Systematics and genome mapping of ferns; molecular phylogenetics of desert-adapted ferns.
Genome Structure and Evolution in Homosporous Ferns — Homosporous ferns are characterized by high chromosome numbers (n average = 57), suggesting that they are polyploids compared to the heterosporous angiosperms (n average = 16), but isozyme gene expression patterns of ferns are the same as those typical of diploid angiosperms. This paradoxical combination of high chromosome numbers and diploid gene expression led to the hypothesis that homosporous ferns are products of ancient polyploidization events (paleopolyploids) with subsequent divergence and silencing of genes in the extra genomes. With support from the National Science Foundation, we are generating and genotyping 500 doubled haploid lines (DHLs) to construct a high resolution genetic linkage map of Ceratopteris richardii, a model homosporous fern, to investigate this hypothesis. In this first characterization of a homosporous fern genome, we use restriction fragment length polymorphism (RFLP) markers to infer the number of gene copies and their distribution in the genome and amplified fragment length polymorphisms (AFLPs) and isozyume markers to increase saturation of the linkage map. We address the following questions. Are the majority of genes duplicated? If so, what is the average number of copies for each gene? Do most genes have a similar number of copies, or do they vary widely in copy number? How are duplicate genes distributed across the genome? Are entire sets of genes duplicated and recognizable as homoeologous chromosomal segments, or are paralogues scattered haphazardly across the genome? If paleopolyploidization is evident, are homoeologous chromosomes recognizable or are they highly rearranged? Duplication of all or most sets of genes combined with collinear gene orders for duplicated chromosomal segments will provide strong evidence of past polyploidization. This work is significant for the following reasons. 1) It will provide the first detailed characterization of a genome of a homosporous vascular plant. 2) It will generate the most comprehensive evidence bearing on paleopolyploidy in homosporous ferns to date, thus providing the foundation for future studies of their biology and evolution. Homosporous ferns compose most of the phylogenetic sister group to seed plants. Therefore this research will significantly broaden our knowledge of the evolution of genome structure in vascular plants. 3) It will make available to the scientific community the 500 fully genotyped DHLs of plants developed in the course of this genome mapping project. 4) If Ceratopteris richardii is shown to be a paleopolyploid, its mapped genome should enable us to test the duplicate gene silencing model of hybrid breakdown.
Molecular Phylogenetics and Systematics of Desert-Adapted Cheilanthoid Ferns — Cheilanthoid ferns are a major evolutionary unit of several hundred species largely adapted to xerically harsh, semi-desert conditions, as in the southwestern U.S. and Mexico. Specialists have long regarded determining natural evolutionary lines within this group by traditional taxonomic means as virtually impossible, perhaps because convergent evolution has strongly modified the morphological features of these species as they became adapted to their harsh environments. We use cladistic analysis of phylogenetically informative molecular data (mutations in chloroplast DNA restriction sites and in the nucleotide sequences of chloroplast and nuclear genes) to infer major evolutionary lineages that can be recognized as natural genera and infragener
Genome Structure and Evolution in Homosporous Ferns — Homosporous ferns are characterized by high chromosome numbers (n average = 57), suggesting that they are polyploids compared to the heterosporous angiosperms (n average = 16), but isozyme gene expression patterns of ferns are the same as those typical of diploid angiosperms. This paradoxical combination of high chromosome numbers and diploid gene expression led to the hypothesis that homosporous ferns are products of ancient polyploidization events (paleopolyploids) with subsequent divergence and silencing of genes in the extra genomes. With support from the National Science Foundation, we are generating and genotyping 500 doubled haploid lines (DHLs) to construct a high resolution genetic linkage map of Ceratopteris richardii, a model homosporous fern, to investigate this hypothesis. In this first characterization of a homosporous fern genome, we use restriction fragment length polymorphism (RFLP) markers to infer the number of gene copies and their distribution in the genome and amplified fragment length polymorphisms (AFLPs) and isozyume markers to increase saturation of the linkage map. We address the following questions. Are the majority of genes duplicated? If so, what is the average number of copies for each gene? Do most genes have a similar number of copies, or do they vary widely in copy number? How are duplicate genes distributed across the genome? Are entire sets of genes duplicated and recognizable as homoeologous chromosomal segments, or are paralogues scattered haphazardly across the genome? If paleopolyploidization is evident, are homoeologous chromosomes recognizable or are they highly rearranged? Duplication of all or most sets of genes combined with collinear gene orders for duplicated chromosomal segments will provide strong evidence of past polyploidization. This work is significant for the following reasons. 1) It will provide the first detailed characterization of a genome of a homosporous vascular plant. 2) It will generate the most comprehensive evidence bearing on paleopolyploidy in homosporous ferns to date, thus providing the foundation for future studies of their biology and evolution. Homosporous ferns compose most of the phylogenetic sister group to seed plants. Therefore this research will significantly broaden our knowledge of the evolution of genome structure in vascular plants. 3) It will make available to the scientific community the 500 fully genotyped DHLs of plants developed in the course of this genome mapping project. 4) If Ceratopteris richardii is shown to be a paleopolyploid, its mapped genome should enable us to test the duplicate gene silencing model of hybrid breakdown.
Molecular Phylogenetics and Systematics of Desert-Adapted Cheilanthoid Ferns — Cheilanthoid ferns are a major evolutionary unit of several hundred species largely adapted to xerically harsh, semi-desert conditions, as in the southwestern U.S. and Mexico. Specialists have long regarded determining natural evolutionary lines within this group by traditional taxonomic means as virtually impossible, perhaps because convergent evolution has strongly modified the morphological features of these species as they became adapted to their harsh environments. We use cladistic analysis of phylogenetically informative molecular data (mutations in chloroplast DNA restriction sites and in the nucleotide sequences of chloroplast and nuclear genes) to infer major evolutionary lineages that can be recognized as natural genera and infragener
Biology, Systematic, Botany, Fern Genome, Taxonomy, Plant
