The Experts below are selected from a list of 918 Experts worldwide ranked by ideXlab platform
Douglas E Soltis - One of the best experts on this subject based on the ideXlab platform.
-
trajectories of homoeolog specific expression in allotetraploid Tragopogon castellanus populations of independent origins
Frontiers in Plant Science, 2021Co-Authors: Lucas J Boatwright, Pamela S. Soltis, Douglas E Soltis, Cheng Ting Yeh, Alfonso Susanna, Patrick S Schnable, William B BarbazukAbstract:Polyploidization can have a significant ecological and evolutionary impact by providing substantially more genetic material that may result in novel phenotypes upon which selection may act. While the effects of polyploidization are broadly reviewed across the plant tree of life, the reproducibility of these effects within naturally occurring, independently formed polyploids is poorly characterized. The flowering plant genus Tragopogon (Asteraceae) offers a rare glimpse into the intricacies of repeated allopolyploid formation with both nascent (< 90 years old) and more ancient (mesopolyploids) formations. Neo- and mesopolyploids in Tragopogon have formed repeatedly and have extant diploid progenitors that facilitate the comparison of genome evolution after polyploidization across a broad span of evolutionary time. Here, we examine four independently formed lineages of the mesopolyploid Tragopogon castellanus for homoeolog expression changes and fractionation after polyploidization. We show that expression changes are remarkably similar among these independently formed polyploid populations with large convergence among expressed loci, moderate convergence among loci lost, and stochastic silencing. We further compare and contrast these results for T. castellanus with two nascent Tragopogon allopolyploids. While homoeolog expression bias was balanced in both nascent polyploids and T. castellanus, the degree of additive expression was significantly different, with the mesopolyploid populations demonstrating more non-additive expression. We suggest that gene dosage and expression noise minimization may play a prominent role in regulating gene expression patterns immediately after allopolyploidization as well as deeper into time, and these patterns are conserved across independent polyploid lineages.
-
application of crispr cas9 to Tragopogon asteraceae an evolutionary model for the study of polyploidy
Molecular Ecology Resources, 2018Co-Authors: Pamela S. Soltis, Evgeny V Mavrodiev, Douglas E Soltis, Shengchen Shan, Zhengzhi Zhang, Bernard A Hauser, Bing YangAbstract:Tragopogon (Asteraceae) is an excellent natural system for studies of recent polyploidy. Development of an efficient CRISPR/Cas9-based genome editing platform in Tragopogon will facilitate novel studies of the genetic consequences of polyploidy. Here, we report our initial results of developing CRISPR/Cas9 in Tragopogon. We have established a feasible tissue culture and transformation protocol for Tragopogon. Through protoplast transient assays, use of the TragCRISPR system (i.e. the CRISPR/Cas9 system adapted for Tragopogon) was capable of introducing site-specific mutations in Tragopogon protoplasts. Agrobacterium-mediated transformation with Cas9-sgRNA constructs targeting the phytoene desaturase gene (TraPDS) was implemented in this model polyploid system. Sequencing of PCR amplicons from the target regions indicated simultaneous mutations of two alleles and four alleles of TraPDS in albino shoots from Tragopogon porrifolius (2x) and Tragopogon mirus (4x), respectively. The average proportions of successfully transformed calli with the albino phenotype were 87% and 78% in the diploid and polyploid, respectively. This appears to be the first demonstration of CRISPR/Cas9-based genome editing in any naturally formed neopolyploid system. Although a more efficient tissue culture system should be developed in Tragopogon, application of a robust CRISPR/Cas9 system will permit unique studies of biased fractionation, the gene-balance hypothesis and cytonuclear interactions in polyploids. In addition, the CRISPR/Cas9 platform enables investigations of those genes involved in phenotypic changes in polyploids and will also facilitate novel functional biology studies in Asteraceae. Our workflow provides a guide for applying CRISPR/Cas9 to other nongenetic model plant systems.
