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1. PAST: The Pathway Association Studies Tool to Infer Biological Meaning from GWAS Datasets

Author:
Daniel G. Peterson,   et al.   ; Adam Thrash; Juliet D. Tang; Mason DeOrnellis; Marilyn L. Warburton;     Show all 5 Authors
Source:
Plants 2020 v.9 no.1 pp. -
ISSN:
2223-7747
Subject:
biochemical pathways; bioinformatics; computer software; genome-wide association study; phenotype; plants (botany); user interface
Abstract:
... In recent years, a bioinformatics method for interpreting genome-wide association study (GWAS) data using metabolic pathway analysis has been developed and successfully used to find significant pathways and mechanisms explaining phenotypic traits of interest in plants. However, the many scripts implementing this method were not straightforward to use, had to be customized for each project, require ...
Handle:
10113/6837744
DOI:
10.3390/plants9010058

2. Quack: A quality assurance tool for high throughput sequence data

Author:
Daniel G. Peterson,   et al.   ; Adam Thrash; Mark Arick;     Show all 3 Authors
Source:
Analytical biochemistry 2018 v.548 pp. 38-43
ISSN:
0003-2697
Subject:
data collection; high-throughput nucleotide sequencing; quality control
Abstract:
... The quality of data generated by high-throughput DNA sequencing tools must be rapidly assessed in order to determine how useful the data may be in making biological discoveries; higher quality data leads to more confident results and conclusions. Due to the ever-increasing size of data sets and the importance of rapid quality assessment, tools that analyze sequencing data should quickly produce ea ...
DOI:
10.1016/j.ab.2018.01.028
CHORUS:
10.1016/j.ab.2018.01.028

3. Evaluation of the MA-10 cell line as a model of insl3 regulation and Leydig cell function

Author:
Daniel G. Peterson,   et al.   ; Mary E. Strong; Matthew A. Burd;     Show all 3 Authors
Source:
Animal reproduction science 2019 v.208 pp. 106116
ISSN:
0378-4320
Subject:
Leydig cells; cell lines; cryptorchidism; cyclic AMP; enzymes; genes; human chorionic gonadotropin; luteinizing hormone; mammals; messenger RNA; models; signal transduction; testosterone; transcription factors
Abstract:
... Cryptorchidism, the failure of one or both testes to descend to an extra-abdominal location during mammalian development, is a common reproductive malady that often requires surgical intervention to remedy. Leydig cells are responsible for producing insulin-like peptide 3 (INSL3), a peptide hormone that is essential for normal testicular descent. The insl3 promoter in Leydig cells can be activated ...
DOI:
10.1016/j.anireprosci.2019.106116

4. Evaluation of optimal droplet size for control of Palmer amaranth (Amaranthus palmeri) with acifluorfen

Author:
Daniel G. Peterson,   et al.   ; Lucas X. Franca; Darrin M. Dodds; Thomas R. Butts; Greg R. Kruger; Daniel B. Reynolds; J. Anthony Mills; Jason A. Bond; Angus L. Catchot;     Show all 9 Authors
Source:
Weed technology 2020 v.34 no.4 pp. 511-519
ISSN:
1550-2740
Subject:
Amaranthus palmeri; Arachis hypogaea; Glycine max; Oryza sativa; acifluorfen; biomass; droplet size; droplets; geographical variation; models; peanuts; plant morphology; population density; rice; selection pressure; soil fertility; soybeans; spray drift; weather; weed control; weeds; Mississippi; Nebraska
Abstract:
... Acifluorfen is a nonsystemic PPO-inhibiting herbicide commonly used for POST Palmer amaranth control in soybean, peanut, and rice across the southern United States. Concerns have been raised regarding herbicide selection pressure and particle drift, increasing the need for application practices that optimize herbicide efficacy while mitigating spray drift. Field research was conducted in 2016, 201 ...
DOI:
10.1017/wet.2020.11

