Viral Metagenome Project A portrait of an analysis

Viral Metagenome Project A portrait of an analysis

Viral metagenome? Sampled directly from the environment Unknown species/strains Assembly of Viral Metagenomes from Yellowstone Hot Springs, T. Schoenfeld, et al. 2008 Two Yellowstone springs, Octopus Hot Springs and Bear Paw Hot Springs

From a read to a contig One read (Oct. HSe. ATYB 2334 -b 2) of ~1 kb 969 nt isn’t long enough! Bio. BIKE: SEQUENCESIMILAR-TO finding overlapping reads ≥ 95% identity, ≥ 20 nt minimum overlap to consider

Building it up MS Word, highlighting Gen. Bank format, then FASTA Align, copy/paste, repeat From 969 nt to 5546 nt

Building it up, cont. 9 reads in total But are there any genes?

Searching for significance Is the sequence similar to known viruses? Known anything, for that matter? What does it mean if it is, or if it isn’t? Common descent

Finding similarities SEQUENCE-SIMILAR -TO in Bio. BIKE NCBI BLAST Translated-nucleotide vs. protein

Finding similarities, cont.

Finding similarities, cont. S. Islandicus E=1 E-120 Per protein S. Islandicus E=1 E-120

What are these? Stygiolobus spp. , Acidianus spp. , Sulfolobus islandicus: hot-springs bacteria in Sulfolobaceae Viruses which infect hot-springs bacteria Does this make sense?

Low identities Bacterial transfer Hot spring 1 Hot spring 2 Hot spring 1 Hot spring 2 Time passes… Hot spring 1 Hot spring 2 Note identities for known viruses: 20 -40% Low compared to the other reads Reproductive isolation? Evolution can occur leading to differentiation Changes in protein structure may or may not alter function

Phylogenetic trees Shows (potential) lines of descent Bio. BIKE has tools for it: TREE-OF Compares genetic/protein sequences Differences permit prediction

Phylogenetic trees, example 20 best matches in SEQUENCESSIMILAR-TO an open reading frame of the contig in Octopus Hot Springs reads (Seq_21 is the contig) Predicts line of descent from common ancestor

Conclusions Metagenome analysis allows one to find similarities between organisms inhabiting an environment and known organisms or sequences This leads to the ability to make inferences about the ecology and biodiversity of an environment