Ashley N Egan

Ashley N Egan
Utah Valley University | UVU · Department of Biology

PhD
Evolutionary genetics and genomics of Phaseoloid legumes; conservation biology of Psoraleeae tribe (Fabaceae)

About

88
Publications
51,714
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Introduction
Evolutionary genetics and genomics of beans and wild relatives, particularly in the phaseoloid clade. Keywords: Transcriptomics, comparative genomics, phylogenomics, phylogenetics, population genetics, population genomics, crop breeding, conservation biology.
Additional affiliations
August 2019 - present
Utah Valley University
Position
  • Professor (Assistant)
August 2018 - August 2019
Aarhus University
Position
  • Research Associate
August 2013 - August 2018
Smithsonian Institution
Position
  • Researcher

Publications

Publications (88)
Preprint
Full-text available
Pattern recognition receptors (PRR) recognize distinct pathogen and herbivore-associated molecular patterns (PAMPs and HAMPs) and mediate activation of immune responses, but the evolution of new PRR sensing functions is not well understood. We employed comparative genomics and functional analysis to define evolutionary events leading to the sensing...
Article
Full-text available
Fabaceae, with 765 genera and ∼19,500 species, are the third-largest angiosperm family and important both economically and ecologically, with global crops intensively studied in part for their nitrogen-fixing ability. However, resolution of Fabaceae phylogeny and divergence times at intrasubfamilial levels have been elusive, precluding a reconstruc...
Chapter
The calcareous glades and barrens of the southeastern United States, often referred to as ‘cedar glades,’ comprise a diverse and unique flora. Many of the plant species in these communities are threatened or endangered. The highest concentration of limestone cedar glades lies in the Central Basin of Middle Tennessee, where these habitats are highly...
Article
Two groups independently and seemingly simultaneously published the new combination of Pediomelum pariense, the Paria River breadroot. Both names were published in the second-quarter issues of separate journals in 1986. Same issue dates have led to confusion over which name takes precedence and is thus accepted. However, one issue was delayed in pr...
Article
Full-text available
Plants in the genus Pueraria DC., including the invasive kudzu, produce large, deep tubers that can weigh upwards of 400 pounds. Within its native Asia, tubers from various Pueraria species have been used for millennia for food and medicine, with more contemporary uses including soil stabilization and enrichment. Three species in particular provide...
Article
Full-text available
The Advances in Legume Systematics (ALS) series has provided the venues for publishing outputs from the series of seven International Legume Conferences (ILC) held over the last four decades. The first two editions arising from the first ILC in 1978 at the Royal Botanic Gardens, Kew, were published in 1981. The first ten parts of ALS were published...
Article
Full-text available
The need for scientists to exchange, share and organise data has resulted in a proliferation of biodiversity research-data portals over recent decades. These cyber-infrastructures have had a major impact on taxonomy and helped the discipline by allowing faster access to bibliographic information, biological and nomenclatural data, and specimen info...
Article
Full-text available
Next-generation sequencing (NGS) technologies and applications have enabled numerous critical advances in legume biology, from marker discovery to whole-genome sequencing, and will provide many new avenues for legume research in the future. The past 6 years in particular have seen revolutionary advances in legume science because of the use of high-...
Article
Full-text available
The need for scientists to exchange, share, and organise data has resulted in a proliferation of research data portals in the past decades. These cyberinfrastructures have had a major impact on taxonomy and helped to revitalise the discipline, by allowing quick access to bibliographic information, biological and nomenclatural data, and specimen inf...
Chapter
Full-text available
The wild relatives of the ve domesticated species of bean (Phaseolus L.) are widely distributed across the tropics and subtropics of the New World, with taxa extending from the Canadian border to Argentina, and on the Caribbean Islands, Bermuda, and the Galapagos Islands. Mesoamerica holds the largest con- centration of species, particularly in the...
Article
Full-text available
Capsaicinoids are compounds synthesized exclusively in the genus Capsicum and are responsible for the burning sensation experienced when consuming hot pepper fruits. To date, only one gene, AT3, a member of the BAHD family of acyltransferases, is currently known to have a measurable quantitative effect on capsaicinoid biosynthesis. Multiple AT3 par...
Data
Tables of Ks estimates for all pairwise comparisons of the 44 individuals shown in the S1 File, inclusive of multiple sheets for Ks estimates from ex1ex2, ex1br, and ex2br. Summary statistics (Sum_stats) are compiled for each data set (Ks_ex1br, Ks_ex2br, Ks_ex1ex2br) with cells in the raw estimates sheets relevant to each comparison color coded to...