-
Sequencing results of TraPDS from regenerated shoots
2018Co-Authors: Shengchen Shan, Pamela S. Soltis, Evgeny V Mavrodiev, Douglas E Soltis, Zhengzhi Zhang, Bernard A Hauser, Bing YangAbstract:Genomic DNAs from regenerated shoots of Tragopogon porrifolius and Tragopogon mirus were extracted. Primers TraPDS-F1 and TraPDS-R2 were used to amplify the fragment covering the CRISPR/Cas9 target sites within the TraPDS gene. PCR amplicons were sequenced using primer TraPDS-F1
-
interpopulation hybridization generates meiotically stable rdna epigenetic variants in allotetraploid Tragopogon mirus
Plant Journal, 2016Co-Authors: Roman Matyasek, Pamela S. Soltis, Douglas E Soltis, Eva Dobesova, Dalibor Huska, Ivana Ježkova, Ales KovařikAbstract:Uniparental silencing of 35S rRNA genes (rDNA), known as nucleolar dominance (ND), is common in interspecific hybrids. Allotetraploid Tragopogon mirus composed of Tragopogon dubius (d) and Tragopogon porrifolius (p) genomes shows highly variable ND. To examine the molecular basis of such variation, we studied the genetic and epigenetic features of rDNA homeologs in several lines derived from recently and independently formed natural populations. Inbred lines derived from T. mirus with a dominant d-rDNA homeolog transmitted this expression pattern over generations, which may explain why it is prevalent among natural populations. In contrast, lines derived from the p-rDNA dominant progenitor were meiotically unstable, frequently switching to co-dominance. Interpopulation crosses between progenitors displaying reciprocal ND resulted in d-rDNA dominance, indicating immediate suppression of p-homeologs in F1 hybrids. Original p-rDNA dominance was not restored in later generations, even in those segregants that inherited the corresponding parental rDNA genotype, thus indicating the generation of additional p-rDNA and d-rDNA epigenetic variants. Despite preserved intergenic spacer (IGS) structure, they showed altered cytosine methylation and chromatin condensation patterns, and a correlation between expression, hypomethylation of RNA Pol I promoters and chromatin decondensation was apparent. Reversion of such epigenetic variants occurred rarely, resulting in co-dominance maintained in individuals with distinct genotypes. Generally, interpopulation crosses may generate epialleles that are not present in natural populations, underlying epigenetic dynamics in young allopolyploids. We hypothesize that highly expressed variants with distinct IGS features may induce heritable epigenetic reprogramming of the partner rDNA arrays, harmonizing the expression of thousands of genes in allopolyploids.
-
cytonuclear coordination is not immediate upon allopolyploid formation in Tragopogon miscellus asteraceae allopolyploids
PLOS ONE, 2015Co-Authors: Tina Sehrish, Pamela S. Soltis, Douglas E Soltis, Vaughan V Symonds, Jennifer A. TateAbstract:Allopolyploids, formed by hybridization and chromosome doubling, face the immediate challenge of having duplicated nuclear genomes that interact with the haploid and maternally inherited cytoplasmic (plastid and mitochondrial) genomes. Most of our knowledge of the genomic consequences of allopolyploidy has focused on the fate of the duplicated nuclear genes without regard to their potential interactions with cytoplasmic genomes. As a step toward understanding the fates of nuclear-encoded subunits that are plastid-targeted, here we examine the retention and expression of the gene encoding the small subunit of Ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco; rbcS) in multiple populations of allotetraploid Tragopogon miscellus (Asteraceae). These polyploids formed recently (~80 years ago) and repeatedly from T. dubius and T. pratensis in the northwestern United States. Examination of 79 T. miscellus individuals from 10 natural populations, as well as 25 synthetic allotetraploids, including reciprocally formed plants, revealed a low percentage of naturally occurring individuals that show a bias in either gene (homeolog) loss (12%) or expression (16%), usually toward maintaining the maternal nuclear copy of rbcS. For individuals showing loss, seven retained the maternally derived rbcS homeolog only, while three had the paternally derived copy. All of the synthetic polyploid individuals examined (S0 and S1 generations) retained and expressed both parental homeologs. These results demonstrate that cytonuclear coordination does not happen immediately upon polyploid formation in Tragopogon miscellus.
Pamela S. Soltis - One of the best experts on this subject based on the ideXlab platform.
