Soft rot Enterobacteriaceae(SRE) are bacterial plant pathogens that cause blackleg, wilt and soft rot diseases on a broad range of important crop and ornamental plants worldwide. These organisms ...(spanning the genera Erwinia, Pectobacterium, Dickeya, and Pantoea) cause significant economic and yield losses in the field, and in storage. They are transmissible through surface water, by trade and other movement of plant material and soil, and in some cases are subject to international legislative and quarantine restrictions. Effective detection and diagnosis in support of food security legislation and epidemiology is dependent on the ability to classify pathogenic isolates precisely. Diagnostics and classification are made more difficult by the influence of horizontal gene transfer on phenotype, and historically complex and sometimes inaccurate nomenclatural and taxonomic assignments that persist in strain collections and online sequence databases. Here, we briefly discuss the relationship between taxonomy, genotype and phenotype in the SRE, and their implications for diagnostic testing and legislation. We present novel whole-genome classifications of the SRE, illustrating inconsistencies between the established taxonomies and evidence from completely sequenced isolates. We conclude with a perspective on the future impact of widespread whole-genome sequencing and classification methods on detection and identification of bacterial plant pathogens in support of legislative and policy efforts in food security.
Complex pigment evolution in the Caryophyllales Brockington, Samuel F.; Walker, Rachel H.; Glover, Beverley J. ...
New Phytologist,
June 2011, Volume:
190, Issue:
4
Journal Article, Book Review
Peer reviewed
Open access
Carotenoids and flavonoids including anthocyanins are the predominant pigments in flowering plants, where they play important roles in pollination, seed dispersal, protection against stress and ...signalling. In certain families within the Pentapetalae order Caryophyllales, an unusual class of pigments, known as betalains, replaces the more common anthocyanins. This isolated occurrence of betalains in the Caryophyllales has stimulated over half a century of debate and experimentation. Numerous hypotheses have been suggested to explain the phylogenetically restricted occurrence of betalains and their apparent mutual exclusion with anthocyanins. In this review, we evaluate these hypotheses in the face of a changing interpretation of Caryophyllales phylogeny and new comparative genetic data. Phylogenetic analyses expose substantial gaps in our knowledge of the early evolution of pigments in the Caryophyllales and suggest pigmentation to be much more labile than previously recognized. Reconstructions of character evolution imply multiple switches from betalain to anthocyanin pigmentation, but also allow for possible multiple origins of betalains. Comparative genetic studies propose possible mechanisms underlying switches between pigment types and suggest that transcriptional down-regulation of late-acting enzymes is responsible for a loss of anthocyanins. Given these insights from molecular phylogenetics and comparative genetics, we discuss outstanding questions and define key goals for future research.
A novel, unbiased approach to plant viral disease diagnosis has been developed which requires no a priori knowledge of the host or pathogen. Next-generation sequencing coupled with metagenomic ...analysis was used to produce large quantities of cDNA sequence in a model system of tomato infected with Pepino mosaic virus. The method was then applied to a sample of Gomphrena globosa infected with an unknown pathogen originally isolated from the flowering plant Liatris spicata. This plant was found to contain a new cucumovirus, for which we suggest the name 'Gayfeather mild mottle virus'. In both cases, the full viral genome was sequenced. This method expedites the entire process of novel virus discovery, identification, viral genome sequencing and, subsequently, the development of more routine assays for new viral pathogens.
Differentiated epidermal cells such as trichomes and conical cells perform numerous essential functions in plant biology and are important for our understanding of developmental patterning and cell ...shape regulation. Many are also commercially significant, such as cotton fibers and trichomes that secrete pharmaceutically useful or herbivore-deterring compounds. Here, we focus on the phylogeny and evolution of the subgroup 9 R2R3 MYB gene transcription factors, which include the MIXTA gene, and that are important for the specification and regulation of plant cellular differentiation. We have sequenced 49 subgroup 9 R2R3 MYB genes from key experimental taxa and combined these sequences with those identified by an exhaustive bioinformatic search, to compile a data set of 223 subgroup 9 R2R3 MYB genes. Our phylogenetic analyses demonstrate, for the first time, the complex evolutionary history of the subgroup 9 R2R3 MYB genes. A duplication event is inferred before the origin of seed plants giving rise to two major gene lineages, here termed SBG9-A and SBG9-B. The evolutionary conservation of the SBG9-B gene lineage has not been previously recognized and its role in cellular differentiation is unknown, thus an entire clade of potential candidate genes for epidermal cell regulation remains to be explored. Using a heterologous transformation bioassay, we provide functional data that implicate members of the SBG9-B lineage in the specification of epidermal projections. Furthermore, we reveal numerous putative duplication events in both SBG9-A and SBG9-B lineages, resolving uncertainty about orthology and paralogy among the subgroup 9 R2R3 MYB genes. Finally, we provide a robust framework over which to interpret existing functional data and to direct ongoing comparative genetic research into the evolution of plant cellular diversity.