5. Influence of flooding period and seed burial depth on Palmer amaranth (Amaranthus palmeri) seed germination

Author:
Daniel G Peterson,   et al.   ; Lucas X Franca; Darrin M Dodds; Daniel B Reynolds; Jason A Bond; Anthony Mills; Angus L Catchot;     Show all 7 Authors
Source:
Pest management science 2020 v.76 no.11 pp. 3832-3837
ISSN:
1526-498X
Subject:
Amaranthus palmeri; Oryza sativa; buried seeds; habitats; herbicide resistance; pest management; rice; sandy loam soils; seed damage; seed germination; silt; silt loam soils; straw; waterfowl; winter; Mississippi
Abstract:
... BACKGROUND: Flooding throughout fall and winter months is an effective practice for rice (Oryza sativa L.) straw decomposition, soil seedbank depletion, and waterfowl habitat in Mississippi. Nevertheless, limited research is available regarding the effects of fall–winter flooding and seed burial depth on Palmer amaranth (Amaranthus palmeri S. Wats.) seed germination. The objective of this study wa ...
DOI:
10.1002/ps.5934

6. Development of a qPCR Protocol to Detect the Cotton Bacterial Blight Pathogen, Xanthomonas citri pv. malvacearum, from Cotton Leaves and Seeds

Author:
Daniel G. Peterson,   et al.   ; Xiao-Qiang Wang; Tom W. Allen; Hui Wang; Robert L. Nichols; Aixin Liu; Xiang-Dong Li; Peng Deng; David Jia; Shi-En Lu;     Show all 10 Authors
Source:
Plant disease 2019 v.103 no.3 pp. 422-429
ISSN:
0191-2917
Subject:
Gossypium hirsutum; Xanthomonas citri; bacteria; blight; bolls; cotton; financial economics; leaves; monitoring; pathogens; plant tissues; planting seed; protocols; quantitative polymerase chain reaction; races; seed-borne diseases; seeds
Abstract:
... Bacterial blight, historically a seed-borne disease of cotton (Gossypium hirsutum) is caused by Xanthomonas citri pv. malvacearum, resulted in significant economic losses prior to development of resistant varieties and implementation of acid-delinting of planting seed. Periodic outbreaks have been associated with seed since the early twentieth century; of note, the disease has experienced a resurg ...
DOI:
10.1094/PDIS-07-18-1150-RE

7. Droplet size impact on lactofen and acifluorfen efficacy for Palmer amaranth (Amaranthus palmeri) control

Author:
Daniel G. Peterson,   et al.   ; Lucas X. Franca; Darrin M. Dodds; Thomas R. Butts; Greg R. Kruger; Daniel B. Reynolds; J. Anthony Mills; Jason A. Bond; Angus L. Catchot;     Show all 9 Authors
Source:
Weed technology 2019 v.34 no.3 pp. 416-423
ISSN:
1550-2740
Subject:
Amaranthus palmeri; acifluorfen; biomass; cost effectiveness; droplet size; droplets; herbicide application; herbicide resistance; lactofen; plant damage; regrowth; sprayers; weeds; weight loss; Mississippi; Nebraska
Abstract:
... Herbicide applications performed with pulse width modulation (PWM) sprayers to deliver specific spray droplet sizes could maintain product efficacy, minimize potential off-target movement, and increase flexibility in field operations. Given the continuous expansion of herbicide-resistant Palmer amaranth populations across the southern and midwestern United States, efficacious and cost-effective me ...
DOI:
10.1017/wet.2019.133

8. Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus

Author:
Daniel G. Peterson,   et al.   ; Arnab Ghosh; Roy N. Platt; Michael W. Vandewege; Rabia Tabassum; Chuan-Yu Hsu; Sally R. Isberg; John W. Finger; Troy J. Kieran; Travis C. Glenn; Jaime Gongora; David A. Ray;     Show all 12 Authors
Source:
Analytical biochemistry 2020 v.602 pp. 113781
ISSN:
0003-2697
Subject:
Crocodylus porosus; DNA; RNA libraries; birds; evolution; gene silencing; genes; genomics; microRNA; retrotransposons; transcription (genetics); transposons
Abstract:
... MicroRNAs (miRNAs) are 18–24 nucleotide regulatory RNAs. They are involved in the regulation of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Data suggests a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to birds, the closest extant relatives of crocodilians. U ...
DOI:
10.1016/j.ab.2020.113781

9. Multiple Herbicide-Resistant Junglerice (Echinochloa colona): Identification of Genes Potentially Involved in Resistance through Differential Gene Expression Analysis