-
trajectories of homoeolog specific expression in allotetraploid Tragopogon castellanus populations of independent origins
Frontiers in Plant Science, 2021Co-Authors: Lucas J Boatwright, Pamela S. Soltis, Douglas E Soltis, Cheng Ting Yeh, Alfonso Susanna, Patrick S Schnable, William B BarbazukAbstract:Polyploidization can have a significant ecological and evolutionary impact by providing substantially more genetic material that may result in novel phenotypes upon which selection may act. While the effects of polyploidization are broadly reviewed across the plant tree of life, the reproducibility of these effects within naturally occurring, independently formed polyploids is poorly characterized. The flowering plant genus Tragopogon (Asteraceae) offers a rare glimpse into the intricacies of repeated allopolyploid formation with both nascent (< 90 years old) and more ancient (mesopolyploids) formations. Neo- and mesopolyploids in Tragopogon have formed repeatedly and have extant diploid progenitors that facilitate the comparison of genome evolution after polyploidization across a broad span of evolutionary time. Here, we examine four independently formed lineages of the mesopolyploid Tragopogon castellanus for homoeolog expression changes and fractionation after polyploidization. We show that expression changes are remarkably similar among these independently formed polyploid populations with large convergence among expressed loci, moderate convergence among loci lost, and stochastic silencing. We further compare and contrast these results for T. castellanus with two nascent Tragopogon allopolyploids. While homoeolog expression bias was balanced in both nascent polyploids and T. castellanus, the degree of additive expression was significantly different, with the mesopolyploid populations demonstrating more non-additive expression. We suggest that gene dosage and expression noise minimization may play a prominent role in regulating gene expression patterns immediately after allopolyploidization as well as deeper into time, and these patterns are conserved across independent polyploid lineages.
-
application of crispr cas9 to Tragopogon asteraceae an evolutionary model for the study of polyploidy
Molecular Ecology Resources, 2018Co-Authors: Pamela S. Soltis, Evgeny V Mavrodiev, Douglas E Soltis, Shengchen Shan, Zhengzhi Zhang, Bernard A Hauser, Bing YangAbstract:Tragopogon (Asteraceae) is an excellent natural system for studies of recent polyploidy. Development of an efficient CRISPR/Cas9-based genome editing platform in Tragopogon will facilitate novel studies of the genetic consequences of polyploidy. Here, we report our initial results of developing CRISPR/Cas9 in Tragopogon. We have established a feasible tissue culture and transformation protocol for Tragopogon. Through protoplast transient assays, use of the TragCRISPR system (i.e. the CRISPR/Cas9 system adapted for Tragopogon) was capable of introducing site-specific mutations in Tragopogon protoplasts. Agrobacterium-mediated transformation with Cas9-sgRNA constructs targeting the phytoene desaturase gene (TraPDS) was implemented in this model polyploid system. Sequencing of PCR amplicons from the target regions indicated simultaneous mutations of two alleles and four alleles of TraPDS in albino shoots from Tragopogon porrifolius (2x) and Tragopogon mirus (4x), respectively. The average proportions of successfully transformed calli with the albino phenotype were 87% and 78% in the diploid and polyploid, respectively. This appears to be the first demonstration of CRISPR/Cas9-based genome editing in any naturally formed neopolyploid system. Although a more efficient tissue culture system should be developed in Tragopogon, application of a robust CRISPR/Cas9 system will permit unique studies of biased fractionation, the gene-balance hypothesis and cytonuclear interactions in polyploids. In addition, the CRISPR/Cas9 platform enables investigations of those genes involved in phenotypic changes in polyploids and will also facilitate novel functional biology studies in Asteraceae. Our workflow provides a guide for applying CRISPR/Cas9 to other nongenetic model plant systems.