The new sequencing technologies are already making a big impact in academic research on medically important microbes and may soon revolutionize diagnostics, epidemiology, and infection control. Plant ...pathology also stands to gain from exploiting these opportunities. This manuscript reviews some applications of these high-throughput sequencing methods that are relevant to phytopathology, with emphasis on the associated computational and bioinformatics challenges and their solutions. Second-generation sequencing technologies have recently been exploited in genomics of both prokaryotic and eukaryotic plant pathogens. They are also proving to be useful in diagnostics, especially with respect to viruses.
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor and a member of the PER-ARNT-SIM (PAS) superfamily of environmental sensors. The AHR is involved in a series of ...biological processes including adaptive metabolism of xenobiotics, toxicity of certain environmental pollutants, vascular development, fertility, and immune function. Mouse models, including the Ahr null and Ahr conditional null (Ahrfx) mice, are widely used for the study of AHR-mediated biology and toxicity. The Ahr conditional null mouse harbors the low-affinity Ahrd allele that exhibits approximately a 10-fold lower binding affinity for certain xenobiotic AHR ligands than the widely used C57BL/6 mouse that harbors the higher affinity Ahrb1 allele. Here, we report a novel mouse model that introduces a V375A polymorphism that converts the low-affinity allele into a high-affinity allele, offering a more sensitive conditional model. In the generation of this novel conditional allele, two additional mutants arose, including a 3-bp deletion in the PAS-B domain (AhrNG367R) and an early termination codon in the PAS-B domain (AhrTer383). The AhrNG367R allele presents as a phenocopy of the null and the AhrTer383 allele presents as an antimorph when assessing for the ductus venosus and liver lobe weight endpoints. These new models represent a series of tools that will be useful in further characterizing AHR biology.
Phenotypic integration, the coordinated covariance of suites of morphological traits, is critical for proper functioning of organisms. Angiosperm flowers are complex structures comprising suites of ...traits that function together to achieve effective pollen transfer. Floral integration could reflect shared genetic and developmental control of these traits, or could arise through pollinator-imposed stabilizing correlational selection on traits. We sought to expose mechanisms underlying floral trait integration in the sexually deceptive daisy, Gorteria diffusa, by testing the hypothesis that stabilizing selection imposed by male pollinators on floral traits involved in mimicry has resulted in tighter integration. To do this, we quantified patterns of floral trait variance and covariance in morphologically divergent G. diffusa floral forms representing a continuum in the levels of sexual deception. We show that integration of traits functioning in visual attraction of male pollinators increases with pollinator deception, and is stronger than integration of non-mimicry trait modules. Consistent patterns of within-population trait variance and covariance across floral forms suggest that integration has not been built by stabilizing correlational selection on genetically independent traits. Instead pollinator specialization has selected for tightened integration within modules of linked traits. Despite potentially strong constraint on morphological evolution imposed by developmental genetic linkages between traits, we demonstrate substantial divergence in traits across G. diffusa floral forms and show that divergence has often occurred without altering within-population patterns of trait correlations.
Structural colour in Chondrus crispus Chandler, Chris J; Wilts, Bodo D; Vignolini, Silvia ...
Scientific reports,
07/2015, Volume:
5, Issue:
1
Journal Article
Peer reviewed
Open access
The marine world is incredibly rich in brilliant and intense colours. Photonic structures are found in many different species and provide extremely complex optical responses that cannot be achieved ...solely by pigments. In this study we examine the cuticular structure of the red alga Chondrus crispus (Irish Moss) using anatomical and optical approaches. We experimentally measure the optical response of the multilayer structure in the cuticle. Using finite-difference time-domain modelling, we demonstrate conclusively for the first time that the dimensions and organisation of lamellae are responsible for the blue structural colouration on the surface of the fronds. Comparison of material along the apical-basal axis of the frond demonstrates that structural colour is confined to the tips of the thalli and show definitively that a lack of structural colour elsewhere corresponds with a reduction in the number of lamellae and the regularity of their ordering. Moreover, by studying the optical response for different hydration conditions, we demonstrate that the cuticular structure is highly porous and that the presence of water plays a critical role in its ability to act as a structural light reflector.
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