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Tripal Developer Toolkit [article]

Bradford Condon, Abdullah Almsaeed, Joe West, Ming Chen, Margaret Staton
2018 bioRxiv   pre-print
Tripal is an open-source biological community database construction toolkit utilizing the content management system Drupal. Tripal is used to make biological, genetic and genomic data more discoverable, shareable, searchable, and standardized. As funding for community level genomics databases declines, Tripal's open source codebase provides a means for sites to be built and maintained with a minimal investment in staff and new development. Tripal is ultimately as strong as the community of
more » ... and developers that use it. We present a set of developer tools that will make building and maintaining Tripal 3 sites easier for new and returning users. These tools break down barriers to entry such as setting up developer and testing environments, acquiring and loading test datasets, working with controlled vocabulary terms, and writing new Drupal classes.
doi:10.1101/328641 fatcat:rmw6hhfc3fdefidqtuou6ddrx4

The Ontology of Process Philosophy in Follett's Administrative Theory

Margaret Stout, Carrie M. Staton
2011 Administrative Theory & Praxis  
Margaret Stout is an assistant professor of public administration at West Virginia University.  ...  Staton is a student in the Master of Public Administration program at West Virginia University.  ... 
doi:10.2753/atp1084-1806330206 fatcat:yyorm2vqvnh4ze7lgfeqc4oak4

Genomics of Fagaceae

Antoine Kremer, Albert G. Abbott, John E. Carlson, Paul S. Manos, Christophe Plomion, Paul Sisco, Margaret E. Staton, Saneyoshi Ueno, Giovanni G. Vendramin
2012 Tree Genetics & Genomes  
An overview of recent achievements and development of genomic resources in the Fagaceae is provided, with major emphasis on the genera Castanea and Quercus. The Fagaceae is a large plant family comprising more than 900 species belonging to 8-10 genera. Using a wide range of molecular markers, population genetics and gene diversity surveys were the focus of many studies during the past 20 years. This work set the stage for investigations in genomics beginning in the early 1990s and facilitated
more » ... e application of genetic and quantitative trait loci mapping approaches. Transferability of markers across species and comparative mapping have indicated tight macrosynteny between Quercus and Castanea. Omic technologies were more recently developed and the corresponding resources are accessible via electronic and physical repositories (expressed sequence tag sequences, single-nucleotide polymorphisms, candidate genes, cDNA clones, bacterial artificial chromosome (BAC) libraries) that have been installed in North America and Europe. BAC libraries and physical maps were also constructed in Castanea and Quercus and provide the necessary resources for full nuclear genome sequencing projects that are currently under way in Castanea mollissima (Chinese chestnut) and Quercus robur (pedunculate oak). Communicated by T. Drudge A contribution to the Special Issue "The genomes of the giants: a walk through the forest of tree genomes" A. Kremer :
doi:10.1007/s11295-012-0498-3 fatcat:cf3aejq4g5hnjmi246ry5l26i4

Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species

Miriam Payá-Milans, James W Olmstead, Gerardo Nunez, Timothy A Rinehart, Margaret Staton
2018 GigaScience  
The usual analysis of RNA sequencing (RNA-seq) reads is based on an existing reference genome and annotated gene models. However, when a reference for the sequenced species is not available, alternatives include using a reference genome from a related species or reconstructing transcript sequences with de novo assembly. In addition, researchers are faced with many options for RNA-seq data processing and limited information on how their decisions will impact the final outcome. Using both a
more » ... d and polyploid species with a distant reference genome, we have tested the influence of different tools at various steps of a typical RNA-seq analysis workflow on the recovery of useful processed data available for downstream analysis. At the preprocessing step, we found error correction has a strong influence on de novo assembly but not on mapping results. After trimming, a greater percentage of reads could be used in downstream analysis by selecting gentle quality trimming performed with Skewer instead of strict quality trimming with Trimmomatic. This availability of reads correlated with size, quality, and completeness of de novo assemblies and with number of mapped reads. When selecting a reference genome from a related species to map reads, outcome was significantly improved when using mapping software tolerant of greater sequence divergence, such as Stampy or GSNAP. The selection of bioinformatic software tools for RNA-seq data analysis can maximize quality parameters on de novo assemblies and availability of reads in downstream analysis.
doi:10.1093/gigascience/giy132 pmid:30418578 pmcid:PMC6275443 fatcat:2bgfv3cdkfa4lb57i6kiu7qrp4

Integration of Transcriptome and Small RNA Sequencing to Decipher Molecular Interaction of Chenopodium quinoa Varieties with Cucumber Mosaic Virus [article]