-
Sequencing results of TraPDS from regenerated shoots
2018Co-Authors: Shengchen Shan, Pamela S. Soltis, Evgeny V Mavrodiev, Douglas E Soltis, Zhengzhi Zhang, Bernard A Hauser, Bing YangAbstract:Genomic DNAs from regenerated shoots of Tragopogon porrifolius and Tragopogon mirus were extracted. Primers TraPDS-F1 and TraPDS-R2 were used to amplify the fragment covering the CRISPR/Cas9 target sites within the TraPDS gene. PCR amplicons were sequenced using primer TraPDS-F1
-
interpopulation hybridization generates meiotically stable rdna epigenetic variants in allotetraploid Tragopogon mirus
Plant Journal, 2016Co-Authors: Roman Matyasek, Pamela S. Soltis, Douglas E Soltis, Eva Dobesova, Dalibor Huska, Ivana Ježkova, Ales KovařikAbstract:Uniparental silencing of 35S rRNA genes (rDNA), known as nucleolar dominance (ND), is common in interspecific hybrids. Allotetraploid Tragopogon mirus composed of Tragopogon dubius (d) and Tragopogon porrifolius (p) genomes shows highly variable ND. To examine the molecular basis of such variation, we studied the genetic and epigenetic features of rDNA homeologs in several lines derived from recently and independently formed natural populations. Inbred lines derived from T. mirus with a dominant d-rDNA homeolog transmitted this expression pattern over generations, which may explain why it is prevalent among natural populations. In contrast, lines derived from the p-rDNA dominant progenitor were meiotically unstable, frequently switching to co-dominance. Interpopulation crosses between progenitors displaying reciprocal ND resulted in d-rDNA dominance, indicating immediate suppression of p-homeologs in F1 hybrids. Original p-rDNA dominance was not restored in later generations, even in those segregants that inherited the corresponding parental rDNA genotype, thus indicating the generation of additional p-rDNA and d-rDNA epigenetic variants. Despite preserved intergenic spacer (IGS) structure, they showed altered cytosine methylation and chromatin condensation patterns, and a correlation between expression, hypomethylation of RNA Pol I promoters and chromatin decondensation was apparent. Reversion of such epigenetic variants occurred rarely, resulting in co-dominance maintained in individuals with distinct genotypes. Generally, interpopulation crosses may generate epialleles that are not present in natural populations, underlying epigenetic dynamics in young allopolyploids. We hypothesize that highly expressed variants with distinct IGS features may induce heritable epigenetic reprogramming of the partner rDNA arrays, harmonizing the expression of thousands of genes in allopolyploids.
-
cytonuclear coordination is not immediate upon allopolyploid formation in Tragopogon miscellus asteraceae allopolyploids
PLOS ONE, 2015Co-Authors: Tina Sehrish, Pamela S. Soltis, Douglas E Soltis, Vaughan V Symonds, Jennifer A. TateAbstract:Allopolyploids, formed by hybridization and chromosome doubling, face the immediate challenge of having duplicated nuclear genomes that interact with the haploid and maternally inherited cytoplasmic (plastid and mitochondrial) genomes. Most of our knowledge of the genomic consequences of allopolyploidy has focused on the fate of the duplicated nuclear genes without regard to their potential interactions with cytoplasmic genomes. As a step toward understanding the fates of nuclear-encoded subunits that are plastid-targeted, here we examine the retention and expression of the gene encoding the small subunit of Ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco; rbcS) in multiple populations of allotetraploid Tragopogon miscellus (Asteraceae). These polyploids formed recently (~80 years ago) and repeatedly from T. dubius and T. pratensis in the northwestern United States. Examination of 79 T. miscellus individuals from 10 natural populations, as well as 25 synthetic allotetraploids, including reciprocally formed plants, revealed a low percentage of naturally occurring individuals that show a bias in either gene (homeolog) loss (12%) or expression (16%), usually toward maintaining the maternal nuclear copy of rbcS. For individuals showing loss, seven retained the maternally derived rbcS homeolog only, while three had the paternally derived copy. All of the synthetic polyploid individuals examined (S0 and S1 generations) retained and expressed both parental homeologs. These results demonstrate that cytonuclear coordination does not happen immediately upon polyploid formation in Tragopogon miscellus.
Evgeny V Mavrodiev - One of the best experts on this subject based on the ideXlab platform.
