Barker, Michael S. .
Inferring Paleopolyploidy in Homosporous Ferns from Age Distributions of Duplicate Genes.
AMONG the unique features of homosporous ferns, the most intriguing may be their high chromosome numbers. Basal chromosome counts for fern genera are significantly higher than similar values from angiosperms (homosporous ferns n=57.05, angiosperms n=16), a result that led early workers to assume that as many as 95% of ferns are polyploids. However, subsequent isozyme investigations found that homosporous fern species with the lowest numbers in their genera demonstrated diploid gene expression patterns. This led Haufler (1987) to hypothesize that homosporous ferns are paleopolyploids that have experienced cycles of ancient polyploidization with subsequent genetic, but not chromosomal, diploidization. To test Haufler’s paleopolyploid hypothesis, I am examining the age distribution of duplicate nuclear gene pairs for evidence of ancient large scale duplication events in two diploid, homosporous fern species; Ceratopteris richardii and Adiantum capillus-veneris. For this analysis, EST datasets for both species were downloaded from Genbank (5,128 sequences for Ceratopteris and 10,421 for Adiantum). Using a custom software pipeline I constructed, the data were cleaned, duplicate gene pairs identified and aligned with their putative protein sequences, and Ks values calculated for each duplicate gene pair using software from the PAML package. The preliminary results indicate that C. richardii has experienced at least two large scale genome duplication events. One of these events occurred in the recent past (ca. Ks = 0.04), whereas the other event is much older (ca. Ks = 1.2). These preliminary results support Haufler’s paleopolyploid hypothesis in homosporous ferns. Ongoing research with these data will reveal the history of duplication events in Adiantum, provide estimates of when putative duplication events occurred, and be compared to available angiosperm data. By coordinating these results with other ongoing research efforts, a clearer picture of the mode and tempo of homosporous fern chromosomal and genome evolution should emerge.
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1 - Indiana University, Department of Biology, Jordan Hall, 1001 East Third Street, Bloomington, Indiana, 47405, USA
Presentation Type: Oral Paper:Papers for Sections
Date: Monday, July 31st, 2006
Time: 4:00 PM