oalib

Publish in OALib Journal

ISSN: 2333-9721

APC: Only $99

Submit

Any time

2019 ( 51 )

2018 ( 313 )

2017 ( 279 )

2016 ( 392 )

Custom range...

Search Results: 1 - 10 of 172353 matches for " Douglas E Soltis "
All listed articles are free for downloading (OA Articles)
Page 1 /172353
Display every page Item
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
Abstract:
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.
Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms
J Gordon Burleigh, Khidir W Hilu, Douglas E Soltis
BMC Evolutionary Biology , 2009, DOI: 10.1186/1471-2148-9-61
Abstract: We performed maximum likelihood bootstrap analyses of the complete, 3-gene 567-taxon data matrix and the incomplete, 5-gene 567-taxon data matrix. Although the 5-gene matrix has more missing data (27.5%) than the 3-gene data matrix (2.9%), the 5-gene analysis resulted in higher levels of bootstrap support. Within the 567-taxon tree, the increase in support is most evident for relationships among the 170 taxa for which both matK and 26S rDNA sequences were added, and there is little gain in support for relationships among the 119 taxa having neither matK nor 26S rDNA sequences. The 5-gene analysis also places the enigmatic Hydrostachys in Lamiales (BS = 97%) rather than in Cornales (BS = 100% in 3-gene analysis). The placement of Hydrostachys in Lamiales is unprecedented in molecular analyses, but it is consistent with embryological and morphological data.Adding available, and often incomplete, sets of sequences to existing data sets can be a fast and inexpensive way to increase support for phylogenetic relationships and produce novel and credible new phylogenetic hypotheses.Molecular data have had an enormous impact on angiosperm phylogenetic hypotheses (e.g. [1-5]), and the abundance of new sequence data provides the potential for further resolving angiosperm relationships. Still, molecular phylogenetic studies across all angiosperms have utilized only a small fraction of the available sequence data. While GenBank currently contains over 1.7 million core nucleotide sequences from angiosperms, with over 160,000 of these being from often phylogenetically useful plastid loci [6], few phylogenetic analyses of angiosperms have included more than a thousand sequences. We examine whether augmenting existing plant data matrices with incomplete data assembled from publicly available sources can enhance the understanding of the backbone phylogenetic relationships across angiosperms.The sampling strategies of phylogenetic studies across angiosperms demonstrate a tradeoff betw
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
Bee Threat Elicits Alarm Call in African Elephants
Lucy E. King,Joseph Soltis,Iain Douglas-Hamilton,Anne Savage,Fritz Vollrath
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0010346
Abstract: Unlike the smaller and more vulnerable mammals, African elephants have relatively few predators that threaten their survival. The sound of disturbed African honeybees Apis meliffera scutellata causes African elephants Loxodonta africana to retreat and produce warning vocalizations that lead other elephants to join the flight. In our first experiment, audio playbacks of bee sounds induced elephants to retreat and elicited more head-shaking and dusting, reactive behaviors that may prevent bee stings, compared to white noise control playbacks. Most importantly, elephants produced distinctive “rumble” vocalizations in response to bee sounds. These rumbles exhibited an upward shift in the second formant location, which implies active vocal tract modulation, compared to rumbles made in response to white noise playbacks. In a second experiment, audio playbacks of these rumbles produced in response to bees elicited increased headshaking, and further and faster retreat behavior in other elephants, compared to control rumble playbacks with lower second formant frequencies. These responses to the bee rumble stimuli occurred in the absence of any bees or bee sounds. This suggests that these elephant rumbles may function as referential signals, in which a formant frequency shift alerts nearby elephants about an external threat, in this case, the threat of bees.
Phylogeographic analysis reveals significant spatial genetic structure of Incarvillea sinensis as a product of mountain building
Shaotian Chen, Yaowu Xing, Tao Su, Zhekun Zhou, Emeritus David L Dilcher, Douglas E Soltis
BMC Plant Biology , 2012, DOI: 10.1186/1471-2229-12-58
Abstract: A total of 16 haplotypes was identified, and significant genetic differentiation was revealed (GST =0.843, NST?=?0.975, P?<?0.05). The survey detected two highly divergent cpDNA lineages connected by a deep gap with allopatric distributions: the southern lineage with higher genetic diversity and differentiation in the eastern Qinghai-Tibet Plateau, and the northern lineage in the region outside the Qinghai-Tibet Plateau. The divergence between these two lineages was estimated at 4.4 MYA. A correlation between the genetic and the geographic distances indicates that genetic drift was more influential than gene flow in the northern clade with lower diversity and divergence. However, a scenario of regional equilibrium between gene flow and drift was shown for the southern clade. The feature of spatial distribution of the genetic diversity of the southern lineage possibly indicated that allopatric fragmentation was dominant in the collections from the eastern Qinghai-Tibet Plateau.The results revealed that the uplift of the Qinghai-Tibet Plateau likely resulted in the significant divergence between the lineage in the eastern Qinghai-Tibet Plateau and the other one outside this area. The diverse niches in the eastern Qinghai-Tibet Plateau created a wide spectrum of habitats to accumulate and accommodate new mutations. The features of genetic diversity of populations outside the eastern Qinghai-Tibet Plateau seemed to reveal the imprints of extinction during the Glacial and the interglacial and postglacial recolonization. Our study is a typical case of the significance of the uplift of the Qinghai-Tibet Plateau and the Quaternary Glacial in spatial genetic structure of eastern Asian plants, and sheds new light on the evolution of biodiversity in the Qinghai-Tibet Plateau at the intraspecies level.Patterns of genetic and geographical structure in natural populations have been strongly influenced not only by intrinsic factors, such as life histories and ecological traits, bu
Page 1 /172353
Display every page Item


Home
Copyright © 2008-2017 Open Access Library. All rights reserved.