-
application of crispr cas9 to Tragopogon asteraceae an evolutionary model for the study of polyploidy
Molecular Ecology Resources, 2018Co-Authors: Pamela S. Soltis, Evgeny V Mavrodiev, Douglas E Soltis, Shengchen Shan, Zhengzhi Zhang, Bernard A Hauser, Bing YangAbstract:Tragopogon (Asteraceae) is an excellent natural system for studies of recent polyploidy. Development of an efficient CRISPR/Cas9-based genome editing platform in Tragopogon will facilitate novel studies of the genetic consequences of polyploidy. Here, we report our initial results of developing CRISPR/Cas9 in Tragopogon. We have established a feasible tissue culture and transformation protocol for Tragopogon. Through protoplast transient assays, use of the TragCRISPR system (i.e. the CRISPR/Cas9 system adapted for Tragopogon) was capable of introducing site-specific mutations in Tragopogon protoplasts. Agrobacterium-mediated transformation with Cas9-sgRNA constructs targeting the phytoene desaturase gene (TraPDS) was implemented in this model polyploid system. Sequencing of PCR amplicons from the target regions indicated simultaneous mutations of two alleles and four alleles of TraPDS in albino shoots from Tragopogon porrifolius (2x) and Tragopogon mirus (4x), respectively. The average proportions of successfully transformed calli with the albino phenotype were 87% and 78% in the diploid and polyploid, respectively. This appears to be the first demonstration of CRISPR/Cas9-based genome editing in any naturally formed neopolyploid system. Although a more efficient tissue culture system should be developed in Tragopogon, application of a robust CRISPR/Cas9 system will permit unique studies of biased fractionation, the gene-balance hypothesis and cytonuclear interactions in polyploids. In addition, the CRISPR/Cas9 platform enables investigations of those genes involved in phenotypic changes in polyploids and will also facilitate novel functional biology studies in Asteraceae. Our workflow provides a guide for applying CRISPR/Cas9 to other nongenetic model plant systems.
-
Sequencing results of TraPDS from regenerated shoots
2018Co-Authors: Shengchen Shan, Pamela S. Soltis, Evgeny V Mavrodiev, Douglas E Soltis, Zhengzhi Zhang, Bernard A Hauser, Bing YangAbstract:Genomic DNAs from regenerated shoots of Tragopogon porrifolius and Tragopogon mirus were extracted. Primers TraPDS-F1 and TraPDS-R2 were used to amplify the fragment covering the CRISPR/Cas9 target sites within the TraPDS gene. PCR amplicons were sequenced using primer TraPDS-F1
-
multiple origins and chromosomal novelty in the allotetraploid Tragopogon castellanus asteraceae
New Phytologist, 2015Co-Authors: Evgeny V Mavrodiev, Victor N Suarezsantiago, Michael Chester, Riccardo M Baldini, Alfonso Susanna, Clayton J Visger, Roseana Rodriguez, Pamela S. SoltisAbstract:Summary Tragopogon includes two classic examples of recently formed allopolyploid species in North America: T. mirus and T. miscellus. Older Tragopogon allotetraploids from Eurasia offer ideal taxa for comparing the longer term outcomes of allopolyploidy. To help resolve the ancestry of one of these older polyploids, phylogenetic analyses of multiple populations of the allotetraploid T. castellanus (2n = 24) and its putative diploid parents, T. crocifolius and T. lamottei, were conducted using sequences from nuclear (internal transcribed spacer, ITS; and alcohol dehydrogenase 1A, Adh) and plastid (trnT-trnL spacer, trnL intron, trnL-trnF spacer and rpl16 intron) loci. Fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used to investigate the chromosomal constitution of T. castellanus. Our data confirm that the widely distributed T. crocifolius and the Iberian endemic, T. lamottei, are the diploid parents of T. castellanus, and that this polyploid formed at least three times. One group of populations of T. castellanus is distinct in exhibiting two pairs of rearranged chromosomes. These data suggest that some of the chromosomal variants that originate in young polyploids (here, an intergenomic translocation) may become fixed in populations, contributing to novelty in older polyploid lineages. The geographical distributions of the allopolyploids and parents are also complex, with allotetraploid populations being disjunct from one or both of the most closely related diploid parental populations.
