Works (10)

Updated: July 5th, 2023 15:54

2018 journal article

Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement

Nature Communications, 9(1).

By: S. Wu*, K. Lau*, Q. Cao*, J. Hamilton*, H. Sun*, C. Zhou*, L. Eserman*, D. Gemenet* ...

MeSH headings : Base Sequence; Carotenoids / metabolism; Diploidy; Ecotype; Genetic Variation; Genome, Plant; Genomics; Ipomoea batatas / genetics; Molecular Sequence Annotation; Multigene Family; Phylogeny; Plant Breeding; Polyploidy; Repetitive Sequences, Nucleic Acid / genetics
TL;DR: Using resequencing data from 16 genotypes widely used in African breeding programs, genes and alleles associated with carotenoid biosynthesis in storage roots are identified, which may enable efficient breeding of varieties with high provitamin A content. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science; OpenAlex)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Sources: Web Of Science, ORCID, Crossref
Added: November 26, 2018

2016 journal article

Development of a universal double-digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa

Molecular Ecology Resources, 16(6), 1303–1314.

By: M. Burford Reiskind n, K. Coyle n, H. Daniels n, P. Labadie n, M. Reiskind n, N. Roberts n, R. Roberts n, J. Schaff n, E. Vargo*

author keywords: double-digest RAD sequencing; high-throughput sequencing; reduced representation sequencing; restriction enzyme digests
MeSH headings : Animals; DNA / chemistry; DNA / metabolism; DNA Restriction Enzymes / metabolism; Fishes / genetics; Genomics / methods; Insecta / genetics; Sequence Analysis, DNA / methods
TL;DR: The results of this study provide empirical evidence of the utility of this method for producing consistent data for diverse nonmodel species and suggest specific considerations for sequencing analysis strategies. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2015 journal article

The plant parasite Pratylenchus coffeae carries a minimal nematode genome

NEMATOLOGY, 17(6), 621–637.

By: M. Burke n, E. Scholl n, D. Bird n, J. Schaff n, S. Colman*, R. Crowell*, S. Diener*, O. Gordon* ...

Contributors: M. Burke n, E. Scholl n, D. Bird n, J. Schaff n, S. Colman*, R. Crowell*, S. Diener*, O. Gordon* ...

author keywords: Caenorhabditis elegans; lesion nematode; Meloidogyne hapla; migratory endoparasitic nematodes; nematode evolution; protein encoding genes
TL;DR: The genome sequence of the lesion nematode, Pratylenchus coffeae, a significant pest of banana and other staple crops in tropical and sub-tropical regions worldwide is reported, and the P. coffeaegenome sequence may help to define timelines related to evolution of parasitism amongst nematodes. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Compartment Proteomics Analysis of White Perch (Morone americana) Ovary Using Support Vector Machines

JOURNAL OF PROTEOME RESEARCH, 13(3), 1515–1526.

By: J. Schilling n, A. Nepomuceno n, J. Schaff n, D. Muddiman n, H. Daniels n & B. Reading n

author keywords: compartment proteomics; support vector machines; modulated modularity clustering; ovary; oocytes; vitellogenin; transcriptome; mitochondria; alternatively spliced variants
MeSH headings : Animals; Bass / metabolism; Chemical Fractionation; Female; Fish Proteins / analysis; Membrane Proteins / analysis; Mitochondrial Proteins / analysis; Molecular Sequence Annotation; Ovary / chemistry; Ovary / metabolism; Proteomics / methods; Support Vector Machine; Tandem Mass Spectrometry
TL;DR: The white perch ovary cytosolic and membrane proteomes and transcriptome presented in this study can support future investigations into oogenesis and early embryogenesis ofwhite perch and other members of the genus Morone. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

De novo Sequencing, Characterization, and Comparison of Inflorescence Transcriptomes of Cornus canadensis and C. florida (Cornaceae)

PLoS ONE, 8(12), e82674.

Contributors: J. Zhang n, R. Franks n, X. Liu n, M. Kang*, J. Keebler n, J. Schaff n, H. Huang*, Q. Xiang n

Ed(s): T. Wang

MeSH headings : Chromosome Mapping; Cornus / genetics; Cornus / growth & development; DNA, Complementary / chemistry; Flowers / genetics; Flowers / growth & development; Gene Library; Polymorphism, Single Nucleotide; Sequence Analysis, DNA; Transcriptome
TL;DR: The study identified putative candidates potentially involved in the genetic regulation of inflorescence evolution and/or disease resistance in dogwoods for future analyses, and built a preliminary source of genome sequence data. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2012 journal article

A sequence-anchored linkage map of the plant-parasitic nematode Meloidogyne hapla reveals exceptionally high genome-wide recombination

G3-Genes Genomes Genetics, 2(7), 815–824.

