A field guide in setting up sequencing workflow, specifically on a moving ship

<p>Figure 2. (A) Molecular bench for procedure including DNA extraction and library preparation was set-up in a clean room, which also serves as one of the bedrooms of scientists on-board. (B) Emulsion PCR was performed using the One-Touch technology located at the laundry room close to the hull of the ship. Damaged touch screen was replaced by re-wiring the display onto a laptop. (C) The sequencer was run at the owner’s cabin where there is an easy and safe access to the nitrogen tank that fuels the microfluidics of the sequencing technology. (D) A modified version of Ion Torrent server was set up to run the data analysis.</p

There is no correlation between genetic and physical distance

<p>Supplemental Figure 7</p> <p>Correlation between physical distance and genetic distance in the microbial species purified on the Line Islands.</p

Heatmap comparing all genomes sequenced to Line Islands metagenomes

<p>Figure 3. The genomes, along the horizontal axis, are clustered by genera. The metagenomes on the vertical axis are organized by the island from which the samples were isolated. Solid gray bars on the top indicate the assembled genome size (bp), and gray bars on the right indicate metagenome size (bp). The cells are colored by distance calculated as described in the text (Equation 1) and as shown in the legend on the lower left.</p

Growth curves in 48 different media showing growth in some wells

<p>Supplemental Figure 4. Growth curve of bacterial isolates in 48 different carbon sources indicated in Supplementary Table 1.</p

Sampling the reefs

<p>Supplemental Figure 2. Examples of sampling surface for bacterial isolates. VRT35 and VRT38 were isolated from coral surfaces, while VRT37 and VRT41 were isolated from algae surfaces.</p> <p></p

Number of bases sequenced and number of contigs generated

<p>Supplemental Figure 3. Number of bases sequenced and number of contigs generated. The best-fit power regression of the data (shown with a gray line) has the equation [number of contigs] = 3.87 * 10^10 [base piars sequenced]^-0.95 with an R^2 of 0.667.</p

2013 Southern Line Islands Research Expedition

<p>Supplemental Figure 1. Expedition route of the 2013 Southern Line Island Expedition. The expedition left Papeete Harbor and circumnavigated the Southern Line Islands in a clockwise direction.</p

Coral Viromes

Coral viromes extracted from Porites rus, Acropora sp., Acropora yongei, Pocillopora verrucos

Summary of known viruses detected in nasopharyngeal samples.

<p>Summary of known viruses detected in nasopharyngeal samples.</p

Maximum likelihood tree showing the clustering of HPV_SD2 with previously documented full-length genomes of human papillomaviruses.

<p>The tree was visualized with the Interactive Tree of Life (iTOL) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058404#pone.0058404-Letunic1" target="_blank">[32]</a>. Bootstrap values with at least 50%, 75% or 100% (100 re-samplings) are indicated. Note, another HPV_SD1 from this study was added in this analysis clustered with reference HPV_49.</p