-
a cryptic taxon rather than a hybrid species of Tragopogon asteraceae from the czech republic
Kew Bulletin, 2013Co-Authors: Evgeny V Mavrodiev, Douglas E Soltis, Frantisek Krahulec, Pamela S. SoltisAbstract:Tragopogon ×mirabilis Rouy is described as a diploid hybrid between T. porrifolius and T. pratensis. A population of T. ×mirabilis from Central Bohemia, Czech Republic, was recently investigated and, unlike previous reports of T. ×mirabilis, was found to be highly fertile. This fertile diploid hybrid population was considered to represent an alternative evolutionary pathway to polyploidy in Tragopogon. To determine the parentage of the plants from Bohemia, we investigated 12 samples of T. ×mirabilis with ITS, ETS, LFY and plastid (rpL16 gene, intron 1, tRNA-Leu (trnL) gene, intron, trnL-trnF intergenic spacer, psbA-trnH intergenic spacer, and trnG-trnT intergenic spacer) sequence data. None of the Bohemian plants have sequences that are consistent with a hybrid origin between T. porrifolius (incl. T. australis) and T. pratensis. Our data suggest that this fertile population of “T. ×mirabilis” may represent an unrecognised diploid species from the Angustissimi clade sensu Mavrodiev et al. (Int. J. Pl. Sci. 164: 1 – 19, 2005), a clade with a centre of distribution in the Caucasus, and hybrids of this unknown species with T. orientalis or T. hayekii (= T. orientalis L. var. hayekii Soo), a species closely related to T. pratensis and native to Bohemia. The Bohemian population of “Tragopogon ×mirabilis” clearly requires more investigation, but based on our data it does not appear to represent T. porrifolius × T. pratensis.
-
rapid diversification of Tragopogon and ecological associates in eurasia
Journal of Evolutionary Biology, 2012Co-Authors: Charles D Bell, Pamela S. Soltis, Evgeny V Mavrodiev, Douglas E Soltis, Andre Calaminus, Dirk C Albach, Nico Cellinese, Nuria GarciajacasAbstract:Tragopogon comprises approximately 150 described species distributed throughout Eurasia from Ireland and the UK to India and China with a few species in North Africa. Most of the species diversity is found in Eastern Europe to Western Asia. Previous phylogenetic analyses identified several major clades, generally corresponding to recognized taxonomic sections, although relationships both among these clades and among species within clades remain largely unresolved. These patterns are consistent with rapid diversification following the origin of Tragopogon, and this study addresses the timing and rate of diversification in Tragopogon. Using BEAST to simultaneously estimate a phylogeny and divergence times, we estimate the age of a major split and subsequent rapid divergence within Tragopogon to be ~2.6 Ma (and 1.7‐5.4 Ma using various clock estimates). Based on the age estimates obtained with BEAST (HPD 1.7‐5.4 Ma) for the origin of crown group Tragopogon and 200 estimated species (to accommodate a large number of cryptic species), the diversification rate of Tragopogon is approximately 0.84‐2.71 species/Myr for the crown group, assuming low levels of extinction. This estimate is comparable in rate to a rapid Eurasian radiation in Dianthus (0.66‐3.89 species/Myr), which occurs in the same or similar habitats. Using available data, we show that subclades of various plant taxa that occur in the same semi-arid habitats of Eurasia also represent rapid radiations occurring during roughly the same window of time (1.7‐5.4 Ma), suggesting similar causal events. However, not all species-rich plant genera from the same habitats diverged at the same time, or at the same tempo. Radiations of several other clades in this same habitat (e.g. Campanula, Knautia, Scabiosa) occurred at earlier dates (45‐4.28 Ma). Existing phylogenetic data and diversification estimates therefore indicate that, although some elements of these semi-arid communities radiated during the Plio-Pleistocene period, other clades sharing the same habitat appear to have diversified earlier.
Jennifer A. Tate - One of the best experts on this subject based on the ideXlab platform.
