A5017588713- Plant Taxonomy and Phylogenetics
- Genomics and Phylogenetic Studies
- African Botany and Ecology Studies
- Plant Diversity and Evolution
- Genetic diversity and population structure
- Bamboo properties and applications
- Ethnobotanical and Medicinal Plants Studies
- Seed and Plant Biochemistry
- Chromosomal and Genetic Variations
- Plant and animal studies
- Natural Antidiabetic Agents Studies
- Ecology and Vegetation Dynamics Studies
- Botany and Plant Ecology Studies
- Agronomic Practices and Intercropping Systems
- Plant Ecology and Taxonomy Studies
- Plant and Fungal Interactions Research
- Genetic factors in colorectal cancer
- Gene expression and cancer classification
- Tree Root and Stability Studies
- Plant Parasitism and Resistance
- Plant nutrient uptake and metabolism
- Cocoa and Sweet Potato Agronomy
- Cancer Genomics and Diagnostics
- Plant Ecology and Soil Science
- Plant and fungal interactions
University of Chicago
2016-2021
Northern Illinois University
2014-2018
Lincoln University - Missouri
2016
The systematics of grasses has advanced through applications plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups Poaceae. Here we present a phylogenomic analysis 250 complete plastomes (179 genera) sampled from 44 the 52 tribes Plastome sequences were determined high throughput sequencing libraries and assemblies represent over 28.7 Mbases sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) plastomes; (2)...
Bambusoideae (Poaceae) comprise three distinct and well-supported lineages: tropical woody bamboos (Bambuseae), temperate (Arundinarieae) herbaceous (Olyreae). Phylogenetic studies using chloroplast markers have generally supported a sister relationship between Bambuseae Olyreae. This suggests either at least two origins of the bamboo syndrome in this subfamily or its loss Olyreae.Here full genome (plastome) phylogenomic study is presented coding noncoding regions 13 complete plastomes from...
Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within subfamily, but largely lack resolution and/or robust support for certain tribal subtribal groups. This study aims resolve these relationships, as well characterize a putative mitochondrial insert one linage. 35 newly sequenced plastomes were combined phylogenomic 37 other species: 15 22 from outgroups. A topology...
Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses these increasing resolution support for relationships that have varied among or been unresolved in earlier single- multi-gene studies. Pooideae, cool-season grass lineage, is largest 12 subfamilies includes important temperate cereals, turf grasses forage species. Although numerous studies phylogeny subfamily undertaken, some 'early-diverging' tribes conflict studies,...
Plastome sequences for 18 species of the PACMAD grasses (subfamilies Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) were analyzed phylogenomically. Next generation sequencing methods used to provide complete plastome 12 species. Sanger was performed determine one species, Hakonechloa macra, a reference annotation. These analyses conducted resolve deep subfamilial relationships within clade. Divergence estimates assessed potential factors that led...
Grass leaf shape is a strong indicator of their habitat with linear leaves predominating in open areas and ovate distinguishing forest-associated grasses. This pattern among extant species suggests that ancestral shifts between forest habitats may have coincided changes or size. We tested relationships habitat, climate, photosynthetic pathway, size phylogenetic framework to evaluate drivers variation over the evolutionary history family. also estimated Poaceae whether margins served as...
Summary Ecosystem restoration is an important tool for mitigating biodiversity loss and recovering critical ecosystem services to humanity, but rarely takes into account the evolutionary attributes of community being restored. Phylogenetic diversity ( PD ) represents a potentially valuable measure success because it can correlate with functional trait that drives function. However, patterns in restored communities are assessed. We surveyed plant tallgrass prairies 2–19 years old calculated...
Studies of complete plastomes have proven informative for our understanding the molecular evolution and phylogenomics grasses. In this study, a plastome phylogenomic analysis sampled species from lineages deeply diverging grasses including Streptochaeta spicata (Anomochlooideae), Leptaspis banksii L. zeylanica (both Pharoideae). Plastomes next generation sequences three were assembled by de novo methods. The unambiguously aligned coding noncoding entire with those 43 other outgroup...
