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Genetics and Genomics

Selected Works

Articles 1 - 6 of 6

Full-Text Articles in Botany

Duplicate Gene Expression In Allopolyploid Gossypium Reveals Two Temporally Distinct Phases Of Expression Evolution, Lex E. Flagel, Joshua A. Udall, Dan Nettleton, Jonathan F. Wendel Jun 2019

Duplicate Gene Expression In Allopolyploid Gossypium Reveals Two Temporally Distinct Phases Of Expression Evolution, Lex E. Flagel, Joshua A. Udall, Dan Nettleton, Jonathan F. Wendel

Dan Nettleton

Polyploidy has played a prominent role in shaping the genomic architecture of the angiosperms. Through allopolyploidization, several modern Gossypium (cotton) species contain two divergent, although largely redundant genomes. Owing to this redundancy, these genomes can play host to an array of evolutionary processes that act on duplicate genes. We compared homoeolog (genes duplicated by polyploidy) contributions to the transcriptome of a natural allopolyploid and a synthetic interspecific F1 hybrid, both derived from a merger between diploid species from the Gossypium A-genome and D-genome groups. Relative levels of A- and D-genome contributions to the petal transcriptome were determined for 1,383 gene …

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Phylogenetics Of Morus (Moraceae) Inferred From Its And Trnl-Trnf Sequence Data., Madhav Nepal Mar 2012

Phylogenetics Of Morus (Moraceae) Inferred From Its And Trnl-Trnf Sequence Data., Madhav Nepal

Madhav Nepal

Morus (Tribe Moreae, Moraceae) consists of ca. 13 species of trees distributed in Asia, Africa, Europe, and North, Central, and South America. The broad geographical distribution of the genus, overlapping ranges of many taxa, and documented hybridization between some species present interesting questions of taxonomy, phylogeny, and biogeography. Phylogenetic data for Morus also contribute to higher level taxonomic work in the family. We used sequence data from ITS of the nrDNA and the chloroplast trnL-trnF intergenic spacer to study phylogenetic relationships of Morus. Phylogenies based on separate data sets were not statistically incongruent, and the combined tree …

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The Plant Structure Ontology, A Unified Vocabulary Of Anatomy And Morphology Of A Flowering Plant, Katica Ilic, Elizabeth A. Kellogg, Pankaj Jaiswal, Felipe Zapata, Peter F. Stevens, Leszek P. Vincent, Shulamit Avraham, Leonore Reiser, Anuradha Pujar, Martin M. Sachs, Noah T. Whitman, Susan R. Mccouch, Mary L. Schaeffer, Doreen H. Ware, Lincoln D. Stein, Seung Y. Rhee Dec 2006

The Plant Structure Ontology, A Unified Vocabulary Of Anatomy And Morphology Of A Flowering Plant, Katica Ilic, Elizabeth A. Kellogg, Pankaj Jaiswal, Felipe Zapata, Peter F. Stevens, Leszek P. Vincent, Shulamit Avraham, Leonore Reiser, Anuradha Pujar, Martin M. Sachs, Noah T. Whitman, Susan R. Mccouch, Mary L. Schaeffer, Doreen H. Ware, Lincoln D. Stein, Seung Y. Rhee

Peter Stevens

Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. The same terms are sometimes applied to different plant structures in different taxonomic groups. Conversely, similar structures are named by their species-specific terms. To address this problem, we created the Plant Structure Ontology (PSO), the first generic ontological …

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Plant Ontology (Po): A Controlled Vocabulary Of Plant Structures And Growth Stages, Pankaj Jaiswal, Shulamit Avraham, Katica Ilic, Elizabeth A. Kellogg, Susan Mccouch, Anuradha Pujar, Leonore Reiser, Seung Y. Rhee, Martin M. Sachs, Mary L. Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Doreen Ware, Felipe Zapata Dec 2004

Plant Ontology (Po): A Controlled Vocabulary Of Plant Structures And Growth Stages, Pankaj Jaiswal, Shulamit Avraham, Katica Ilic, Elizabeth A. Kellogg, Susan Mccouch, Anuradha Pujar, Leonore Reiser, Seung Y. Rhee, Martin M. Sachs, Mary L. Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Doreen Ware, Felipe Zapata

Peter Stevens

The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. These provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize and rice (Oryza sp.) anatomy, morphology and growth stages. Using the ontology browser, …

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The Unusual Life History Of Alseis Blackiana: A Shade-Persistent Pioneer Tree?, Jason D. Nason, J. W. Dalling, K. Winter, S. P. Hubbell, D. A. Murawski, J. L. Hamrick Jan 2001

The Unusual Life History Of Alseis Blackiana: A Shade-Persistent Pioneer Tree?, Jason D. Nason, J. W. Dalling, K. Winter, S. P. Hubbell, D. A. Murawski, J. L. Hamrick

Jason D Nason

Classifications of tree species into regeneration guilds or functional groups are often based on a limited number of life history characteristics indicative of requirements for early establishment, with the assumption that these traits are correlated with growth requirements of larger individuals. We tested the validity of this assumption for Alseis blackiana, a common canopy tree in central Panama, by examining its seed germination, seedling growth, and sapling distribution, growth, and mortality. We found that the early life history of Alseis is characteristic of pioneer species: the seed germination rate was much higher in forest gaps than in the forest understory, …

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Genetic Divergence Within The Genus Liriodendron (Magnoliaceae), Jonathan F. Wendel, Clifford R. Parks, Norton G. Miller, Karen M. Mcdougal Jan 1983

Genetic Divergence Within The Genus Liriodendron (Magnoliaceae), Jonathan F. Wendel, Clifford R. Parks, Norton G. Miller, Karen M. Mcdougal

Jonathan F. Wendel

The genus Liriodendron L. consists of a southeast Asian-eastern North American disjunct species pair, but the genus had a much wider distribution in the Northern Hemisphere during the late Cretaceous and the Tertiary. Although generally similar in morphology, the two extant species are measurably different. In 1973 and 1977 they were hybridized, and interspecific heterosis was observed in the progeny. After seven years, the interspecific hybrids synthesized in 1973 had a significantly greater biomass than intraspecific hybrids of L. tulipifera. The growth rate of interspecific and intraspecific F2 seedlings was approximately equal. A preliminary survey of flavonoid extracts in L. …

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