A Multiplex TaqMan qPCR Assay for Detection and Quantification of Clade 1 and Clade 2 Isolates of and .

The ability to detect and quantify aerially dispersed plant pathogens is essential for developing effective disease control measures and epidemiological models that optimize the timing for control. There is an acute need for managing the downy mildew pathogens infecting cucurbits and hop incited by members of the genus ( clade 1 and 2 isolates and , respectively). A highly specific multiplex TaqMan quantitative polymerase chain reaction (PCR) assay targeting unique sequences in the pathogens' mitochondrial genomes was developed that enables detection of all three taxa in a single multiplexed amplification.

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts.

Background: Macrophomina phaseolina is a fungal plant pathogen with a broad host range, but one genotype was shown to exhibit host preference/specificity on strawberry. This pathogen lacked a high-quality genome assembly and annotation, and little was known about genomic differences among isolates from different hosts.

Results: We used PacBio sequencing and Hi-C scaffolding to provide nearly complete genome assemblies for M.

Variable gene transcription underlies phenotypic convergence of hypoxia tolerance in sculpins.

Background: The degree by which mechanisms underlying phenotypic convergence are similar among taxa depends on the number of evolutionary paths available for selection to act upon. Likelihood of convergence will be influenced by an interplay of factors such as genetic architecture, phylogenetic history and population demography. To determine if there is convergence or divergence in mechanisms underlying phenotypic similarity, we assessed whether gene transcription patterns differed among species with similar levels of hypoxia tolerance.

Development of Molecular Methods to Detect Macrophomina phaseolina from Strawberry Plants and Soil.

Macrophomina phaseolina is a broad-host-range fungus that shows some degree of host preference on strawberry, and causes symptoms that include crown rot and root rot. Recently, this pathogen has affected strawberry production as fumigation practices have changed, leaving many growers in California and around the world in need of accurate, rapid diagnostic tools for M. phaseolina in soil and infected plants.

Divergent transcriptional patterns are related to differences in hypoxia tolerance between the intertidal and the subtidal sculpins.

Transcriptionally mediated phenotypic plasticity as a mechanism of modifying traits in response to an environmental challenge remains an important area of study. We compared the transcriptional responses to low oxygen (hypoxia) of the hypoxia-tolerant intertidal fish, the tidepool sculpin (Oligocottus maculosus) with the closely related hypoxia-intolerant subtidal fish, the silverspotted sculpin (Blepsias cirrhosus) to determine whether these species use different mechanisms to cope with hypoxia. Individuals from each species were exposed to environmental O(2) tensions chosen to yield a similar level of tissue hypoxia, and gene transcription was assessed in the liver over time.

Molecular support for marine sculpin (Cottidae; Oligocottinae) diversification during the transition from the subtidal to intertidal habitat in the Northeastern Pacific Ocean.

Sculpins in the genera Ruscarius, Artedius, Clinocottus, and Oligocottus are common intertidal and subtidal benthic fishes of the Northeastern Pacific Ocean. While there has been a long history of attempts to reconstruct the evolutionary relationships within this clade, studies have largely resulted in conflicting conclusions. Current ideas regarding the limits of species and genera in this subfamily (Oligocottinae) and their branching order are based primarily on morphology [Bolin, R.

Lack of mitochondrial genetic structure in hamlets (Hypoplectrus spp.): recent speciation or ongoing hybridization?

Species in the genus Hypoplectrus (hamlet fish) have been recognized primarily on the basis of colour morphology, which varies substantially. Limited differentiation in other morphological characters, however, has led to ongoing debate about their taxonomy. Our analysis of mtDNA sequences demonstrates neither reciprocal monophyly nor significant genetic differentiation among hamlet colour morphs.