Matching Items (13)

128805-Thumbnail Image.png

Oberholzeria (Fabaceae subfam. Faboideae), a New Monotypic Legume Genus from Namibia

Description

Oberholzeria etendekaensis, a succulent biennial or short-lived perennial shrublet is described as a new species, and a new monotypic genus. Discovered in 2012, it is a rare species known only

Oberholzeria etendekaensis, a succulent biennial or short-lived perennial shrublet is described as a new species, and a new monotypic genus. Discovered in 2012, it is a rare species known only from a single locality in the Kaokoveld Centre of Plant Endemism, north-western Namibia. Phylogenetic analyses of molecular sequence data from the plastid matK gene resolves Oberholzeria as the sister group to the Genisteae clade while data from the nuclear rDNA ITS region showed that it is sister to a clade comprising both the Crotalarieae and Genisteae clades. Morphological characters diagnostic of the new genus include: 1) succulent stems with woody remains; 2) pinnately trifoliolate, fleshy leaves; 3) monadelphous stamens in a sheath that is fused above; 4) dimorphic anthers with five long, basifixed anthers alternating with five short, dorsifixed anthers, and 5) pendent, membranous, one-seeded, laterally flattened, slightly inflated but indehiscent fruits.

Contributors

Created

Date Created
  • 2015-03-27

136816-Thumbnail Image.png

Characterization of Transgenic Arabidopsis thaliana Overexpressing a Type I H+ Pyrophosphatase and the Phloem Lipid-Associated Family Protein

Description

Overexpression of AVP1 (Arabidopsis vacuolar pyrophosphatase), a type I H+ pyrophosphatase, results in greater biomass, possibly due to a function in sucrose transport within the phloem. Overexpression of the phloem

Overexpression of AVP1 (Arabidopsis vacuolar pyrophosphatase), a type I H+ pyrophosphatase, results in greater biomass, possibly due to a function in sucrose transport within the phloem. Overexpression of the phloem lipid-associated family protein (PLAFP) was shown to increase the number of vascular bundles in Arabidopsis. Could these two phenotypes complement one another additively? In this work, double mutants overexpressing both AVP1 and PLAFP were characterized. These double mutants have enhanced biomass, greater leaf area, and a larger number of vascular bundles than the single mutant lines. Overexpression of PLAFP does not result in any increase in rhizosphere acidification capacity.

Contributors

Agent

Created

Date Created
  • 2014-05

136838-Thumbnail Image.png

Phenotypes associated with over-expression of type I H+-PPases: Is there a common mechanism?

Description

Type I H+-PPase encoding genes, such as AVP1 (Arabidopsis thaliana), TsVP (Thellungiella halophilla), TaVP,( Triticum aestivum), and OVP1 (Oryza sativa) are highly conserved and.traditionally known to operate as vacuolar proton

Type I H+-PPase encoding genes, such as AVP1 (Arabidopsis thaliana), TsVP (Thellungiella halophilla), TaVP,( Triticum aestivum), and OVP1 (Oryza sativa) are highly conserved and.traditionally known to operate as vacuolar proton translocating pyrophosphatases. It is worth mentioning that Rocha-Facanha and de Meis presented in vitro evidence with tonoplast fractions of maize coleoptiles and seeds consistent with the reverse function of the H+-PPase (1998). These authors suggested that given the appropriate thermodynamic conditions in vivo, the H+-PPase could operate as a system of energy conservation with a role in the maintenance of cytosolic PPi levels. Further evidence in support for a PPi-synthase activity of plant H+-PPases came from work done on tonoplasts from mature oranges where PPi synthesis was demonstrated when a ΔpH of 3 units was imposed (Marsh et al. 2000).

Futher research has shown that transgenics overexpressing type I H+-PPases develop more root and shoot biomass, and have enhanced rhizosphere acidification capacity than wild types. The increased root biomass suggests that previous reports describing the response of these plants to water scarcity as drought tolerance are incomplete. Larger root systems indicate that an important component of the response is drought resistance. The enhanced rhizosphere acidification capacity has also been associated with an increase in nutrient use efficiency, conferring a growth advantage under nitrogen and phosphorous deficient conditions.
While a vacuolar localized H+-PPase easily explains the salt tolerant phenotypes, it does little to provide a mechanism for an increase in root and shoot biomass and/or an augmented rhizosphere acidification capacity. Several groups have argued that higher levels and transport of the growth hormone auxin could be responsible for the above phenotypes. An alternative model focusing on the function of a plasma membrane bound H+-PPase in sieve elements and companion cells links these phenotypes with enhanced phloem sucrose loading and transport.
The following paper reviews publications in which the H+-PPase overexpression technology has been used since 2006 in an attempt to identify cues that could help us test the compatibility of the the proposed models with the actual data.

