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Blaine D Marchant - One of the best experts on this subject based on the ideXlab platform.
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the c Fern ceratopteris richardii genome insights into plant genome evolution with the first partial homosporous Fern genome assembly
Scientific Reports, 2019Co-Authors: Emily B. Sessa, Paul G Wolf, Pamela S. Soltis, Blaine D Marchant, Brad W Barbazuk, Douglas E. SoltisAbstract:Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of Ferns are unclear, largely due to the absence of a sequenced homosporous Fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous Ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model Fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous Ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous Fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.
Emily B. Sessa - One of the best experts on this subject based on the ideXlab platform.
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the c Fern ceratopteris richardii genome insights into plant genome evolution with the first partial homosporous Fern genome assembly
Scientific Reports, 2019Co-Authors: Emily B. Sessa, Paul G Wolf, Pamela S. Soltis, Blaine D Marchant, Brad W Barbazuk, Douglas E. SoltisAbstract:Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of Ferns are unclear, largely due to the absence of a sequenced homosporous Fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous Ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model Fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous Ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous Fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.
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Evolution and Classification of Ferns and Lycophytes
Current Advances in Fern Research, 2018Co-Authors: Emily B. SessaAbstract:The last several decades have seen a transformation in our understanding of the evolutionary history of Ferns and lycophytes. Historically the plants belonging to these lineages were grouped together and referred to as “pteridophytes” or “Ferns and Fern allies.” These terms both describe what we now recognize to be non-monophyletic assemblages, and both reflect a lack of understanding of the relationships of Ferns and lycophytes that was only dispelled in the late 1990s and early 2000s. Thanks to the emergence of molecular systematics and the efforts of researchers in the Fern and lycophyte community, we now have well-sampled and highly resolved phylogenies that include all tracheophytes, including substantial numbers of Ferns and lycophytes. These trees have generated numerous insights about the evolutionary history of all land plants and have clarified the relationships between major groups of tracheophytes and vastly improved our understanding of Fern and lycophyte evolution. This chapter reviews the major lineages, diversification events, and transitions in Fern and lycophyte evolution and summarizes our current understanding of Fern and lycophyte classification based on a modern, community-derived classification system that was recently produced for all 11,916 extant species of Ferns and lycophytes.
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Evolutionary Genomics of Ferns and Lycophytes
Advances in Botanical Research, 2016Co-Authors: Emily B. SessaAbstract:Abstract Ferns and lycophytes are ubiquitous and charismatic members of many terrestrial ecosystems. Members of these lineages play key ecological roles in many of Earth's biomes and have an ancient fossil record dating back to the Devonian. Modern Ferns underwent significant diversification in the Cretaceous, and the clade as a whole occupies a pivotal position in land plant evolution as the sister lineage to seed plants; lycophytes, in turn, are sister to Ferns plus seed plants together. Both Ferns and lycophytes are spore-bearing vascular plants, and each clade includes both homosporous and heterosporous members. Many taxa have large genomes with high numbers of chromosomes, particularly among the homosporous members of both lineages. They are the only two lineages of land plants that maintain independent gametophyte and sporophyte phases in their life cycle. Ferns are known to be prone to hybridization and polyploidy, but the roles these events have played in producing their large genomes are still unclear. Genome science has advanced dramatically in recent years, but genomic research in lycophytes and Ferns has lagged behind other groups of plants. While nuclear genome sequences are now available for over 100 species of seed plants, there is only one sequenced genome of a lycophyte available (heterosporous Selaginella moellendorffii ), and none from any Fern, or from any homosporous vascular plant. This chapter reviews what is known about Fern and lycophyte genomes (nuclear, chloroplast, and mitochondrial) and transcriptomes and presents an outlook on the future of genome research in these groups, including outstanding challenges in plant biology that will be illuminated by incorporating information on Ferns and lycophytes.
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an exploration into Fern genome space
Genome Biology and Evolution, 2015Co-Authors: Paul G Wolf, Emily B. Sessa, Daniel Blaine Marchant, Faywei Li, Carl J Rothfels, Erin M Sigel, Matthew A GitzendannerAbstract:Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in Ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize Ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into Fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (~0.4X to 2X) for six Fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of Fern genomes can provide information useful for selecting a promising candidate Fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between Ferns and seed plants.
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between two Fern genomes
GigaScience, 2014Co-Authors: Emily B. Sessa, Jo Ann Banks, Faywei Li, Michael S Barker, Aaron M Duffy, Sean W Graham, Mitsuyasu Hasebe, Jane A Langdale, D B Marchant, Kathleen M PryerAbstract:Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in Ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first Ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant Ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across Ferns and all land plants. Here we review the unique biological characteristics of Ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of Ferns to the set of taxa with sequenced nuclear genomes. We explain why the Fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of Fern genomes will enable progress in research beyond the Ferns themselves.
Faywei Li - One of the best experts on this subject based on the ideXlab platform.