Next-generation sequencing now allows for total RNA extracts to be sequenced in non-model organisms such as bamboos, an economically and ecologically important group of grasses. Bamboos are divided into three lineages, two which woody perennials with bisexual flowers, undergo gregarious monocarpy. The third lineage, herbaceous perennials, possesses unisexual flowers that annual flowering events.Transcriptomes were assembled using both reference-based de novo methods. These methods tested by...
Premise of research. Studies complete plastomes have proven informative for our understanding the molecular evolution and phylogenomics grasses, but subfamily Chloridoideae has not been included in this In previous multilocus studies, specific deep branches, as large clade corresponding to Cynodonteae, are uniformly well supported.Methodology. study, a plastome phylogenomic analysis sampled 14 species representing 4 tribes 10 genera Chloridoideae. One was Sanger sequenced, other species,...
Abstract Technological advances have allowed phylogenomic studies of plants, such as full chloroplast genome (plastome) analysis, to become increasingly popular and economically feasible. Although next–generation short–read sequencing allows for plastomes be sequenced relatively rapidly, it requires additional attention using software assemble these reads into comprehensive sequences. Here we compare the use three de novo assemblers combined with contig assembly methods. Seven plastome...
Abstract Wood betony, Orobanchaceae ( Pedicularis canadensis ) and bastard toadflax, Santalaceae Comandra umbellata are two root‐hemiparasitic plant species found in tallgrass prairie communities. Natural resource managers interested utilizing these as “pseudograzers” grasslands to reduce competitively dominant grasses thereby increase ecological diversity quality restorations urban plantings. We performed an observational field study at 5 sites investigate the association of hemiparasite...
Joinvilleaceae is a family of tropical grass-like monocots that comprises only the genus Joinvillea. Previous studies have placed in close phylogenetic proximity to well-studied grass family. A full plastome sequence was determined and characterized for J. ascendens. The sequenced with next generation methods, fully assembled de novo annotated. assembly revealed two novel inversions specific lineage at least one plastid inversion Joinvilleaceae-Poaceae lineage. Two previously documented...
We investigated the little-studied Arundinoideae/Micrairoideae clade of grasses with an innovative plastome phylogenomic approach. This method gives robust results for taxa uncertain phylogenetic placement. Arundinoideae comprise ∼45 species, although historically was much larger. is notable widely invasive Phragmites australis. Micrairoideae nine genera and ∼200 species. Some are threatened extinction, including Hubbardia, some Isachne spp., Limnopoa. Two micrairoid genera, Eriachne...
The bamboos (Bambusoideae, Poaceae) comprise a major grass lineage with complex evolutionary history involving ancient hybridization and allopolyploidy. About 1700 described species are classified into three tribes, Olyreae (herbaceous bamboos), Bambuseae (tropical woody Arundinarieae (temperate bamboos). Nuclear analyses strongly support monophyly of the whereas plastome paraphyly, sister to Olyreae. Our objectives were clarify origin(s) bamboo tribes resolve nuclear vs. plastid conflict...
Neighbor-joining gene tree representing the SOC-like and E-class MADS box genes. Gene copies assembled in this study are labeled by genus, colored according to taxa (orange: G. inermis, green: O. acuminata, dark red: P. aurea, blue: L. pauciflora) numbered redundantly distinguish copies. Reference not colored, abbreviated binomial (At: Arabidopsis thaliana, Bd: Brachypodium distachyon, Os: Oryza sativa) their labeling Genbank. Nodes that were supported at over 50Â % bootstrap indicated. (PDF 465 kb)
Neighbor-joining gene tree representing the A and C/D-class MADS box genes. Gene copies assembled in this study are labeled by genus, colored according to taxa (orange: G. inermis, green: O. acuminata, dark red: P. aurea, blue: L. pauciflora) numbered redundantly distinguish copies. Reference not colored, abbreviated binomial (At: Arabidopsis thaliana, Bd: Brachypodium distachyon, Os: Oryza sativa) their labeling Genbank. Nodes that were supported at over 50Â % bootstrap indicated. (PDF 331 kb)