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Originally published as Genetics Published Articles Ahead of Print on April 28, 2006.
Genetics, Vol. 173, 1585-1597, July 2006, Copyright © 2006
doi:10.1534/genetics.106.055624
Genetic Map-Based Analysis of Genome Structure in the Homosporous Fern Ceratopteris richardii
Takuya Nakazato*,1,
Min-Kyung Jung
,
Elizabeth A. Housworth,
Loren H. Rieseberg* and
Gerald J. Gastony*
* Department of Biology and Department of Mathematics, Indiana University, Bloomington, Indiana 47405-7005
1 Corresponding author: Department of Biology, Indiana University, 1001 E. Third St., Bloomington, IN 47405-7005.
E-mail: tnakazat{at}indiana.edu
Homosporous ferns have extremely high chromosome numbers relative to flowering plants, but the species with the lowest chromosome numbers show gene expression patterns typical of diploid organisms, suggesting that they may be diploidized ancient polyploids. To investigate the role of polyploidy in fern genome evolution, and to provide permanent genetic resources for this neglected group, we constructed a high-resolution genetic linkage map of the homosporous fern model species, Ceratopteris richardii (n = 39). Linkage map construction employed 488 doubled haploid lines (DHLs) that were genotyped for 368 RFLP, 358 AFLP, and 3 isozyme markers. Forty-one linkage groups were recovered, with average spacing between markers of 3.18 cM. Most loci (
76%) are duplicated and most duplicates occur on different linkage groups, indicating that as in other eukaryotic genomes, gene duplication plays a prominent role in shaping the architecture of fern genomes. Although past polyploidization is a potential mechanism for the observed abundance of gene duplicates, a wide range in the number of gene duplicates as well as the absence of large syntenic regions consisting of duplicated gene copies implies that small-scale duplications may be the primary mode of gene duplication in C. richardii. Alternatively, evidence of past polyploidization(s) may be masked by extensive chromosomal rearrangements as well as smaller-scale duplications and deletions following polyploidization(s).
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