By: V. Thomas, S. Fudali, J. Schaff, Q. Liu, E. Scholl, C. Opperman, D. Bird, V. Williamson

Source: NC State University Libraries
Added: August 6, 2018

2010 journal article

A method for release and multiple strand amplification of small quantities of DNA from endospores of the fastidious bacterium Pasteuria penetrans

LETTERS IN APPLIED MICROBIOLOGY, 50(5), 515–521.

By: T. Mauchline*, S. Mohan*, K. Davies*, J. Schaff n, C. Opperman n, B. Kerry*, P. Hirsch*

author keywords: 16S rRNA gene; bead-beating; endospores; gyrB; microLYSIS (R)-PLUS; multiple strand amplification; Pasteuria penetrans; phi29
MeSH headings : Bacillales / genetics; Bacillales / isolation & purification; Bacterial Proteins / genetics; DNA Gyrase / genetics; DNA Primers / genetics; DNA, Bacterial / genetics; DNA, Bacterial / isolation & purification; DNA, Ribosomal / genetics; Polymerase Chain Reaction / methods; RNA, Ribosomal, 16S / genetics; Spores, Bacterial / genetics; Spores, Bacterial / isolation & purification
TL;DR: A reliable protocol to extract DNA from Pasteuria penetrans endospores for use as template in multiple strand amplification, thus providing sufficient material for genetic analyses, and to develop a highly sensitive PCR‐based diagnostic tool for P. penetrans. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science; OpenAlex)
13. Climate Action (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2008 journal article

A sequence-anchored genetic linkage map for the moss, Physcomitrella patens

Plant Journal, 56(5), 840–854.

By: J. Schaff, F. Mbeunkui, K. Blackburn, D. Bird & M. Goshe

Source: NC State University Libraries
Added: August 6, 2018

2008 journal article

Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105(39), 14802–14807.

By: C. Opperman n, D. Bird n, V. Williamson*, D. Rokhsar*, M. Burke n, J. Cohn n, J. Cromer n, S. Diener n ...

Contributors: C. Opperman n, D. Bird n, V. Williamson*, D. Rokhsar*, M. Burke n, J. Cohn n, J. Cromer n, S. Diener n ...

author keywords: compaction; dauer; development; horizontal gene transfer; gene
MeSH headings : Animals; Base Sequence; Caenorhabditis elegans / genetics; Chromosome Mapping; Evolution, Molecular; Gene Duplication; Gene Transfer, Horizontal; Genome, Helminth; Host-Parasite Interactions / genetics; Molecular Sequence Data; Multigene Family; Operon; Phylogeny; Plants / parasitology; Synteny; Tylenchoidea / genetics
TL;DR: Meloidogyne hapla is established as a tractable model plant-parasitic nematode amenable to forward and reverse genetics, and a complete genome sequence is presented that defines a platform to elucidate mechanisms of parasitism by what is the largest uncontrolled group of plant pathogens worldwide. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2007 journal article

Comprehensive Transcriptome Profiling in Tomato Reveals a Role for Glycosyltransferase in Mi-Mediated Nematode Resistance

Plant Physiology, 144(2), 1079–1092.

By: J. Schaff n, D. Nielsen n, C. Smith n, E. Scholl n & D. Bird n

Contributors: J. Schaff n, D. Nielsen n, C. Smith n, E. Scholl n & D. Bird n

MeSH headings : Animals; Feeding Behavior / physiology; Gene Expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene Silencing; Genomics; Glycosyltransferases / metabolism; Host-Parasite Interactions / physiology; Solanum lycopersicum / enzymology; Solanum lycopersicum / genetics; Solanum lycopersicum / parasitology; Oligonucleotide Array Sequence Analysis; Plant Roots / enzymology; Plant Roots / metabolism; Plant Roots / parasitology; Reproduction / physiology; Tylenchoidea / physiology
TL;DR: The root transcriptome of the resistant and susceptible cultivars ‘Motelle’ and ‘Moneymaker’ is interrogated, providing a picture of global gene expression changes in roots during compatible and incompatible associations with RKN, and point to candidates for further investigation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

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