host-associated microbiota, or by targeting host-specific mitochondrial DNA (mtDNA).
Our results show that several dozen actively transcribed, largely nuclear, genes are of host origin.
Additionally, a number of putative homologs of genes for host resistance were also found.
The other three models describe snoRNA genes located outside of host genes and putatively transcribed from their own promoters.
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