Nourolah Soltani, Margaret E Staton, Kimberly D Gwinn
2020 bioRxiv   pre-print
Saponins are secondary metabolites with antiviral properties. Low saponin (sweet) varieties of quinoa (Chenopodium quinoa) have been developed because seeds high in saponins taste bitter. The aim of this study was to elucidate the role of saponin in resistance of quinoa to Cucumber mosaic virus (CMV). Differential gene expression was studied in time-series study of CMV infection. High-throughput transcriptome sequence data were obtained from 36 samples (3 varieties, (with/without) CMV, 1 or 4
more » ... ys after inoculation, 3 replicates). Translation, lipid, nitrogen, amino acid metabolism, and mono- and sesquiterpenoid biosynthesis genes were upregulated in CMV infections. In 'Red Head', (bitter), CMV-induced systemic symptoms were concurrent with downregulation of a key saponin biosynthesis gene, TSARL1, four days after inoculation. In local lesion responses (sweet and semi-sweet), TSARL1 levels remained up-regulated. Known microRNAs (miRNA) (81) from 11 miR families and 876 predicted novel miRNAs were identified. Differentially expressed miRNA and short interfering RNA clusters (24nt) induced by CMV infection are predicted to target genomic and intergenic regions enriched in repetitive elements. This is the first report of integrated RNASeq and sRNASeq data in quinoa-virus interactions and provides comprehensive understanding of involved genes, non-coding regions, and biological pathways in virus resistance.
doi:10.1101/2020.07.20.212795 fatcat:3sjzavqe6ncfph47qtmzht23va

Cross amplification of 15 EST-SSR markers in the genus Fraxinus

Andi G. Noakes, Teodora Best, Margaret E. Staton, Jennifer Koch, Jeanne Romero-Severson
2014 Conservation Genetics Resources  
Ash (Fraxinus, Oleaceae) species occur on most continents, within a wide range of forest tree communities. Emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), introduced into the U.S. from Asia in the late twentieth century, has caused widespread mortality, primarily in green ash, Fraxinus pennsylvanica Marsh. (Section: Melioides) and now impacts other North American ash species. The development and successful reintroduction of resistant trees requires genetic tools to
more » ... aluate population dynamics and aid in species identification. Here, we report 15 novel EST-SSR markers developed in green ash, most of which amplify and are polymorphic across 18 species of Fraxinus, including six species native to North America. The high average polymorphism information content (0.741) and allelic richness (15.3) revealed in six disparate populations of green ash indicate that these markers also have utility for investigating population dynamics in this species.
doi:10.1007/s12686-014-0260-2 fatcat:4mvcqcganjc2pkv74ntkv65muq

Complete chloroplast genome comparisons for Pityopsis (Asteraceae)

E. Anne Hatmaker, Phillip A. Wadl, Timothy A. Rinehart, Jennifer Carroll, Thomas S. Lane, Robert N. Trigiano, Margaret E. Staton, Edward E. Schilling, Tzen-Yuh Chiang
2020 PLoS ONE  
Pityopsis includes several regionally and one federally endangered species of herbaceous perennials. Four species are highly localized, including the federally endangered P. ruthii. The genus includes several ploidy levels and interesting ecological traits such as drought tolerance and fire-dependent flowering. Results from previous cladistic analyses of morphology and from initial DNA sequence studies did not agree with one another or with the infrageneric taxonomic classification, with the
more » ... ult that infrageneric relationships remain unresolved. We sequenced, assembled, and compared the chloroplast (cp) genomes of 12 species or varieties of Pityopsis to better understand generic evolution. A reference cp genome 152,569 bp in length was assembled de novo from P. falcata. Reads from other sampled species were then aligned to the P. falcata reference and individual chloroplast genomes were assembled for each, with manual gapfilling and polishing. After removing the duplicated second inverted region, a multiple sequence alignment of the cp genomes was used to construct a maximum likelihood (ML) phylogeny for the twelve cp genomes. Additionally, we constructed a ML phylogeny from the nuclear ribosomal repeat region after mapping reads to the Helianthus annuus region. The chloroplast phylogeny supported two clades. Previously proposed clades and taxonomic sections within the genus were largely unsupported by both nuclear and chloroplast phylogenies. Our results provide tools for exploring hybridity and examining the physiological and genetic basis for drought tolerance and fire-dependent flowering. This study will inform breeding and conservation practices, and general knowledge of evolutionary history, hybridization, and speciation within Pityopsis.
doi:10.1371/journal.pone.0241391 pmid:33370297 fatcat:wimmpfscezfjzjyxti37pt42oq

Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly

Fang Liu, Tarek Hewezi, Sarah L. Lebeis, Vince Pantalone, Parwinder S. Grewal, Margaret E. Staton
2019 BMC Microbiology  
Grewal, and Margaret E.  ...  Staton This article is available at Trace: Tennessee Research and Creative Exchange: utk_entopubs/14 Table 1 1 Network topological characteristics.  ... 
doi:10.1186/s12866-019-1572-x pmid:31477026 pmcid:PMC6720100 fatcat:prpldy2vk5ecbkf4ogpkurj6ha

