Arabidopsis thaliana, the thale cress, mouse-ear cress or arabidopsis, is a small plant from the mustard family (Brassicaceae), native to Eurasia and Africa. Commonly found along the shoulders of roads and in disturbed land, it is generally considered a weed.
The Oomycetes, or Oomycota, form a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms within the Stramenopiles. They are filamentous and heterotrophic, and can reproduce both sexually and asexually. Sexual reproduction of an oospore is the result of contact between hyphae of male antheridia and female oogonia; these spores can overwinter and are known as resting spores. Asexual reproduction involves the formation of chlamydospores and sporangia, producing motile zoospores. Oomycetes occupy both saprophytic and pathogenic lifestyles, and include some of the most notorious pathogens of plants, causing devastating diseases such as late blight of potato and sudden oak death. One oomycete, the mycoparasite Pythium oligandrum, is used for biocontrol, attacking plant pathogenic fungi. The oomycetes are also often referred to as water molds, although the water-preferring nature which led to that name is not true of most species, which are terrestrial pathogens.
The transfer DNA is the transferred DNA of the tumor-inducing (Ti) plasmid of some species of bacteria such as Agrobacterium tumefaciens and Agrobacterium rhizogenes . The T-DNA is transferred from bacterium into the host plant's nuclear DNA genome. The capability of this specialized tumor-inducing (Ti) plasmid is attributed to two essential regions required for DNA transfer to the host cell. The T-DNA is bordered by 25-base-pair repeats on each end. Transfer is initiated at the right border and terminated at the left border and requires the vir genes of the Ti plasmid.
The Pathogen-Host Interactions database (PHI-base) is a biological database that contains manually curated information on genes experimentally proven to affect the outcome of pathogen-host interactions. The database has been maintained by researchers at Rothamsted Research and external collaborators since 2005. PHI-base has been part of the UK node of ELIXIR, the European life-science infrastructure for biological information, since 2016.
Albugo candida, commonly known as white rust or white blister rust, is an obligate plant pathogen in the family Albuginaceae that infects Brassicaceae species. It has a relatively smaller genome than other oomycetes.
Hyaloperonospora is a genus of oomycete, obligate, plant pathogens that was originally considered to be part of Peronospora. Species in this group produce a disease called downy mildew and can infect many important crops. From the 19 downy mildew producing genera, Hyaloperonospora has been grouped with Perofascia in the brassicolous downy mildews. In the group of downy mildews, Hyaloperonospora is the third biggest genus. The most famous species in the genus is the Hyaloperonospora parasitica, or also known as Hyaloperonospora arabidopsis. This species has become a model organism from its ability to infect the model plant Arabidopsis thaliana. It is used to study plant-pathogen interactions, and is currently the only Hyaloperonospora species that has an assembled genome.
Hyaloperonospora parasitica is an oomycete from the family Peronosporaceae. It has been considered for a long time to cause downy mildew of a variety of species within the Brassicaceae, on which the disease can cause economically important damage by killing seedlings or affecting the quality of produce intended for freezing. Hyaloperonospora parasitica causes downy mildew on a wide range of many different plants. It belongs to the Kingdom Chromista, the phylum Oomycota, and the family Peronosporaceae. The former name for H. parasitica was Peronospora parasitica until it was reclassified and put in the genus Hyaloperonospora. It is an especially vicious disease on crops of the family Brassicaceae. It is most famous for being a model pathogen of Arabidopsis thaliana which is a model organism used for experimental purposes. Accordingly, the former Hyaloperonospora parasitica has been split into a large number of species. For instance, the taxonomically correct name of the parasite of the well-known model organism Arabidopsis thaliana is Hyaloperonospora arabidopsidis, not H. parasitica, whereas the pathogen of Brassica has to be called Hyaloperonospora brassicae.
Pseudomonas syringae is a rod-shaped, Gram-negative bacterium with polar flagella. As a plant pathogen, it can infect a wide range of species, and exists as over 50 different pathovars, all of which are available to researchers from international culture collections such as the NCPPB, ICMP, and others.
Pythium ultimum is a plant pathogen. It causes damping off and root rot diseases of hundreds of diverse plant hosts including corn, soybean, potato, wheat, fir, and many ornamental species. P. ultimum belongs to the peronosporalean lineage of oomycetes, along with other important plant pathogens such as Phytophthora spp. and many genera of downy mildews. P. ultimum is a frequent inhabitant of fields, freshwater ponds, and decomposing vegetation in most areas of the world. Contributing to the widespread distribution and persistence of P. ultimum is its ability to grow saprotrophically in soil and plant residue. This trait is also exhibited by most Pythium spp. but not by the related Phytophthora spp., which can only colonize living plant hosts.
LTR retrotransposons are class I transposable element characterized by the presence of long terminal repeats (LTRs) directly flanking an internal coding region. As retrotransposons, they mobilize through reverse transcription of their mRNA and integration of the newly created cDNA into another location. Their mechanism of retrotransposition is shared with retroviruses, with the difference that most LTR-retrotransposons do not form infectious particles that leave the cells and therefore only replicate inside their genome of origin. Those that do (occasionally) form virus-like particles are classified under Ortervirales.
Hyaloperonospora arabidopsidis is a species from the family Peronosporaceae. It is an obligate parasite and the causal agent of the downy mildew of the plant model organism Arabidopsis thaliana. While H. arabidopsidis has for a long time been subsumed under Peronospora parasitica, recent studies have shown that H. parasitica is restricted to Capsella bursa-pastoris as a host plant. Like the other Hyaloperonospora species, H. arabidopsidis is highly specialized to Arabidopsis thaliana.
Chloroplast DNA (cpDNA) is the DNA located in chloroplasts, which are photosynthetic organelles located within the cells of some eukaryotic organisms. Chloroplasts, like other types of plastid, contain a genome separate from that in the cell nucleus. The existence of chloroplast DNA was identified biochemically in 1959, and confirmed by electron microscopy in 1962. The discoveries that the chloroplast contains ribosomes and performs protein synthesis revealed that the chloroplast is genetically semi-autonomous. The first complete chloroplast genome sequences were published in 1986, Nicotiana tabacum (tobacco) by Sugiura and colleagues and Marchantia polymorpha (liverwort) by Ozeki et al. Since then, a great number of chloroplast DNAs from various species have been sequenced.
Martin Edward Kreitman is an American geneticist at the University of Chicago, most well known for the McDonald–Kreitman test that is used to infer the amount of adaptive evolution in population genetic studies.
PhytoPath was a joint scientific project between the European Bioinformatics Institute and Rothamsted Research, running from January 2012 to May 30, 2017. The project aimed to enable the exploitation of the growing body of “-omics” data being generated for phytopathogens, their plant hosts and related model species. Gene mutant phenotypic information is directly displayed in genome browsers.
In molecular biology mir-396 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms.
Arabidopsis thaliana is a first class model organism and the single most important species for fundamental research in plant molecular genetics.
Joy Michele Bergelson is an American evolutionary biologist. She is currently the Dorothy Schiff Professor of Genomics at New York University. Bergelson was previously and James D. Watson Distinguished Service Professor of Ecology and Evolution at the University of Chicago, where she chaired the department for ecology and evolution. Her research focuses on the evolution and ecology of plants.
John M. McDowell is the J.B. Stroobants Professor of Biotechnology at Virginia Polytechnic Institute and State University. His major area of research is phytopathology and plant-pathogen interactions. He has used gene-sequencing technology to examine the genome of Phytophthora capsici and to develop strains of soybean plants that are better able to defend against pathogens.
