A similar pattern of habitat-driven taxonomic bias was seen in the first ecogenomic survey of sequenced microbial genomes, whereby 67% of the buy inhibitor sequenced marine microbes were phototrophs [8]. Genome Pairs The study of phages and hosts intrinsically lends itself to taking advantage of what Martiny and Field describe as “one of the most exciting and underutilized aspects of the genome collection” [8]: genome pairs. A genome pair occurs when organisms with potential natural interactions are both sequenced, e.g., a phage and host. These associations have revealed patterns in genome biology, such as how well pairs correlate based on %G+C content or tetranucleotide genome signatures [8,32]. Such pairs can (and soon will) rapidly evolve to complex networks as multiple phages infecting the same host, or multiple hosts infected by the same phage, are sequenced.

This complexity obviates the need for the basic units, the pairs, to be explicitly documented (as called for by MIGS) in a structured form. This is possible through the GCDML ‘original host’ and ‘alternate host’ fields, where they can be stored for automated retrieval and network visualization. This process was just barely possible by hand with the 27 marine phage genomes, and reveals interesting trends (Figure 7). Thus far, most cyanophage-cyanobacteria associations are one-to-one pairs, though many cyanophages are known with broad host ranges [33]. Furthermore, such visualization leads to hypotheses about the ‘lone phages’, such as Phage phiJL001, Halomonas phage HAP-1, and Cyanophage Syn5, which lack a sequenced host, but which exist in phylogenetic groups with related sequenced hosts (Figure 7).

The current map is useful in designing future sequencing ventures to answer targeted questions, such as “What drives phage host range�� and ��what are the genomic consequences of all members belonging to the same network?” Figure 7 Network of ‘genome pairs’ and interactions between sequenced marine phages and sequenced hosts. Solid lines link phages (empty circles) to the host strain (solid circles) they infect; dashed lines connect phages to the host species (but not necessarily … Environmental parameters Additionally, the 27 ��mappable�� genomes can be further analyzed in their environmental context using emerging resources, such as megx.

net, to (i) ��put them on the map�� (Panel a of Figure 4; [14]), and (ii) extract interpolated environmental data, though only possible for the eight genomes Brefeldin_A where depth is reported and which are not too close to the coast (Table 1). Preliminary analysis of the megx.net interpolated data available in the GCDML reports revealed that, based on physical-chemical parameters across sample sites, e.g., the four phages isolated from the Sargasso Sea cluster together, while Cyanophage PSS2 appears to be an outlier (Panel b of Figure 4).