Contributors

Agent

Created

Date Created
  • 2014-05

Species delimitation of flowering plant genus Medicago section Buceras (Fabaceae)

Description

There is a relative lack of basic information about early diverging species of the genus Medicago that, for the most part, were formerly considered to be in the genus Trigonella.

There is a relative lack of basic information about early diverging species of the genus Medicago that, for the most part, were formerly considered to be in the genus Trigonella. Species boundaries are not always clear, for example, the most recent treatment of the genus Medicago submerged four previously recognized species into Medicago monantha, a widely distributed species in the Middle East. These species are recognized on the basis of morphological characters such as fruit number, shape, length and areole shape and size, but species identification is still challenging and further clarification of species boundaries is needed. There is also a lack of cytogenetic information. Some of the relatively few published chromosome numbers, e.g. 2n=28, and 44, differ from those of the rest of the genus, which are mostly 2n=16 or multiples thereof, although seven species are 2n=14. As part of a larger study of the genome and chromosome number evolution in the genus Medicago, we obtained genome size data using flow cytometry for 44 accessions of 14 currently recognized early diverging species, with a focus on Medicago monantha. Chromosome numbers were obtained using standard cytological methods. Our chromosome number data confirm a chromosome number of 2n=16 for M. brachycarpa (genome size of 1.33 pg), and M. monspeliaca (1.88 pg), and 2n=28 for M. polyceratia (2.77 pg) and give new numbers for some species; 2n=16 for M. biflora (2.7 pg), and a previously unknown chromosome number for these early diverging species of 2n=14 for Medicago fischeriana (~1.35 pg). Interestingly, our data support the hypothesis that there are at least two entities within M. monantha as currently recognized that differ in chromosome number and genome size; two accessions had chromosome numbers of 2n=26 and 30 with corresponding genome sizes of 2.68 and 2.85 pg and three other accessions had chromosome numbers 2n=36,44, and another 44 with genome sizes of 3.94, 3.89, and 4.04 pg. There are also some significant morphological differences between these two entities, such as fruit length and areole area. These data lead to both further clarification of the relationships of early diverging Medicago and help build a platform for more in-depth research concerning the evolution of chromosome number and genome size within Medicago.

Contributors

Agent

Created

Date Created
  • 2016-05

130373-Thumbnail Image.png

Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat

Description

Premise of the study: Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of

Premise of the study: Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of such genome-scale structural changes.
Methods: Using next-generation sequence data, we assembled the plastid genome of saguaro cactus and probed the nuclear genome for transferred plastid genes and functionally related nuclear genes. We combined these results with available data across Cactaceae and seed plants more broadly to infer the history of gene loss and to assess the strength of phylogenetic association between gene loss and loss of the inverted repeat (IR).
Key results: The saguaro plastid genome is the smallest known for an obligately photosynthetic angiosperm (∼113 kb), having lost the IR and plastid ndh genes. This loss supports a statistically strong association across seed plants between the loss of ndh genes and the loss of the IR. Many nonplastid copies of plastid ndh genes were found in the nuclear genome, but none had intact reading frames; nor did three related nuclear-encoded subunits. However, nuclear pgr5, which functions in a partially redundant pathway, was intact.
Conclusions: The existence of an alternative pathway redundant with the function of the plastid NADH dehydrogenase-like complex (NDH) complex may permit loss of the plastid ndh gene suite in photoautotrophs like saguaro. Loss of these genes may be a recurring mechanism for overall plastid genome size reduction, especially in combination with loss of the IR.

Contributors

Created

Date Created
  • 2015-07-01

129046-Thumbnail Image.png

Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species

Description

Background
Parasitic plants, represented by several thousand species of angiosperms, use modified structures known as haustoria to tap into photosynthetic host plants and extract nutrients and water. As a result