TreeSnap: A citizen science app connecting tree enthusiasts and forest scientists

Ellen Crocker, Bradford Condon, Abdullah Almsaeed, Benjamin Jarret, C. Dana Nelson, Albert G. Abbott, Doreen Main, Margaret Staton
2019 Plants, People, Planet  
ACK N OWLED G M ENTS O RCI D Margaret Staton of 28 January 2019, the TreeSnap database contains 2,684 submissions from 1684 registered users.  ... 
doi:10.1002/ppp3.41 fatcat:x5qzebokczgehldiyttbtexsny

Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes

Sook Jung, Dorrie Main, Margaret Staton, Ilhyung Cho, Tatyana Zhebentyayeva, Pere Arús, Albert Abbott
2006 BMC Genomics  
Due to the lack of availability of large genomic sequences for peach or other Prunus species, the degree of synteny conservation between the Prunus species and Arabidopsis has not been systematically assessed. Using the recently available peach EST sequences that are anchored to Prunus genetic maps and to peach physical map, we analyzed the extent of conserved synteny between the Prunus and the Arabidopsis genomes. The reconstructed pseudo-ancestral Arabidopsis genome, existed prior to the
more » ... sed recent polyploidy event, was also utilized in our analysis to further elucidate the evolutionary relationship. We analyzed the synteny conservation between the Prunus and the Arabidopsis genomes by comparing 475 peach ESTs that are anchored to Prunus genetic maps and their Arabidopsis homologs detected by sequence similarity. Microsyntenic regions were detected between all five Arabidopsis chromosomes and seven of the eight linkage groups of the Prunus reference map. An additional 1097 peach ESTs that are anchored to 431 BAC contigs of the peach physical map and their Arabidopsis homologs were also analyzed. Microsyntenic regions were detected in 77 BAC contigs. The syntenic regions from both data sets were short and contained only a couple of conserved gene pairs. The synteny between peach and Arabidopsis was fragmentary; all the Prunus linkage groups containing syntenic regions matched to more than two different Arabidopsis chromosomes, and most BAC contigs with multiple conserved syntenic regions corresponded to multiple Arabidopsis chromosomes. Using the same peach EST datasets and their Arabidopsis homologs, we also detected conserved syntenic regions in the pseudo-ancestral Arabidopsis genome. In many cases, the gene order and content of peach regions was more conserved in the ancestral genome than in the present Arabidopsis region. Statistical significance of each syntenic group was calculated using simulated Arabidopsis genome. We report here the result of the first extensive analysis of the conserved microsynteny using DNA sequences across the Prunus genome and their Arabidopsis homologs. Our study also illustrates that both the ancestral and present Arabidopsis genomes can provide a useful resource for marker saturation and candidate gene search, as well as elucidating evolutionary relationships between species.
doi:10.1186/1471-2164-7-81 pmid:16615871 pmcid:PMC1479338 fatcat:guosyw7n4jdv3o7tok2g6owzim

Nuclear microsatellite markers for population genetic studies in sugar maple (Acer saccharum Marsh.)

Sudhir Khodwekar, Margaret Staton, Mark V. Coggeshall, John E. Carlson, Oliver Gailing
2015 Annals of Forest Research  
A total of 10,152 di-, tri and tetranucleotide microsatellite motifs were identified using an SSR finder script (Staton et al. submitted).  ...  Thus, AT-rich, relatively short motifs were preferentially recovered from Illumina sequencing for all ten species (Owusu et al. 2013, Staton et al. submitted) .  ... 
doi:10.15287/afr.2015.360 fatcat:3kvr3w2qojav7klfnik7cfzoum

Economic adversity and children's sleep problems: Multiple indicators and moderation of effects

Mona El-Sheikh, Erika J. Bagley, Margaret Keiley, Lori Elmore-Staton, Edith Chen, Joseph A. Buckhalt
2013 Health Psychology  
Objective: Toward explicating relations between economic adversity and children's sleep, we examined associations between multiple indicators of socioeconomic status (SES)/adversity and children's objectively and subjectively derived sleep parameters; ethnicity was examined as potential moderator. Methods: Participants were 276 third-and fourth-grade children and their families (133 girls; M age ϭ 9.44 years; SD ϭ .71): 66% European American (EA) and 34% African American (AA). Four SES
more » ... s were used: income-to-needs ratio, perceived economic well-being, maternal education, and community poverty. Children wore actigraphs for 7 nights and completed a self-report measure to assess sleep problems. Results: Objectively and subjectively assessed sleep parameters were related to different SES indicators, and overall worse sleep was evident for children from lower SES homes. Specifically, children from homes with lower income-to-needs ratios had higher levels of reported sleep/wake problems. Parental perceived economic well-being was associated with shorter sleep minutes and greater variability in sleep onset for children. Lower mother's education was associated with lower sleep efficiency. Children who attended Title 1 schools had shorter sleep minutes. Ethnicity was a significant moderator of effects in the link between some SES indicators and children's sleep. AA children's sleep was more negatively affected by income-to-needs ratio and mother's education than was the sleep of EA children. Conclusions: The results advocate for the importance of specifying particular SES and sleep variables used because they may affect the ability to detect associations between sleep and economic adversity.
doi:10.1037/a0030413 pmid:23148451 pmcid:PMC4008970 fatcat:gszy6eg34vgg5kidkmyi47zp7y

