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Search Results: 1 - 10 of 326418 matches for " Pamela S. Soltis "
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Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae)
Jin Koh, Pamela S Soltis, Douglas E Soltis
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-97
Abstract: Using cDNA-AFLPs, we found differential band patterns that could be attributable to gene silencing, novel expression, and/or maternal/paternal effects between T. mirus and its diploid parents. Subsequent cleaved amplified polymorphic sequence (CAPS) analyses of genomic DNA and cDNA revealed that 20 of the 30 genes identified through cDNA-AFLP analysis showed additivity, whereas nine of the 30 exhibited the loss of one parental homeolog in at least one individual. Homeolog loss (versus loss of a restriction site) was confirmed via sequencing. The remaining gene (ADENINE-DNA GLYCOSYLASE) showed ambiguous patterns in T. mirus because of polymorphism in the diploid parent T. dubius. Most (63.6%) of the homeolog loss events were of the T. dubius parental copy. Two genes, NUCLEAR RIBOSOMAL DNA and GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, showed differential expression of the parental homeologs, with the T. dubius copy silenced in some individuals of T. mirus.Genomic and cDNA CAPS analyses indicated that plants representing multiple populations of this young natural allopolyploid have experienced frequent and preferential elimination of homeologous loci. Comparable analyses of synthetic F1 hybrids showed only additivity. These results suggest that loss of homeologs and changes in gene expression are not the immediate result of hybridization, but are processes that occur following polyploidization, occurring during the early (<40) generations of the young polyploid. Both T. mirus and a second recently formed allopolyploid, T. miscellus, exhibit more homeolog losses than gene silencing events. Furthermore, both allotetraploids undergo biased loss of homeologs contributed by their shared diploid parent, T. dubius. Further studies are required to assess whether the results for the 30 genes so far examined are representative of the entire genome.Polyploidy is a particularly important evolutionary mechanism in flowering plants [1-4]. During the past 70 years, many plant biologi
Plant Reproductive Genomics at the Plant and Animal Genome Conference
Jim Leebens-Mack,Douglas E. Soltis,Pamela S. Soltis
Comparative and Functional Genomics , 2006, DOI: 10.1002/cfg.469
On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae)
Jennifer A Tate, Prashant Joshi, Kerry A Soltis, Pamela S Soltis, Douglas E Soltis
BMC Plant Biology , 2009, DOI: 10.1186/1471-2229-9-80
Abstract: Of the 13 loci analyzed in 84 T. miscellus individuals, 11 showed loss of at least one parental homoeolog in the young allopolyploids. Two loci were retained in duplicate for all polyploid individuals included in this study. Nearly half (48%) of the individuals examined lost a homoeolog of at least one locus, with several individuals showing loss at more than one locus. Patterns of loss were stochastic among individuals from the independently formed populations, except that the T. dubius copy was lost twice as often as T. pratensis.This study represents the most extensive survey of the fate of genes duplicated by allopolyploidy in individuals from natural populations. Our results indicate that the road to genome downsizing and ultimate genetic diploidization may occur quickly through homoeolog loss, but with some genes consistently maintained as duplicates. Other genes consistently show evidence of homoeolog loss, suggesting repetitive aspects to polyploid genome evolution.Allopolyploidy combines the processes of hybridization with genome doubling, and together, these provide a potential avenue for instantaneous speciation [1-3]. Whole-genome sequencing efforts have revolutionized our thinking about the significance of polyploidy, as it is clear that paleopolyploidy is a common phenomenon. Ancient whole-genome duplications have been detected in many eukaryotic lineages, including angiosperms, vertebrates, and yeast [4-12]. Polyploidy has been particularly prevalent in flowering plants, where previous estimates indicated that 30–70% of angiosperm species had polyploidy in their ancestry [reviewed in [13]]. In the last decade, the view of polyploidy in angiosperms has changed, and it is now appreciated that perhaps all angiosperm lineages have experienced at least one round of polyploidy, with many lineages undergoing two or more such episodes [14-18]. On more recent timescales, molecular data have also revealed that most extant polyploid plant species have formed rec
Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants
Mi-Jeong Yoo, Victor A Albert, Pamela S Soltis, Douglas E Soltis
BMC Plant Biology , 2006, DOI: 10.1186/1471-2229-6-3