Background
Parasitic plants, represented by several thousand species of angiosperms, use modified structures known as haustoria to tap into photosynthetic host plants and extract nutrients and water. As a result of their direct plant-plant connections with their host plant, parasitic plants have special opportunities for horizontal gene transfer, the nonsexual transmission of genetic material across species boundaries. There is increasing evidence that parasitic plants have served as recipients and donors of horizontal gene transfer (HGT), but the long-term impacts of eukaryotic HGT in parasitic plants are largely unknown.
Results
Here we show that a gene encoding albumin 1 KNOTTIN-like protein, closely related to the albumin 1 genes only known from papilionoid legumes, where they serve dual roles as food storage and insect toxin, was found in Phelipanche aegyptiaca and related parasitic species of family Orobanchaceae, and was likely acquired by a Phelipanche ancestor via HGT from a legume host based on phylogenetic analyses. The KNOTTINs are well known for their unique “disulfide through disulfide knot” structure and have been extensively studied in various contexts, including drug design. Genomic sequences from nine related parasite species were obtained, and 3D protein structure simulation tests and evolutionary constraint analyses were performed. The parasite gene we identified here retains the intron structure, six highly conserved cysteine residues necessary to form a KNOTTIN protein, and displays levels of purifying selection like those seen in legumes. The albumin 1 xenogene has evolved through >150 speciation events over ca. 16 million years, forming a small family of differentially expressed genes that may confer novel functions in the parasites. Moreover, further data show that a distantly related parasitic plant, Cuscuta, obtained two copies of albumin 1 KNOTTIN-like genes from legumes through a separate HGT event, suggesting that legume KNOTTIN structures have been repeatedly co-opted by parasitic plants.
Conclusions
The HGT-derived albumins in Phelipanche represent a novel example of how plants can acquire genes from other plants via HGT that then go on to duplicate, evolve, and retain the specialized features required to perform a unique host-derived function.

Contributors

Created

Date Created
  • 2013-02-20

156011-Thumbnail Image.png

Developing a virtual flora portal for vascular plants of Saudi Arabia

Description

A floristic analysis is essential to understanding the current diversity and structure

of community associations of plants in a region. Also, a region’s floristic analysis is key not only to investigating

A floristic analysis is essential to understanding the current diversity and structure

of community associations of plants in a region. Also, a region’s floristic analysis is key not only to investigating their geographical origin(s) but is necessary to their management and protection as a reservoir of greater biodiversity. With an area of 2,250,000 square kilometers, the country of Saudi Arabia covers almost four-fifths of the Arabian Peninsula. Efforts to document information on the flora of Saudi Arabia began in the 1700s and have resulted in several comprehensive publications over the last 25 years. There is no doubt that these studies have helped both the community of scientific researchers as well as the public to gain knowledge about the number of species, types of plants, and their distribution in Saudi Arabia. However, there has been no effort to use digital technology to make the data contained in various Saudi herbarium collections easily accessible online for research and teaching purposes. This research project aims to develop a “virtual flora” portal for the vascular plants of Saudi Arabia. Based on SEINet and the Symbiota software used to power it, a preliminary website portal was established to begin an effort to make information of Saudi Arabia’s flora available on the world- wide web. Data comprising a total of 12,834 specimens representing 175 families were acquired from different organizations and used to create a database for the designed website. After analyzing the data, the Fabaceae family (“legumes”) was identified as a largest family and chosen for further analysis. This study contributes to help scientific researchers, government workers and the general public to have easy, unlimited access to the plant information for a variety of purposes.

Contributors

Agent

Created

Date Created
  • 2017

157712-Thumbnail Image.png

Glycoside Hydrolase Gene Families Of Termite Hindgut Protists

Description

This project was completed to understand the evolution of the ability to digest wood in termite symbiotic protists. Lower termites harbor bacterial and protist symbionts which are essential to the

This project was completed to understand the evolution of the ability to digest wood in termite symbiotic protists. Lower termites harbor bacterial and protist symbionts which are essential to the termite ability to use wood as a nutritional source, producing glycoside hydrolases to break down the polysaccharides found in lignocellulose. Yet, only a few molecular studies have been done to confirm the protist species responsible for particular enzymes. By mining publicly available and newly generated genomic and transcriptomic data, including three transcriptomes from isolated protist cells, I identify over 200 new glycoside hydrolase sequences and compute the phylogenies of eight glycoside hydrolase families (GHFs) reported to be expressed by termite hindgut protists.

Of those families examined, the results are broadly consistent with Todaka et al. 2010, though none of the GHFs found were expressed in both termite-associated protist and non-termite-associated protist transcriptome data. This suggests that, rather than being inherited from their free-living protist ancestors, GHF genes were acquired by termite protists while within the termite gut, potentially via lateral gene transfer (LGT). For example one family, GHF10, implies a single acquisition of a bacterial xylanase into termite protists. The phylogenies from GHF5 and GHF11 each imply two distinct acquisitions in termite protist ancestors, each from bacteria. In eukaryote-dominated GHFs, GHF7 and GHF45, there are three apparent acquisitions by termite protists. Meanwhile, it appears prior reports of GHF62 in the termite gut may have been misidentified GHF43 sequences. GHF43 was the only GHF found to contain sequences from the protists not found in the termite gut. These findings generally all support the possibility termite-associated protists adapted to a lignocellulosic diet after colonization of the termite hindgut. Nonetheless, the poor resolution of GHF phylogeny and limited termite and protist sampling constrain interpretation.

