Skip to content

Home

Jump to bottom
eolesin edited this page Aug 12, 2022 · 24 revisions

Welcome to the AMOR_Indiv_Assembly_Protocol wiki!

ISME18: Interpretation of microbial food webs from metagenomic data in deep-sea hydrothermal vents across the Arctic Mid-Ocean Ridge

pdf of poster

Methods

  1. Sampling was accomplished over the course of numerous research expeditions to the Arctic Mid-Ocean Ridge by members of the Centre for Deep Sea Research between 2007-2019.
  2. DNA extraction was performed using the DNEasy Powersoil DNA extraction and isolation kit.
  3. Bioinformatic analysis consisted of the following steps, details of which can be found to the right side bar of this wiki:
  • QC analysis and filtration
  • 16s rRNA read detection, extraction, taxonomic affiliation and counting (using PhyloFlash)
  • Metagenome contiguous sequence assembly (Megahit)
  • Read mapping to contigs (bowtie2)
  • Gene detection/annotation within contigs and counting (Prodigal, anvio scripts)
  • Metagenome-assembled genome binning, completeness/contamination checking (multiple algorithms + dasTool, checkM)
  • Dereplication of genomes (dRep)
  • Read mapping to non-redundant MAGs (bowtie2)

Supporting Figures

Supp. Figure 1. A) PCA of 16s rRNA reads extracted from metagenomes of chimney and biosyringe samples. Data source is the same table used for sample percent composition figure on the poster. Components are counts from all individiual NTUs per sample in this plot. Data was additive logratio transformed before principle component analysis was performed.** B) **PCA of Metagenome assembled-genomes (MAGs). Data source is coverages of MAGs, additive logratio transformed.

Supp. Figure 2. Additive logratios of 16S rRNA reads collapsed by functional group of NTUs as predicted by taxonomic assignment. This visualization demonstrates beta diversity of functional groups between samples regardless of the presence of other taxa in the sample due to compositional nature of sequence data.

Supp. Figure 3. Venn diagram of the overlap of presence of metagenome assembled genomes (MAGs) between hydrothermal vents along the Arctic Mid-Ocean Ridge (AMOR). Presence of a MAG was determined using an arbitrary genome coverage cutoff value of 0.25 after testing of several more arbitrarily-chosen cutoffs (10,1,0.25,0.1,0.001).

Supp. Figure 4. Seven MAGs belonging to the aerobic methane oxidizer lineage Methylococcales represent the lineage with the most genomes out of the 28 genomes deemed present among all 5 AMOR vent sites. Additive log ratios of these MAG coverages are visualized to demonstrate beta diversity of these 7 MAGs.

Clone this wiki locally