Data
Supplementary figures, including: Figure A–RAxML maximum likelihood phylogeny of the 44-sample Ks ex1ex2 dataset; Figure B–RAxML maximum likelihood phylogeny of the 44-sample Ks ex1br dataset; Figure C–RAxML maximum likelihood phylogeny of the 44-sample Ks ex2br dataset. (PDF)
Data
Reduced alignments used for Ks estimation within PAML for 44 sequences parsed by exon 1 and exon 2 and presented in phylip format. (TXT)
Article
Full-text available
Background: Kudzu, Pueraria montana var. lobata, is a woody vine native to Southeast Asia that has been introduced globally for cattle forage and erosion control. The vine is highly invasive in its introduced areas, including the southeastern US. Modern molecular marker resources are limited for the species, despite its importance. Transcriptomes...
Article
Full-text available
Premise of the Study The development of pipelines for locus discovery has spurred the use of target enrichment for plant phylogenomics. However, few studies have compared pipelines from locus discovery and bait design, through validation, to tree inference. We compared three methods within Leguminosae (Fabaceae) and present a workflow for future ef...
Article
Full-text available
Winged bean, Psophocarpus tetragonolobus (L.) DC., is analogous to soybean in yield and nutritional quality, proving a valuable alternative to soybean in tropical regions of the world. The presence of anti-nutritional factors and high costs associated with indeterminate plant habit have been major concerns in this crop. But occurrence of good genet...
Article
Full-text available
Background The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson’s drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is li...
Article
Full-text available
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK...
Article
Full-text available
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK...
Article
Full-text available
Several taxonomic and phylogenetic studies have hypothesized polyphyly within Pueraria DC., a genus comprising 19 species (24 with varieties) including the highly invasive Pueraria montana var. lobata (Kudzu) introduced to the U.S.A. about 150 years ago. Previous efforts to investigate monophyly of the genus have been hampered by limited taxon samp...
Article
Full-text available
Winged bean, Psophocarpus tetragonolobus (L.) DC., is similar to soybean in yield and nutritional value but more viable in tropical conditions. Here, we strengthen genetic resources for this orphan crop by producing a de novo transcriptome assembly and annotation of two Sri Lankan accessions (denoted herein as CPP34 [PI 491423] and CPP37 [PI 639033...
Article
Full-text available
Toxicopueraria peduncularis (Graham ex Benth.) A.N.Egan & B.Pan bis is reported for the first time in Thailand. Genus and species descriptions are provided, along with vernacular names, distributional data and specimens examined. This Thailand population is shown to be a distant outlier from the known range for T. peduncularis and its closely relat...
Article
Full-text available
A synopsis of the genus Haymondia A.N.Egan & B.Pan bis in Thailand, comprised of a single species: H. wallichii (DC.) A.N.Egan & B.Pan bis, is given. The genus and species descriptions are provided, along with nomenclature, vernacular names, distributional data and specimens examined.
Article
Full-text available
Recent molecular phylogenetic studies (Egan et al., in prep.) have demonstrated widespread polyphyly within the genus Pueraria. A new classification is presented here that delineates monophyletic groups previously considered congeneric with Pueraria. This taxonomic treatment provides several new species combinations and a more natural circumscripti...
Article
Full-text available
Pueraria stracheyi has long been recognized as erroneously placed in the genus Pueraria. Here we examined the history behind this collection, past hypotheses concerning its taxonomic affinities, and morphological and ecological comparisons with Shuteria and Apios carnea, wherein we conclude that Pueraria stracheyi represents a synonym of the latter...
Article
Full-text available
Pediomelum is a genus endemic to North America comprising about 26 species, including the megalanthum complex, which consists of Pediomelummegalanthum and its varieties retrorsum and megalanthum, Pediomelummephiticum, and the recently described Pediomelumverdiense and Pediomelumpauperitense. Historically, species of the megalanthum complex have bee...
Chapter
Full-text available
Abstract Transcriptome sequencing or RNA-Seq is one of the most efficient and cost-effective methods currently available for gene discovery in non-model organisms. Recent studies have demonstrated the utility of these data for resolving the relationships of diverse lineages of organisms, by extracting sequences of a large number of single-copy nucl...
Article
Full-text available
The accumulation of over 30 years of basic research on the biology, genetic variation, and evolution of the wild perennial relatives of soybean (Glycine max) provides a foundation to improve cultivated soybean. The cultivated soybean and its wild progenitor, G. soja, have a center of origin in eastern Asia and are the only two species in the annual...