Response of bitter and sweet Chenopodium quinoa varieties to cucumber mosaic virus: Transcriptome and small RNASeq perspective

Nourolah Soltani, Margaret Staton, Kimberly D Gwinn
2021 PLoS ONE  
Writing -review & editing: Nourolah Soltani, Margaret Staton, Kimberly D. Gwinn.  ...  Soltani N, Staton M, Gwinn K. RNA Seq: virus infection alters terpenoid biosynthesis in Chenopodium quinoa.  ...  Soltani N, Staton M, Gwinn K. Small RNA profile in the Chenopodium quinoa-Cucumber mosaic virus interaction.  ... 
doi:10.1371/journal.pone.0244364 pmid:33621238 pmcid:PMC7901783 fatcat:omdgujlbjbd6hnkvcocgvhrkj4

Development and Characterization of 15 Novel Genomic SSRs for Viburnum farreri

Trinity P Hamm, Marcin Nowicki, Sarah L Boggess, William E Klingeman, Denita Hadziabdic, Matthew L Huff, Margaret E Staton, Robert N Trigiano
2021 Plants  
The Viburnum genus is of particular interest to horticulturalists, phylogeneticists, and biogeographers. Despite its popularity, there are few existing molecular markers to investigate genetic diversity in this large genus, which includes over 160 species. There are also few polymorphic molecular tools that can delineate closely related species within the genus. Viburnum farreri, a member of the Solenotinus subclade and one of the centers of diversity for Viburnum, was selected for DNA
more » ... g and development of genomic simple sequence repeats (gSSRs). In this study, 15 polymorphic gSSRs were developed and characterized for a collection of 19 V. farreri samples. Number of alleles per locus ranged from two- to- eight and nine loci had four or more alleles. Observed heterozygosity ranged from 0 to 0.84 and expected heterozygosity ranged from 0.10 to 0.80 for the 15 loci. Shannon diversity index values across these loci ranged from 0.21 to 1.62. The markers developed in this study add to the existing molecular toolkit for the genus and will be used in future studies investigating cross-transferability, genetic variation, and species and cultivar delimitation in the Viburnum genus and closely allied genera in the Adoxaceae and Caprifoliaceae.
doi:10.3390/plants10030487 pmid:33807587 pmcid:PMC8000228 fatcat:hol2vckmbrehxc7q6i2ow7hpvy

Overexpression of strigolactone-associated genes exerts fine-tuning selection on soybean rhizosphere bacterial and fungal microbiome

Fang Liu, John Hollis Rice, Valeria Lopes, Parwinder Grewal, Sarah Lebeis, Tarek Hewezi, Margaret Staton
2020 Phytobiomes Journal  
Strigolactones are a recently discovered class of carotenoid-derived plant hormones with a wide variety of functions, including acting as signaling molecules in the rhizosphere to promote arbuscular mycorrhizal fungi colonization and parasitic seed germination. To determine whether strigolactones influence the recruitment of microbes to the rhizosphere, we characterized both bacterial and fungal communities in response to the overexpression of genes involved in strigolactone biosynthesis
more » ... and signaling perception (D14 and MAX2a) in soybean (Glycine max). The amplicon sequencing-based results suggest that strigolactone overexpression lines had altered soybean rhizosphere bacteria composition at both the community level and individual taxa level with genera including Shinella and Bdellovibrio consistently more abundant across all three overexpression constructs. In addition, the responses of the soybean rhizosphere bacteria community differed significantly across the genes, with lines overexpressing genes involved in strigolactone biosynthesis (MAX1d) yielding a divergent bacterial community in comparison with those with altered expression of strigolactone perception genes (D14 and MAX2a). The overexpressed genes did not significantly impact the overall fungal community distribution; however, some individual taxa were altered in abundance. MAX1d and D14 overexpression lines had significantly enriched abundance of Fusarium solani. The mediating role of strigolactone biosynthesis and signaling genes on soybean rhizosphere bacterial and fungal communities confirmed strigolactone's importance in the rhizosphere host-microbe communication and microbial community structure.
doi:10.1094/pbiomes-01-20-0003-r fatcat:dqrpvytcnrgxla5kgkzmkowsze
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