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A Roadmap for Fern Genome Sequencing
American Fern Journal, 2019Co-Authors: Faywei LiAbstract:The large genomes of Ferns have long deterred genome sequencing efforts. To date, only two heterosporous Ferns with remarkably small genomes, Azolla filiculoides and Salvinia cucullata, have been sequenced. However, as sequencing technologies continue to improve and become more affordable, generating high-quality, “normal-sized” Fern genomes is within reach. Here we provide new genome size data and discuss candidates for whole genome sequencing. In particular, we identified 18 species representing major branches in the Fern phylogeny that are worth pursuing. We also review the current sequencing technologies and offer our opinions on the best sequencing approach for these Fern species.
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is there foul play in the leaf pocket the metagenome of floating Fern azolla reveals endophytes that do not fix n2 but may denitrify
New Phytologist, 2018Co-Authors: Laura W Dijkhuizen, Faywei Li, Paul Brouwer, Henk Bolhuis, Gertjan Reichart, Nils Koppers, Bruno Huettel, Anthony Bolger, Shifeng ChengAbstract:Summary Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating Fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla Ferns were characterized. A metagenomic approach was taken complemented by detection of N2O released and nitrogen isotope determinations of Fern biomass. Ribosomal RNA genes in sequenced DNA of natural Ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct nearly full-length Rhizobiales genomes were identified in leaf-pocket-enriched samples from ditch grown A. filiculoides. Their annotation revealed genes for denitrification but not N2-fixation. 15N2 incorporation was active in Ferns with N. azollae but not in Ferns without. N2O was not detectably released from surface-sterilized Ferns with the Rhizobiales. N2-fixing N. azollae, we conclude, dominated the microbiome of Azolla Ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2O.
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an exploration into Fern genome space
Genome Biology and Evolution, 2015Co-Authors: Paul G Wolf, Emily B. Sessa, Daniel Blaine Marchant, Faywei Li, Carl J Rothfels, Erin M Sigel, Matthew A GitzendannerAbstract:Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in Ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize Ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into Fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (~0.4X to 2X) for six Fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of Fern genomes can provide information useful for selecting a promising candidate Fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between Ferns and seed plants.
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between two Fern genomes
GigaScience, 2014Co-Authors: Emily B. Sessa, Jo Ann Banks, Faywei Li, Michael S Barker, Aaron M Duffy, Sean W Graham, Mitsuyasu Hasebe, Jane A Langdale, D B Marchant, Kathleen M PryerAbstract:Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in Ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first Ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant Ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across Ferns and all land plants. Here we review the unique biological characteristics of Ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of Ferns to the set of taxa with sequenced nuclear genomes. We explain why the Fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of Fern genomes will enable progress in research beyond the Ferns themselves.
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An Exploration of Fern Genome Space
Botany, 2014Co-Authors: Paul G Wolf, Faywei Li, Carl J Rothfels, Matthew A Gitzendanner, Clayton J. Visger, Marchant D. Blaine, Douglas E. Soltis, Pamela S. Soltis, Kathleen M PryerAbstract:Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in Ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolutionacrossgreenplants, and shed lightongenetic and genomic features that characterize Ferns, suchas their highchromosome numbers and large genome sizes. As part of an initial exploration into Fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (~0.4X to2X) for six Fern species fromthePolypodiales (Ceratopteris,Pteridium, Polypodium,Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of Ferngenomescanprovide informationuseful for selectingapromisingcandidate Fern species forwholegenomesequencing.Wealso describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between Ferns and seed plants.
Kathleen M Pryer - One of the best experts on this subject based on the ideXlab platform.
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between two Fern genomes
GigaScience, 2014Co-Authors: Emily B. Sessa, Jo Ann Banks, Faywei Li, Michael S Barker, Aaron M Duffy, Sean W Graham, Mitsuyasu Hasebe, Jane A Langdale, D B Marchant, Kathleen M PryerAbstract:Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in Ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first Ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant Ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across Ferns and all land plants. Here we review the unique biological characteristics of Ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of Ferns to the set of taxa with sequenced nuclear genomes. We explain why the Fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of Fern genomes will enable progress in research beyond the Ferns themselves.
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An Exploration of Fern Genome Space
Botany, 2014Co-Authors: Paul G Wolf, Faywei Li, Carl J Rothfels, Matthew A Gitzendanner, Clayton J. Visger, Marchant D. Blaine, Douglas E. Soltis, Pamela S. Soltis, Kathleen M PryerAbstract:Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in Ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolutionacrossgreenplants, and shed lightongenetic and genomic features that characterize Ferns, suchas their highchromosome numbers and large genome sizes. As part of an initial exploration into Fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (~0.4X to2X) for six Fern species fromthePolypodiales (Ceratopteris,Pteridium, Polypodium,Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of Ferngenomescanprovide informationuseful for selectingapromisingcandidate Fern species forwholegenomesequencing.Wealso describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between Ferns and seed plants.