Abstract: We found that the structure of GSK genes is generally conserved in Arabidopsis and rice, although we documented examples of exon expansion and intron loss. Our phylogenetic analyses of 139 sequences revealed four major clades of GSK genes that correspond to the four subgroups initially recognized in Arabidopsis. ESTs from basal angiosperms were represented in all four major clades; GSK homologs from the basal angiosperm Persea americana (avocado) appeared in all four clades. Gymnosperm sequences occurred in clades I, III, and IV, and a sequence of the red alga Porphyra was sister to all green plant sequences.Our results indicate that (1) the plant-specific GSK gene lineage was established early in the history of green plants, (2) plant GSKs began to diversify prior to the origin of extant seed plants, (3) three of the four major clades of GSKs present in Arabidopsis and rice were established early in the evolutionary history of extant seed plants, and (4) diversification into four major clades (as initially reported in Arabidopsis) occurred either just prior to the origin of the angiosperms or very early in angiosperm history.The glycogen synthase kinase 3 (GSK3)/SHAGGY-like kinases are non-receptor serine/threonine protein kinases that are involved in a variety of signal transduction pathways [1]. In animals, they are involved in cell fate determination, in metazoan pattern formation, and in tumorigenesis [2-6]. In mammals, two enzymes, GSK3α and GSK3β, are involved in the regulation of glycogen metabolism [7], in stability of the cytoskeleton [8], and in numerous processes related to oncogenesis [9]. In Saccharomyces cerevisiae, the GSK3 homologs MCK1 and MDS1 play a role in chromosomal segregation [10], and in Schizosaccharomyces pombe the GSK3 homolog Skp1 regulates cytokinesis [11].In contrast to the two members of the GSK3 family found in mammals, plants appear to have a much larger set of divergent GSK3/SHAGGY-like kinase genes [12-28], with functions as nume
Review of the Application of Modern Cytogenetic Methods (FISH/GISH) to the Study of Reticulation (Polyploidy/Hybridisation)
Michael Chester,Andrew R. Leitch,Pamela S. Soltis,Douglas E. Soltis
Genes , 2010, DOI: 10.3390/genes1020166
Abstract: The convergence of distinct lineages upon interspecific hybridisation, including when accompanied by increases in ploidy (allopolyploidy), is a driving force in the origin of many plant species. In plant breeding too, both interspecific hybridisation and allopolyploidy are important because they facilitate introgression of alien DNA into breeding lines enabling the introduction of novel characters. Here we review how fluorescence in situ hybridisation (FISH) and genomic in situ hybridisation (GISH) have been applied to: 1) studies of interspecific hybridisation and polyploidy in nature, 2) analyses of phylogenetic relationships between species, 3) genetic mapping and 4) analysis of plant breeding materials. We also review how FISH is poised to take advantage of nextgeneration sequencing (NGS) technologies, helping the rapid characterisation of the repetitive fractions of a genome in natural populations and agricultural plants.
Rapid and accurate pyrosequencing of angiosperm plastid genomes
Michael J Moore, Amit Dhingra, Pamela S Soltis, Regina Shaw, William G Farmerie, Kevin M Folta, Douglas E Soltis
BMC Plant Biology , 2006, DOI: 10.1186/1471-2229-6-17
Abstract: More than 99.75% of each plastid genome was simultaneously obtained during two GS 20 sequence runs, to an average depth of coverage of 24.6× in Nandina and 17.3× in Platanus. The Nandina and Platanus plastid genomes shared essentially identical gene complements and possessed the typical angiosperm plastid structure and gene arrangement. To assess the accuracy of the GS 20 sequence, over 45 kilobases of sequence were generated for each genome using conventional sequencing. Overall error rates of 0.043% and 0.031% were observed in GS 20 sequence for Nandina and Platanus, respectively. More than 97% of all observed errors were associated with homopolymer runs, with ~60% of all errors associated with homopolymer runs of 5 or more nucleotides and ~50% of all errors associated with regions of extensive homopolymer runs. No substitution errors were present in either genome. Error rates were generally higher in the single-copy and noncoding regions of both plastid genomes relative to the inverted repeat and coding regions.Highly accurate and essentially complete sequence information was obtained for the Nandina and Platanus plastid genomes using the GS 20 System. More importantly, the high accuracy observed in the GS 20 plastid genome sequence was generated for a significant reduction in time and cost over traditional shotgun-based genome sequencing techniques, although with approximately half the coverage of previously reported GS 20 de novo genome sequence. The GS 20 should be broadly applicable to angiosperm plastid genome sequencing, and therefore promises to expand the scale of plant genetic and phylogenetic research dramatically.Plastid genome sequence information is of central importance to several fields of plant biology, including phylogenetics, molecular biology and evolution, and plastid genetic engineering [1-6]. The relatively small size of the plastid genome (~150 kb) has made its complete sequencing technically feasible since the mid-1980s, although limitatio
Similar patterns of rDNA evolution in synthetic and recently formed natural populations of Tragopogon (Asteraceae) allotetraploids
