Transcript INBRE POSTER080515Final

Determining the reliability of 16S ribosomal RNA sequences as a proxy for whole genome
taxonomic characterization
Shane
1
Kochvi ,
Jordan
2
Ramsdell ,
Phillip
1
Hatcher ,
W. Kelley
2
Thomas
1. Department of Computer Science, University of New Hampshire
2. Department of Genetics, University of New Hampshire
NH-INBRE
Background
16S ribosomal RNA is often used
as a marker to cluster
prokaryotes functionally and
taxonomically
into
quasiphylogenetic clusters known as
Operational Taxonomic Units
(OTUs). However, organisms with
similar or even identical 16S
sequences can differ greatly in
their protein coding sequences.
Objective
To investigate the similarity of
genomes within OTUs on a
gene-by-gene basis.
Hypothesis
We hypothesized that genomes
belonging prokaryotes with
similar 16S sequences will be
nearly identical in gene content.
This poster was made possible by the
IDeA Program, NIH Grant No.
P20GM103506 (National Institute of
General Medical Sciences)
Procedure
Download all complete prokaryotic
genomes from the NCBI RefSeq database
Extract 16S rRNA sequences from each
genome.
Use UCLUST algorithm to cluster 16S
sequences into OTUs at four different levels
of similarity: 97, 98, 99, and 100 percent.
Two of the most important observations were the numbers of
unique and related genes. We found that the number of unique
genes the number of genes in families at a given percent
similarity was distributed approximately normally.
At all levels of cluster similarity, the median percentages of
unique and shared genes in each two genome cluster were
approximately 30% and 65% respectively. Our hypothesis was
rejected.
Below is a graph of the mean percentages of unique and
shared genes in every two genome cluster at each level of
similarity.
Mean Percentage of Unique/Shared Genes for Two Genome Clusters
Run each cluster through a pipeline which
compares all genes within each OTU, and
identifies genes that are shared among
genomes and unique to specific genomes.
Below are two Venn diagrams representing
OTUs with different numbers of unique and
related genes. Each circle represents the
genes within a single genome, with shared
genes in cyan and unique genes in magenta.
Percentage Unique/Shared
Goals
Results
80%
70%
60%
50%
40%
% Unique Genes
% Shared Genes
30%
20%
10%
0%
97
98
99
Cluster % Similarity
100
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