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is morphology really at odds with molecules in estimating Fern phylogeny
Systematic Botany, 2009Co-Authors: Harald Schneider, Alan R Smith, Kathleen M PryerAbstract:Using a morphological dataset of 136 vegetative and reproductive characters, we infer the tracheophyte phylogeny with an emphasis on early divergences of Ferns (monilophytes). The dataset comprises morphological, anatomical, biochemical, and some DNA structural characters for a taxon sample of 35 species, including representatives of all major lineages of vascular plants, especially Ferns. Phylogenetic relationships among vascular plants are reconstructed using maximum parsimony and Bayesian inference. Both approaches yield similar relationships and provide evidence for three major lineages of extant vascular plants: lycophytes, Ferns, and seed plants. Lycophytes are sister to the euphyllophyte clade, which comprises the Fern and seed plant lineages. The Fern lineage consists of five clades: horsetails, whisk Ferns, ophioglossoids, marattioids, and leptosporangiate Ferns. This lineage is supported by characters of the spore wall and has a parsimony bootstrap value of 76%, although the Bayesian posterior probability is only 0.53. Each of the five Fern clades is well supported, but the relationships among them lack statistical support. Our independent phylogenetic analyses of morphological evidence recover the same deep phylogenetic relationships among tracheophytes as found in previous studies utilizing DNA sequence data, but differ in some ways within seed plants and within Ferns. We discuss the extensive independent evolution of the five extant Fern clades and the evidence for the placement of whisk Ferns and horsetails in our morphological analyses.
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Fern phylogeny inferred from 400 leptosporangiate species and three plastid genes
Taxon, 2007Co-Authors: Eric Schuettpelz, Kathleen M PryerAbstract:In an effort to obtain a solid and balanced approximation of global Fern phylogeny to serve as a tool for addressing large-scale evolutionary questions, we assembled and analyzed the most inclusive molecular dataset for leptosporangiate Ferns to date. Three plastid genes (rbcL, atpB, atpA), totaling more than 4,000 bp, were sequenced for each of 400 leptosporangiate Fern species (selected using a proportional sampling approach) and five outgroups. Maximum likelihood analysis of these data yielded an especially robust phylogeny: 80% of the nodes were supported by a maximum likelihood bootstrap percentage ≥ 70. The scope of our analysis provides unprecedented insight into overall Fern relationships, not only delivering additional support for the deepest leptosporangiate divergences, but also uncovering the composition of more recently emerging clades and their relationships to one another.
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Ferns diversified in the shadow of angiosperms
Nature, 2004Co-Authors: Harald Schneider, Kathleen M Pryer, Eric Schuettpelz, Raymond Cranfill, Susana Magallón, Richard LupiaAbstract:The rise of angiosperms during the Cretaceous period is often portrayed as coincident with a dramatic drop in the diversity and abundance of many seed-free vascular plant lineages, including Ferns1,2,3,4,5. This has led to the widespread belief that Ferns, once a principal component of terrestrial ecosystems6, succumbed to the ecological predominance of angiosperms and are mostly evolutionary holdovers from the late Palaeozoic/early Mesozoic era. The first appearance of many modern Fern genera in the early Tertiary fossil record implies another evolutionary scenario; that is, that the majority of living Ferns resulted from a more recent diversification7,8,9,10. But a full understanding of trends in Fern diversification and evolution using only palaeobotanical evidence is hindered by the poor taxonomic resolution of the Fern fossil record in the Cretaceous11. Here we report divergence time estimates for Ferns and angiosperms based on molecular data, with constraints from a reassessment of the fossil record. We show that polypod Ferns (> 80% of living Fern species) diversified in the Cretaceous, after angiosperms, suggesting perhaps an ecological opportunistic response to the diversification of angiosperms, as angiosperms came to dominate terrestrial ecosystems.
Paul G Wolf - One of the best experts on this subject based on the ideXlab platform.
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the c Fern ceratopteris richardii genome insights into plant genome evolution with the first partial homosporous Fern genome assembly
Scientific Reports, 2019Co-Authors: Emily B. Sessa, Paul G Wolf, Pamela S. Soltis, Blaine D Marchant, Brad W Barbazuk, Douglas E. SoltisAbstract:Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of Ferns are unclear, largely due to the absence of a sequenced homosporous Fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous Ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model Fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous Ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous Fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.
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an exploration into Fern genome space
Genome Biology and Evolution, 2015Co-Authors: Paul G Wolf, Emily B. Sessa, Daniel Blaine Marchant, Faywei Li, Carl J Rothfels, Erin M Sigel, Matthew A GitzendannerAbstract:Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in Ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize Ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into Fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (~0.4X to 2X) for six Fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of Fern genomes can provide information useful for selecting a promising candidate Fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between Ferns and seed plants.
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An Exploration of Fern Genome Space
Botany, 2014Co-Authors: Paul G Wolf, Faywei Li, Carl J Rothfels, Matthew A Gitzendanner, Clayton J. Visger, Marchant D. Blaine, Douglas E. Soltis, Pamela S. Soltis, Kathleen M PryerAbstract:Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in Ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolutionacrossgreenplants, and shed lightongenetic and genomic features that characterize Ferns, suchas their highchromosome numbers and large genome sizes. As part of an initial exploration into Fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (~0.4X to2X) for six Fern species fromthePolypodiales (Ceratopteris,Pteridium, Polypodium,Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of Ferngenomescanprovide informationuseful for selectingapromisingcandidate Fern species forwholegenomesequencing.Wealso describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between Ferns and seed plants.