Hana Malinska, Jennifer A Tate, Roman Matyasek, Andrew R Leitch, Douglas E Soltis, Pamela S Soltis, Ales Kovarik
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-291
Abstract: Using Southern blot hybridization and fluorescent in situ hybridization (FISH), we analyzed copy numbers and distribution of these highly reiterated genes in seven lines of synthetic T. mirus (110 individuals) and four lines of synthetic T. miscellus (71 individuals). Variation among diploid parents accounted for most of the observed gene imbalances detected in F1 hybrids but cannot explain frequent deviations from repeat additivity seen in the allotetraploid lines. Polyploid lineages involving the same diploid parents differed in rDNA genotype, indicating that conditions immediately following genome doubling are crucial for rDNA changes. About 19% of the resynthesized allotetraploid individuals had equal rDNA contributions from the diploid parents, 74% were skewed towards either T. porrifolius or T. pratensis-type units, and only 7% had more rDNA copies of T. dubius-origin compared to the other two parents. Similar genotype frequencies were observed among natural populations. Despite directional reduction of units, the additivity of 35S rDNA locus number is maintained in 82% of the synthetic lines and in all natural allotetraploids.Uniparental reductions of homeologous rRNA gene copies occurred in both synthetic and natural populations of Tragopogon allopolyploids. The extent of these rDNA changes was generally higher in natural populations than in the synthetic lines. We hypothesize that locus-specific and chromosomal changes in early generations of allopolyploids may influence patterns of rDNA evolution in later generations.Chromosome counts suggest that between 30 and 100% of angiosperm species are polyploids [1], and Wood et al. [2] propose that 15% of angiosperm speciation events are associated with polyploidy whereas recent genomic studies of selected model and crop species have revealed that all plant genomes sequenced to date have signatures of one or more whole-genome duplications in their evolutionary history [3,4]. The success of newly formed angiosperm
Exploring Diversification and Genome Size Evolution in Extant Gymnosperms through Phylogenetic Synthesis
J. Gordon Burleigh,W. Brad Barbazuk,John M. Davis,Alison M. Morse,Pamela S. Soltis
Journal of Botany , 2012, DOI: 10.1155/2012/292857
Abstract: Gymnosperms, comprising cycads, Ginkgo, Gnetales, and conifers, represent one of the major groups of extant seed plants. Yet compared to angiosperms, little is known about the patterns of diversification and genome evolution in gymnosperms. We assembled a phylogenetic supermatrix containing over 4.5 million nucleotides from 739 gymnosperm taxa. Although 93.6% of the cells in the supermatrix are empty, the data reveal many strongly supported nodes that are generally consistent with previous phylogenetic analyses, including weak support for Gnetales sister to Pinaceae. A lineage through time plot suggests elevated rates of diversification within the last 100 million years, and there is evidence of shifts in diversification rates in several clades within cycads and conifers. A likelihood-based analysis of the evolution of genome size in 165 gymnosperms finds evidence for heterogeneous rates of genome size evolution due to an elevated rate in Pinus. 1. Introduction Recent advances in sequencing technology offer the possibility of identifying the genetic mechanisms that influence evolutionarily important characters and ultimately drive diversification. Within angiosperms, large-scale phylogenetic analyses have identified complex patterns of diversification (e.g., [1–3]), and numerous genomes are at least partially sequenced. Yet the other major clade of seed plants, the gymnosperms, have received far less attention, with few comprehensive studies of diversification and no sequenced genomes. Note that throughout this paper “gymnosperms” specifies only the approximately 1000 extant species within cycads, Ginkgo, Gnetales, and conifers. These comprise the Acrogymnospermae clade described by Cantino et al. [4]. Many gymnosperms have exceptionally large genomes (e.g., [5–7]), and this has hindered whole-genome sequencing projects, especially among economically important Pinus species. This large genome size is interesting because one suggested mechanism for rapid increases in genome size, polyploidy, is rare among gymnosperms [8]. Recent sequencing efforts have elucidated some of genomic characteristics associated with the large genome size in Pinus. Morse et al. [9] identified a large retrotransposon family in Pinus, that, with other retrotransposon families, accounts for much of the genomic complexity. Similarly, recent sequencing of 10 BAC (bacterial artificial chromosome) clones from Pinus taeda identified many conifer-specific LTR (long terminal repeat) retroelements [10]. These studies suggest that the large genome size may be caused by rapid expansion of
The Genomes of All Angiosperms: A Call for a Coordinated Global Census
David W. Galbraith,Jeffrey L. Bennetzen,Elizabeth A. Kellogg,J. Chris Pires,Pamela S. Soltis
Journal of Botany , 2011, DOI: 10.1155/2011/646198