Author:
Daniel G. Peterson,   et al.   ; Alice A. Wright; Marianela Rodriguez-Carres; Rajkumar Sasidharan; Liisa Koski; Vijay K. Nandula; Jeffery D. Ray; Jason A. Bond; David R. Shaw;     Show all 9 Authors
Source:
Weed science 2018 v.66 no.3 pp. 347-354
ISSN:
0043-1745
Subject:
Echinochloa colona; F-box proteins; Helianthus annuus; biotypes; cytochrome P-450; dose response; food security; gene expression; gene expression regulation; genes; glutathione transferase; herbicide resistance; imazamox; malathion; mechanism of action; point mutation; propanil; quantitative polymerase chain reaction; quinclorac; resistance mechanisms; single nucleotide polymorphism; weed science; Mississippi
Abstract:
... Herbicide resistance, and in particular multiple-herbicide resistance, poses an ever-increasing threat to food security. A biotype of junglerice [Echinochloa colona (L.) Link] with resistance to four herbicides, imazamox, fenoxaprop-P-ethyl, quinclorac, and propanil, each representing a different mechanism of action, was identified in Sunflower County, MS. Dose responses were performed on the resi ...

10. Transcriptomic changes in Echinochloa colona in response to treatment with the herbicide imazamox

Author:
Daniel G. Peterson,   et al.   ; Alice A. Wright; Rajkumar Sasidharan; Liisa Koski; Marianela Rodriguez-Carres; Vijay K. Nandula; Jeffery D. Ray; Jason A. Bond; David R. Shaw;     Show all 9 Authors
Source:
Planta 2018 v.247 no.2 pp. 369-379
ISSN:
0032-0935
Subject:
Echinochloa colona; abiotic stress; biotypes; cDNA libraries; complementary DNA; enzymes; gene expression regulation; genome; imazamox; leaves; messenger RNA; metabolism; stress response; transcription factors; transcriptome; transcriptomics; weed control
Abstract:
... MAIN CONCLUSION: Presented here is the first Echinochloa colona leaf transcriptome. Analysis of gene expression before and after herbicide treatment reveals that E. colona mounts a stress response upon exposure to herbicide. Herbicides are the most frequently used means of controlling weeds. For many herbicides, the target site is known; however, it is considerably less clear how plant gene expres ...
DOI:
10.1007/s00425-017-2784-7

11. Insights into the Evolution of the New World Diploid Cottons (Gossypium, SubgenusHouzingenia) Based on Genome Sequencing

Author:
Daniel G. Peterson,   et al.   ; Corrinne E. Grover; Mark A. Arick; Adam Thrash; Justin L. Conover; William S. Sanders; James E. Frelichowski; Jodi A. Scheffler; Brian E. Scheffler; Jonathan F. Wendel;     Show all 10 Authors
Source:
Genome Biology and Evolution 2019 v.11 no.1 pp. 53-71
ISSN:
1759-6653
Subject:
Gossypium; biodiversity; diploidy; genome; genomics; introgression; mutation; phylogeny; sequence analysis; transposons; Africa; Arizona; Peru
Abstract:
... We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the geographically widely dispersed New World diploid cottons (Gossypium, subg. Houzingenia). Whole genome resequencing data (average of 33× genomic coverage) were generated to reassess the phylogenetic history of the subgenus and provide a temporal framework for its diversification. Phylogenetic analyses i ...
DOI:
10.1093/gbe/evy256
CHORUS:
10.1093/gbe/evy256

12. Bacterial Diversity Patterns Differ in Soils Developing in Sub-tropical and Cool-Temperate Ecosystems

Author:
Daniel G. Peterson,   et al.   ; Shankar G. Shanmugam; Zenaida V. Magbanua; Mark A. Williams; Kamlesh Jangid; William B. Whitman; William L. Kingery;     Show all 7 Authors
Source:
Microbial ecology 2017 v.73 no.3 pp. 556-569
ISSN:
0095-3628
Subject:
bacterial communities; biogeography; chronosequences; climate; community structure; ecological function; ecological resilience; ecosystems; environmental factors; sequence analysis; soil formation; soil properties; variance; Georgia; Michigan
Abstract:
... Microbial diversity patterns have been surveyed in many different soils and ecosystems, but we are unaware of studies comparing similar soils developing from similar parent materials in contrasting climates. In 2008, developmental chronosequences with ages ranging from 105 to 500,000 years across Georgia (GA) and Michigan (MI) were studied to investigate how bacterial community composition and div ...
DOI:
10.1007/s00248-016-0884-8

13. Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis

Author:
Daniel G. Peterson,   et al.   ; Dinum Perera; Zenaida V. Magbanua; Supaphan Thummasuwan; Dipaloke Mukherjee; Mark Arick; Philippe Chouvarine; Campbell J. Nairn; Jeremy Schmutz; Jane Grimwood; Jeffrey F.D. Dean;     Show all 11 Authors
Source:
Gene 2018 v.663 pp. 165-177
ISSN:
0378-1119
Subject:
Arabidopsis; Pinus taeda; bacterial artificial chromosomes; carbon metabolism; cell walls; evolution; fungi; nucleotide sequences; prediction; pseudogenes; wood; Southeastern United States
Abstract:
... Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the loblolly pine (LP; Pinus taeda L.) genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive, moderately-repetitive, and single/low-copy sequenc ...
DOI:
10.1016/j.gene.2018.04.024

14. Sub genome-anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids

Author:
Daniel G. Peterson,   et al.   ; Christopher A. Saski; Brian E. Scheffler; Amanda M. Hulse-Kemp; Bo Liu; Qingxin Song; Atsumi Ando; David M. Stelly; Jodi A. Scheffler; Jane Grimwood; Don C. Jones; Jeremy Schmutz; Z. Jeffery Chen;     Show all 13 Authors
Source:
Scientific reports 2017 v.7 no.15274 pp. -
ISSN:
2045-2322
Subject:
Gossypium hirsutum; allotetraploidy; bacterial artificial chromosomes; chromosome mapping; cotton; crops; diploidy; fluorescence in situ hybridization; genome; genome assembly; single nucleotide polymorphism
Abstract:
... Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a ...
Handle:
10113/5934974
DOI:
10.1038/s41598-017-14885-w
PubMed:
29127298
PubMed Central:
PMC5681701

15. Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing

Author:
Daniel G. Peterson,   et al.   ; Corrinne E. Grover; Mark A. Arick; Justin L. Conover; Adam Thrash; Guanjing Hu; William S. Sanders; Chuan-Yu Hsu; Rubab Zahra Naqvi; Muhammad Farooq; Xiaochong Li; Lei Gong; Joann Mudge; Thiruvarangan Ramaraj; Joshua A. Udall; Jonathan F. Wendel;     Show all 16 Authors
Source:
Genome Biology and Evolution 2017 v.9 no.12 pp. 3328-3344
ISSN:
1759-6653
Subject:
Gossypium; ancestry; cotton; genes; genetic drift; genomics; geographical distribution; phylogeny; transposons; Eastern Africa; Madagascar
Abstract:
... Long-distance insular dispersal is associated with divergence and speciation because of founder effects and strong genetic drift. The cotton tribe (Gossypieae) has experienced multiple transoceanic dispersals, generating an aggregate geographic range that encompasses much of the tropics and subtropics worldwide. Two genera in the Gossypieae, Kokia and Gossypioides, exhibit a remarkable geographic ...
DOI:
10.1093/gbe/evx248
CHORUS:
10.1093/gbe/evx248

16. Draft Genome Sequence of Burkholderia pyrrocinia Lyc2, a Biological Control Strain That Can Suppress Multiple Plant Microbial Pathogens

Author:
Daniel G. Peterson,   et al.   ; Xiao-Qiang Wang; Kurt C. Showmaker; Xiao-Qing Yu; Tao Bi; Chuan-Yu Hsu; Sonya M. Baird; Xiang-Dong Li; Shi-En Lu;     Show all 9 Authors
Source:
Genome announcements 2014 v.2 no.5 pp. e00991-14
ISSN:
2169-8287
Subject:
Burkholderia pyrrocinia; bacteria; biological control; cotton; damping off; genome; nucleotide sequences; pathogens; rhizosphere; seedlings; tobacco; China
Abstract:
... Burkholderia pyrrocinia strain Lyc2 was isolated from the tobacco rhizosphere in China. This bacterium exhibits a remarkable capacity to inhibit the growth of multiple pathogens and shows strong suppression of cotton seedling damping-off. Here, we present the draft genome sequence of Burkholderia pyrrocinia strain Lyc2. ...
DOI:
10.1128/genomeA.00991-14
PubMed:
25278535
PubMed Central:
PMC4183879

17. Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus

Author:
Daniel G. Peterson,   et al.   ; Felix D. Guerrero; Paula Moolhuijzen; Shelby Bidwell; Elisabet Caler; Matthew Bellgard; Vishvanath M. Nene; Appolinaire Djikeng;     Show all 8 Authors
Source:
BMC genomics 2010 v.11 no.1 pp. 374
ISSN:
1471-2164
Subject:
ticks; transposons; bacterial artificial chromosomes; Rhipicephalus microplus; DNA; expressed sequence tags; clones; amino acids; databases
Abstract:
... Background: The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence fiscally and technically problematic. To selectively obtain gene-enriched regions of this tick's genome, Cot filtration was performed, and Cot-filtered DNA was sequenced via 454 FLX pyrosequencing. Results: The sequenced Cot-filtered genomic DNA was assembled with an EST-based ge ...
Handle:
10113/55726
DOI:
10.1186/1471-2164-11-374
PubMed:
20540747
PubMed Central:
PMC2893602

18. CattleTickBase: An integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus

Author:
Daniel G. Peterson,   et al.   ; Matthew I. Bellgard; Paula M. Moolhuijzen; Felix D. Guerrero; David Schibeci; Manuel Rodriguez-Valle; Scot E. Dowd; Roberto Barrero; Adam Hunter; Robert J. Miller; Ala E. Lew-Tabor;     Show all 11 Authors
Source:
International journal for parasitology 2012 v.42 no.2 pp. 161-169
ISSN:
0020-7519
Subject:
Rhipicephalus microplus; genome; DNA; bioinformatics; gene expression; Rhipicephalus annulatus
Abstract:
... The Rhipicephalus microplus genome is large and complex in structure, making it difficult to assemble a genome sequence and costly to resource the required bioinformatics. In light of this, a consortium of international collaborators was formed to pool resources to begin sequencing this genome. We have acquired and assembled genomic DNA into contigs that represent over 1.8 Gigabase pairs of DNA fr ...
Handle:
10113/55423
DOI:
10.1016/j.ijpara.2011.11.006

19. The complexity of Rhipicephalus (Boophilus) microplus genome characterised through detailed analysis of two BAC clones

Author:
Daniel G. Peterson,   et al.   ; Paula M. Moolhuijzen; Ala E. Lew-Tabor; Jess A. T. Morgan; Manuel Rodríguez Valle; Scot E. Dowd; Felix D. Guerrero; Matthew I. Bellgard; Rudi Appels;     Show all 9 Authors
Source:
BMC Research Notes 2011 v.4 no. pp. 254
ISSN:
1756-0500
Subject:
ticks; Crustacea; bacterial artificial chromosomes; Rhipicephalus microplus; vector-borne diseases; mites; clones; genes; Rhipicephalus annulatus; Araneae; genomics; Anopheles; Scorpiones; Drosophila
Abstract:
... Rhipicephalus (Boophilus) microplus (Rmi) a major cattle ectoparasite and tick borne disease vector, impacts on animal welfare and industry productivity. In arthropod research there is an absence of a complete Chelicerate genome, which includes ticks, mites, spiders, scorpions and crustaceans. Model arthropod genomes such as Drosophila and Anopheles are too taxonomically distant for a reference in ...
Handle:
10113/55757
DOI:
10.1186/1756-0500-4-254
PubMed:
21777481
PubMed Central:
PMC3160391

20. Towards decoding the conifer giga-genome

Author:
Daniel G. Peterson,   et al.   ; John Mackay; Jeffrey F. D. Dean; Christophe Plomion; Francisco M. Cánovas; Nathalie Pavy; Pär K. Ingvarsson; Outi Savolainen; M. Ángeles Guevara; Silvia Fluch; Barbara Vinceti; Dolores Abarca; Carmen Díaz-Sala; María-Teresa Cervera;     Show all 14 Authors
Source:
Plant molecular biology 2012 v.80 no.6 pp. 555-569
ISSN:
0167-4412
Subject:
Picea; Pinus; chromosome mapping; complementary DNA; coniferous forests; conifers; evolution; genome; genotype; phenotype
Abstract:
... Several new initiatives have been launched recently to sequence conifer genomes including pines, spruces and Douglas-fir. Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions afforded by next generation sequencers. The purpose of this review is to desc ...
DOI:
10.1007/s11103-012-9961-7
PubMed:
22960864