-
cytonuclear coordination is not immediate upon allopolyploid formation in Tragopogon miscellus asteraceae allopolyploids
PLOS ONE, 2015Co-Authors: Tina Sehrish, Pamela S. Soltis, Douglas E Soltis, Vaughan V Symonds, Jennifer A. TateAbstract:Allopolyploids, formed by hybridization and chromosome doubling, face the immediate challenge of having duplicated nuclear genomes that interact with the haploid and maternally inherited cytoplasmic (plastid and mitochondrial) genomes. Most of our knowledge of the genomic consequences of allopolyploidy has focused on the fate of the duplicated nuclear genes without regard to their potential interactions with cytoplasmic genomes. As a step toward understanding the fates of nuclear-encoded subunits that are plastid-targeted, here we examine the retention and expression of the gene encoding the small subunit of Ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco; rbcS) in multiple populations of allotetraploid Tragopogon miscellus (Asteraceae). These polyploids formed recently (~80 years ago) and repeatedly from T. dubius and T. pratensis in the northwestern United States. Examination of 79 T. miscellus individuals from 10 natural populations, as well as 25 synthetic allotetraploids, including reciprocally formed plants, revealed a low percentage of naturally occurring individuals that show a bias in either gene (homeolog) loss (12%) or expression (16%), usually toward maintaining the maternal nuclear copy of rbcS. For individuals showing loss, seven retained the maternally derived rbcS homeolog only, while three had the paternally derived copy. All of the synthetic polyploid individuals examined (S0 and S1 generations) retained and expressed both parental homeologs. These results demonstrate that cytonuclear coordination does not happen immediately upon polyploid formation in Tragopogon miscellus.
-
gene silencing via dna methylation in naturally occurring Tragopogon miscellus asteraceae allopolyploids
BMC Genomics, 2014Co-Authors: Tina Sehrish, Pamela S. Soltis, Douglas E Soltis, Vaughan V Symonds, Jennifer A. TateAbstract:Hybridization coupled with whole-genome duplication (allopolyploidy) leads to a variety of genetic and epigenetic modifications in the resultant merged genomes. In particular, gene loss and gene silencing are commonly observed post-polyploidization. Here, we investigated DNA methylation as a potential mechanism for gene silencing in Tragopogon miscellus (Asteraceae), a recent and recurrently formed allopolyploid. This species, which also exhibits extensive gene loss, was formed from the diploids T. dubius and T. pratensis. Comparative bisulfite sequencing revealed CG methylation of parental homeologs for three loci (S2, S18 and TDF-44) that were previously identified as silenced in T. miscellus individuals relative to the diploid progenitors. One other locus (S3) examined did not show methylation, indicating that other transcriptional and post-transcriptional mechanisms are likely responsible for silencing that homeologous locus. These results indicate that Tragopogon miscellus allopolyploids employ diverse mechanisms, including DNA methylation, to respond to the potential shock of genome merger and doubling.
-
similar patterns of rdna evolution in synthetic and recently formed natural populations of Tragopogon asteraceae allotetraploids
BMC Evolutionary Biology, 2010Co-Authors: Hana Malinska, Pamela S. Soltis, Jennifer A. Tate, Andrew R. Leitch, Roman Matyasek, Douglas E Soltis, Ales KovarikAbstract:Tragopogon mirus and T. miscellus are allotetraploids (2n = 24) that formed repeatedly during the past 80 years in eastern Washington and adjacent Idaho (USA) following the introduction of the diploids T. dubius, T. porrifolius, and T. pratensis (2n = 12) from Europe. In most natural populations of T. mirus and T. miscellus, there are far fewer 35S rRNA genes (rDNA) of T. dubius than there are of the other diploid parent (T. porrifolius or T. pratensis). We studied the inheritance of parental rDNA loci in allotetraploids resynthesized from diploid accessions. We investigate the dynamics and directionality of these rDNA losses, as well as the contribution of gene copy number variation in the parental diploids to rDNA variation in the derived tetraploids. 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.
-
rapid chromosome evolution in recently formed polyploids in Tragopogon asteraceae
PLOS ONE, 2008Co-Authors: Yoong K Lim, Pamela S. Soltis, Jennifer A. Tate, Roman Matyasek, Hana Srubarova, Ales Kovarik, Chris J Pires, Zhiyong Xiong, Andrew R. LeitchAbstract: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.