Abstract: Recent advances in biological instrumentation and associated experimental technologies now permit an unprecedented efficiency and scale for the acquisition of genomic data, at ever-decreasing costs. Further advances, with accompanying decreases in cost, are expected in the very near term. It now becomes appropriate to discuss the best uses of these technologies in the context of the angiosperms. This white paper proposes a complete genomic census of the approximately 500,000 species of flowering plants, outlines the goals of this census and their value, and provides a road map towards achieving these goals in a timely manner. 1. Introduction The angiosperms (flowering plants) are believed to comprise somewhere around 360,000 species [1, 2] in 415 families [3]. An exact enumeration of the total number of existing species is impossible, because this includes a guess at the number of species that have not yet been discovered. If these were all found, a final total of somewhere between 400,000 and 500,000 species seems likely [4]. The enumeration and description of all angiosperm species takes on particular urgency because thousands of species become extinct every year, largely due to the impact of human activities. The risks accompanying the depletion of angiosperm biodiversity resources relate to ecosystem maintenance, to food production, for example, by the loss of wild relatives of crops that may have desirable alleles, and to drug discovery, given the observation that plant secondary products represent not simply the primary source of drugs and drug leads, but also the chemical inspiration for synthetic organic syntheses. These observations lead us to propose the timely establishment of a global network of coordinated research activities across the angiosperms with the objectives listed below. 2. Objectives The main objective is to establish vibrant and efficient communication among scientific experts in the disparate disciplines of taxonomy, systematics, cytometry, genomics, and bioinformatics, with the aim of planning a comprehensive molecular census of the angiosperms. This census is envisaged to start with measurement of nuclear genome sizes (C-value) for all angiosperms and would progress, over a five-year period, through sample survey sequencing to complete genome sequencing for a subset of these species. The census would start with planning activities preparative to coordinated research. Such planning would involve face-to-face meetings, the establishment of virtual communications, training courses and workshops, support for student internships,
Rapid Chromosome Evolution in Recently Formed Polyploids in Tragopogon (Asteraceae)
K. Yoong Lim, Douglas E. Soltis, Pamela S. Soltis, Jennifer Tate, Roman Matyasek, Hana Srubarova, Ales Kovarik, J. Chris Pires, Zhiyong Xiong, Andrew R. Leitch
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003353
Abstract: Background Polyploidy, frequently termed “whole genome duplication”, is a major force in the evolution of many eukaryotes. Indeed, most angiosperm species have undergone at least one round of polyploidy in their evolutionary history. Despite enormous progress in our understanding of many aspects of polyploidy, we essentially have no information about the role of chromosome divergence in the establishment of young polyploid populations. Here we investigate synthetic lines and natural populations of two recently and recurrently formed allotetraploids Tragopogon mirus and T. miscellus (formed within the past 80 years) to assess the role of aberrant meiosis in generating chromosomal/genomic diversity. That diversity is likely important in the formation, establishment and survival of polyploid populations and species. Methodology/Principal Findings Applications of fluorescence in situ hybridisation (FISH) to natural populations of T. mirus and T. miscellus suggest that chromosomal rearrangements and other chromosomal changes are common in both allotetraploids. We detected extensive chromosomal polymorphism between individuals and populations, including (i) plants monosomic and trisomic for particular chromosomes (perhaps indicating compensatory trisomy), (ii) intergenomic translocations and (iii) variable sizes and expression patterns of individual ribosomal DNA (rDNA) loci. We even observed karyotypic variation among sibling plants. Significantly, translocations, chromosome loss, and meiotic irregularities, including quadrivalent formation, were observed in synthetic (S0 and S1 generations) polyploid lines. Our results not only provide a mechanism for chromosomal variation in natural populations, but also indicate that chromosomal changes occur rapidly following polyploidisation. Conclusions/Significance These data shed new light on previous analyses of genome and transcriptome structures in de novo and establishing polyploid species. Crucially our results highlight the necessity of studying karyotypes in young (<150 years old) polyploid species and synthetic polyploids that resemble natural species. The data also provide insight into the mechanisms that perturb inheritance patterns of genetic markers in synthetic polyploids and populations of young natural polyploid species.
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