RT Journal
A1 Beaulaurier, John
A1 Luo, Elaine
A1 Eppley, John M.
A1 Uyl, Paul Den
A1 Dai, Xiaoguang
A1 Burger, Andrew
A1 Turner, Daniel J.
A1 Pendelton, Matthew
A1 Juul, Sissel
A1 Harrington, Eoghan
A1 DeLong, Edward F.
T1 Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities
JF Genome Research 
JO Genome Research 
YR 2020 
FD March 01 
VO 30 
IS 3 
SP 437 
OP 446 
DO 10.1101/gr.251686.119 
UL http://genome.cshlp.org/content/30/3/437.abstract 
AB Viruses are the most abundant biological entities on Earth and play key roles in host ecology, evolution, and horizontal gene transfer. Despite recent progress in viral metagenomics, the inherent genetic complexity of virus populations still poses technical difficulties for recovering complete virus genomes from natural assemblages. To address these challenges, we developed an assembly-free, single-molecule nanopore sequencing approach, enabling direct recovery of complete virus genome sequences from environmental samples. Our method yielded thousands of full-length, high-quality draft virus genome sequences that were not recovered using standard short-read assembly approaches. Additionally, our analyses discriminated between populations whose genomes had identical direct terminal repeats versus those with circularly permuted repeats at their termini, thus providing new insight into native virus reproduction and genome packaging. Novel DNA sequences were discovered, whose repeat structures, gene contents, and concatemer lengths suggest they are phage-inducible chromosomal islands, which are packaged as concatemers in phage particles, with lengths that match the size ranges of co-occurring phage genomes. Our new virus sequencing strategy can provide previously unavailable information about the genome structures, population biology, and ecology of naturally occurring viruses and viral parasites.