Abundant non-canonical DNA viruses in seawater revealed by high-throughput single particle sequencing (Reference data)

PREPRINT: https://www.researchsquare.com/article/rs-6227375/v1DATASET FILES:I. SAG Datasets: These consist of three zipped folders containing Single Amplified Genomes. Each of the three datasets was generated from the same seawater sample using a different method:cSAGS.zip contains 260 fasta.gz files. Each fasta is a final SAG assembly. These "cell-like" SAGs were generated from DNA-containing particles captured by FACS targeting prokaryote-sized particles. While these FACS settings enriched for prokaryotes, the SAGs may stem from other sources as well.vSAGs.zip contains 190 fasta.gz files. Each fasta is a final SAG assembly. These "virus-like" SAGs were generated from DNA-containing particles captured by FACS targeting virus-sized particles. Though these FACS settings enriched for viruses, these SAGs may stem from other sources as well.emSAGs.zip contains 2,037 fasta.gz files. Each fasta is a final SAG assembly. emSAGs were captured from seawater using the novel EMCG approach (described in manuscript), wherein DNA was whole-genome-amplified within a semi-permeable capsule. These picoliter-volume capsules may result in SAGs generated from viruses, prokaryotes or free DNA, but are generally too small to enclose eukaryotes.II. Metagenome Dataset: These metagenome reads were obtained from the same seawater sample as for the SAGs above.seawater_metagenome_trimmed_interleaved.fastq.gz is the 16 GB file of interleaved paired-end Illumina reads.ABSTRACT: Viruses and other extracellular genetic elements play essential roles in marine ecology and evolution, yet their composition remains elusive. In this study, we compartmentalized a coastal seawater sample into picoliter-sized semipermeable capsules for in-capsule amplification and barcoding of DNA from individual particles. We obtained genomic sequences of 2,037 particles from a 250 nanoliter sample, capturing a broad range of cellular and extracellular entities. The ratio of viruses to cells (9:1), the predominance of Caudoviricetes viruses, and the taxonomy of cellular genomes indicated quantitative genome recovery. The virus-like genomes included an abundant population of Naomiviridae that lacked metagenomic representation and were linked to several abundant cellular host lineages, suggesting their use of non-canonical DNA and a potentially overlooked ecological significance. The reported Environment Micro-Compartment Genomics (EMCG) technology provides a new opportunity for high-throughput, quantitative, and cost-effective genome analyses of extracellular genetic elements at the resolution of individual particles.