A new family of “megaphages” abundant in the marine environment

Abstract

Megaphages, bacteriophages harbouring extremely large genomes, have recently been found to be ubiquitous, being described from a variety of microbiomes ranging from the animal gut to soil and freshwater systems. However, no complete marine megaphage has been identified to date. Here, using both short and long read sequencing, we assembled >900 high-quality draft viral genomes from water in the English Channel. One of these genomes included a novel megaphage, Mar_Mega_1 at >650 Kb, making it one of the largest phage genomes assembled to date. Utilising phylogenetic and network approaches, we found this phage represents a new family of megaphages. Genomic analysis showed Mar_Mega_1 shares relatively few homologues with its closest relatives, but, as with other megaphages Mar_Mega_1 contained a variety of auxiliary metabolic genes responsible for carbon metabolism and nucleotide biosynthesis, including a NADP-dependent isocitrate dehydrogenase [Idh] and nicotinamide-nucleotide amidohydrolase [PncC], which have not previously been identified in megaphages. Mar_Mega_1 was abundant in a marine virome sample and related phages are widely prevalent in the oceans.

The long and short of it: Benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies

“…While the number of viromes that utilise ONT alone or in combination with Illumina sequencing is slowly increasing [14,[22][23][24][25], reports of utilising PacBio sequencing for viromes are scarce [26]. A recent study predicted phages from a bacterial metagenome assembled from PacBio reads, identifying phages not identified when the same sample was sequenced with short reads [26].…”

Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities

“…The current results provide evidence that the viruses play a role in the budget of vitamins at the bathypelagic. DHFR genes have previously been reported in the genomes of marine bacteriophages [37]. Yet, to our knowledge, this is the first time this gene is reported in bathypelagic viruses, in association with other genes directly involved in nucleotide metabolism, and with differential abundances between free-living and particle-attached fractions or water masses.…”

Viral Complexity

“…Although still a minority compared to smaller phages, over 300 jumbo phages have been cultivated and had their genomes sequenced [ 23 ]. Moreover, cultivation-independent approaches have reconstructed genomes of many more of these phages, some with genome sizes >700 kbp, and suggested that they are ubiquitous in the biosphere [ 24 , 25 , 26 , 27 ].…”

“…Relatively less is known about the functional repertoires of jumbo phages owing to the lack of detectable homologs in many genomes and the relatively recent discovery of many new groups [ 24 , 25 , 27 , 81 ]. Moreover, given the small number of jumbo phage genomes currently available, it is at present unclear if these viruses have any distinct functional capabilities that distinguish them from their smaller relatives.…”

“…The mosaic genomes of large DNA viruses are particularly perplexing because so few of the genes in these genomes have recognizable homologs in any sequence databases [ 27 , 81 , 160 ]. It therefore remains an enigma exactly how many of these genes arise.…”