-
evolution and expression of homeologous loci in Tragopogon miscellus asteraceae a recent and reciprocally formed allopolyploid
Genetics, 2006Co-Authors: Jennifer A. Tate, Pamela S. Soltis, Jin Koh, Annecathrine Scheen, Candace A Gilbert, David Lefkowitz, Jeffrey Z Chen, Douglas E SoltisAbstract:On both recent and ancient time scales, polyploidy (genome doubling) has been a significant evolutionary force in plants. Here, we examined multiple individuals from reciprocally formed populations of Tragopogon miscellus, an allotetraploid that formed repeatedly within the last 80 years from the diploids T. dubius and T. pratensis. Using cDNA–AFLPs followed by genomic and cDNA cleaved amplified polymorphic sequence (CAPS) analyses, we found differences in the evolution and expression of homeologous loci in T. miscellus. Fragment variation within T. miscellus, possibly attributable to reciprocal formation, comprised 0.6% of the cDNA–AFLP bands. Genomic and cDNA CAPS analyses of 10 candidate genes revealed that only one “transcript-derived fragment” (TDF44) showed differential expression of parental homeologs in T. miscellus; the T. pratensis homeolog was preferentially expressed by most polyploids in both populations. Most of the cDNA–AFLP polymorphisms apparently resulted from loss of parental fragments in the polyploids. Importantly, changes at the genomic level have occurred stochastically among individuals within the independently formed populations. Synthetic F1 hybrids between putative diploid progenitors are additive of their parental genomes, suggesting that polyploidization rather than hybridization induces genomic changes in Tragopogon.
Shengchen Shan - One of the best experts on this subject based on the ideXlab platform.
-
application of crispr cas9 to Tragopogon asteraceae an evolutionary model for the study of polyploidy
Molecular Ecology Resources, 2018Co-Authors: Pamela S. Soltis, Evgeny V Mavrodiev, Douglas E Soltis, Shengchen Shan, Zhengzhi Zhang, Bernard A Hauser, Bing YangAbstract:Tragopogon (Asteraceae) is an excellent natural system for studies of recent polyploidy. Development of an efficient CRISPR/Cas9-based genome editing platform in Tragopogon will facilitate novel studies of the genetic consequences of polyploidy. Here, we report our initial results of developing CRISPR/Cas9 in Tragopogon. We have established a feasible tissue culture and transformation protocol for Tragopogon. Through protoplast transient assays, use of the TragCRISPR system (i.e. the CRISPR/Cas9 system adapted for Tragopogon) was capable of introducing site-specific mutations in Tragopogon protoplasts. Agrobacterium-mediated transformation with Cas9-sgRNA constructs targeting the phytoene desaturase gene (TraPDS) was implemented in this model polyploid system. Sequencing of PCR amplicons from the target regions indicated simultaneous mutations of two alleles and four alleles of TraPDS in albino shoots from Tragopogon porrifolius (2x) and Tragopogon mirus (4x), respectively. The average proportions of successfully transformed calli with the albino phenotype were 87% and 78% in the diploid and polyploid, respectively. This appears to be the first demonstration of CRISPR/Cas9-based genome editing in any naturally formed neopolyploid system. Although a more efficient tissue culture system should be developed in Tragopogon, application of a robust CRISPR/Cas9 system will permit unique studies of biased fractionation, the gene-balance hypothesis and cytonuclear interactions in polyploids. In addition, the CRISPR/Cas9 platform enables investigations of those genes involved in phenotypic changes in polyploids and will also facilitate novel functional biology studies in Asteraceae. Our workflow provides a guide for applying CRISPR/Cas9 to other nongenetic model plant systems.
-
Sequencing results of TraPDS from regenerated shoots
2018Co-Authors: Shengchen Shan, Pamela S. Soltis, Evgeny V Mavrodiev, Douglas E Soltis, Zhengzhi Zhang, Bernard A Hauser, Bing YangAbstract:Genomic DNAs from regenerated shoots of Tragopogon porrifolius and Tragopogon mirus were extracted. Primers TraPDS-F1 and TraPDS-R2 were used to amplify the fragment covering the CRISPR/Cas9 target sites within the TraPDS gene. PCR amplicons were sequenced using primer TraPDS-F1
