Recent Topics Posters
Margheim, Stephanie R. , Peery, Rhiannon , Kuehl, Jennifer V. , Boore, Jeffrey L. , Raubeson, Linda A. .
Mutation patterns of highly similar chloroplast genomes.
The number of angiosperm chloroplast genome sequences available has been growing rapidly. As this sampling has increased, multiple genomes now have been characterized from within the same genus or family. This provides the opportunity to compare similar sequences and characterize mutation patterns from data with fewer superimposed events. We have completed chloroplast genome sequences for Acorus americanus, Anethum graveolens (dill), and Foeniculum vulgare (fennel). When we compared our Acorus americanus sequence to the published Acorus calamus, we found that the two genomes differ by only 21 mismatches and 15 indels. The dill and fennel genomes differ by 447 substitutions and 549 indels. To place our comparisons in context, we obtained other genome pairs from GenBank that we could align contiguously using Mulan. Some genomes failed to align in one piece, and thus were excluded from the analysis, either because they have regions of greater dissimilarity or because they are not collinear. For those that did align, we determined the percent similarity (93.08-100%), the number of mismatches (0-6401), and the number of indels (0-3885) for each genome pair that aligned (48 pairs). We found the number of mismatches and the number of indels to be correlated (spearman rank correlation statistic = 0.905, p < 0.00001). For more detailed comparisons, we limited our scope to those genome pairs (16) with similarities equal to or greater than 99%. There we found, as expected, that single copy regions show more (3-28 times as much) differences than the inverted repeat regions. The number of substitutions is about equal on average to the number of indels but ranges from three-fourths to more than twice as many. We are continuing our comparisons to look at coding versus non-coding regions, transitions versus transversions and other aspects of the mutational differences between these highly similar pairs of sequences.
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1 - Central Washington University, Biological Sciences, 400 E University Way, Ellensburg, WA, 98926-7537, USA
2 - DOE Joint Genome Institute, Department of Evolutionary Genomics, 2800 Mitchell Drive, Walnut Creek, California, 94598, USA
Presentation Type: Recent Topics Poster
Location: Exhibit Hall (Northeast, Southwest & Southeast)/Hilton
Date: Sunday, July 8th, 2007
Time: 8:00 AM