Contributors

Agent

Created

Date Created
  • 2019

154093-Thumbnail Image.png

The effect of plant neighbors on a common desert shrub's physiology and evapotranspiration

Description

Hydrological models in arid and semi-arid ecosystems can be subject to high uncertainties. Spatial variability in soil moisture and evapotranspiration, key components of the water cycle, can contribute to model

Hydrological models in arid and semi-arid ecosystems can be subject to high uncertainties. Spatial variability in soil moisture and evapotranspiration, key components of the water cycle, can contribute to model uncertainty. In particular, an understudied source of spatial variation is the effect of plant-plant interactions on water fluxes. At patch scales (plant and associated soil), plant neighbors can either negatively or positively affect soil water availability via competition or hydraulic redistribution, respectively. The aboveground microclimate can also be altered via canopy shading effects by neighbors. Across longer timescales (years), plants may adjust their physiological (water-use) traits in response to the neighbor-altered microclimate, which subsequently affects transpiration rates. The influence of physiological adjustments and neighbor-altered microclimate on water fluxes was assessed around Larrea tridentata in the Sonoran Desert. Field measurements of Larrea’s stomatal behavior and vertical root distributions were used to examine the effects of neighbors on Larrea’s physiological controls on transpiration. A modeling based approach was implemented to explore the sensitivity of evapotranspiration and soil moisture to neighbor effects. Neighbors significantly altered both above- and belowground physiological controls on evapotranspiration. Compared to Larrea growing alone, neighbors increased Larrea’s annual transpiration by up to 75% and 30% at the patch and stand scales, respectively. Estimates of annual transpiration were highly sensitive to the presence/absence of competition for water, and on seasonal timescales, physiological adjustments significantly influenced transpiration estimates. Plant-plant interactions can be a significant source of spatial variation in ecohydrological models, and both physiological adjustments to neighbors and neighbor effects on microclimate affect small scale (patch to ecosystem) water fluxes.

Contributors

Agent

Created

Date Created
  • 2015

150180-Thumbnail Image.png

Protist and cyanobacterial contributions to particle flux in oligotrophic ocean regions

Description

The oceans play an essential role in global biogeochemical cycles and in regulating climate. The biological carbon pump, the photosynthetic fixation of carbon dioxide by phytoplankton and subsequent sequestration of

The oceans play an essential role in global biogeochemical cycles and in regulating climate. The biological carbon pump, the photosynthetic fixation of carbon dioxide by phytoplankton and subsequent sequestration of organic carbon into deep water, combined with the physical carbon pump, make the oceans the only long-term net sink for anthropogenic carbon dioxide. A full understanding of the workings of the biological carbon pump requires a knowledge of the role of different taxonomic groups of phytoplankton (protists and cyanobacteria) to organic carbon export. However, this has been difficult due to the degraded nature of particles sinking into particle traps, the main tools employed by oceanographers to collect sinking particulate matter in the ocean. In this study DNA-based molecular methods, including denaturing gradient gel electrophoresis, cloning and sequencing, and taxon-specific quantitative PCR, allowed for the first time for the identification of which protists and cyanobacteria contributed to the material collected by the traps in relation to their presence in the euphotic zone. I conducted this study at two time-series stations in the subtropical North Atlantic Ocean, one north of the Canary Islands, and one located south of Bermuda. The Bermuda study allowed me to investigate seasonal and interannual changes in the contribution of the plankton community to particle flux. I could also show that small unarmored taxa, including representatives of prasinophytes and cyanobacteria, constituted a significant fraction of sequences recovered from sediment trap material. Prasinophyte sequences alone could account for up to 13% of the clone library sequences of trap material during bloom periods. These observations contradict a long-standing paradigm in biological oceanography that only large taxa with mineral shells are capable of sinking while smaller, unarmored cells are recycled in the euphotic zone through the microbial loop. Climate change and a subsequent warming of the surface ocean may lead to a shift in the protist community toward smaller cell size in the future, but in light of these findings these changes may not necessarily lead to a reduction in the strength of the biological carbon pump.

Contributors

Agent

Created

Date Created
  • 2011