Impact of Globodera ellingtonae on yield of potato (Solanum tuberosum).

Globodera ellingtonae was described from Oregon and Idaho in 2012. Due to the close phylogenetic relationship of this nematode to the potato cyst nematodes G. pallida and G. rostochiensis, and evidence that G. ellingtonae reproduces on potato (Solanum tuberosum), potential damaging effects to potato by this nematode are of great concern. To evaluate the pathogenic effects of G. ellingtonae on potato, five field and two microplot trials were conducted over a four-year period including comparisons of a range of G. ellingtonae initial population densities (Pi) and potato cultivars. In two field trials, potato 'Russet Burbank' was inoculated with Pi of G. ellingtonae ranging from 0 to 80 eggs/g soil; a similar trial was conducted with potato 'Désirée.' In another field trial, potato cultivars varying in maturity lengths were either inoculated (80 eggs/g soil) or not with G. ellingtonae. In a final field trial, 'Ranger Russet' was inoculated with Pi of G. ellingtonae ranging from 0 to 360 eggs/g soil. Additionally, Russet Burbank was inoculated with G. ellingtonae Pi ranging from 0 to 169 eggs/g soil in microplots. In all trials, data on tuber yield, aboveground biomass, final eggs/cyst, final population densities (Pf), and reproduction factor (RF = Pf/Pi) were collected. In only two of six trials conducted with increasing levels of Pi, was there a significant negative correlation between Pi of G. ellingtonae and yield of potato. Based on the linear regression model of tuber yield on logPi for Russet Burbank, 30.5 to 40.9% yield loss was predicted at a Pi of 40 and 80 eggs/g soil, respectively, and for Ranger Russet, 16.5 and 19.7% yield loss was predicted at a Pi of 40 and 80 eggs/g soil, respectively. None of the potato cultivars inoculated with 80 G. ellingtonae eggs/g soil had significantly reduced yields compared to non-inoculated plants. Reproduction factor values across trials ranged from 4.0 to 8.3 when inoculated with Pi of 40 eggs/g soil, demonstrating that the nematode successfully invaded and reproduced on potato in all trials. Care should be taken in extrapolating the results from these experiments conducted in Oregon to probable effects of G. ellingtonae on potato in other environments.KeywordsPotato, Damage, Globodera, Regression.Globodera ellingtonae was described from Oregon and Idaho in 2012. Due to the close phylogenetic relationship of this nematode to the potato cyst nematodes G. pallida and G. rostochiensis, and evidence that G. ellingtonae reproduces on potato (Solanum tuberosum), potential damaging effects to potato by this nematode are of great concern. To evaluate the pathogenic effects of G. ellingtonae on potato, five field and two microplot trials were conducted over a four-year period including comparisons of a range of G. ellingtonae initial population densities (Pi) and potato cultivars. In two field trials, potato 'Russet Burbank' was inoculated with Pi of G. ellingtonae ranging from 0 to 80 eggs/g soil; a similar trial was conducted with potato 'Désirée.' In another field trial, potato cultivars varying in maturity lengths were either inoculated (80 eggs/g soil) or not with G. ellingtonae. In a final field trial, 'Ranger Russet' was inoculated with Pi of G. ellingtonae ranging from 0 to 360 eggs/g soil. Additionally, Russet Burbank was inoculated with G. ellingtonae Pi ranging from 0 to 169 eggs/g soil in microplots. In all trials, data on tuber yield, aboveground biomass, final eggs/cyst, final population densities (Pf), and reproduction factor (RF = Pf/Pi) were collected. In only two of six trials conducted with increasing levels of Pi, was there a significant negative correlation between Pi of G. ellingtonae and yield of potato. Based on the linear regression model of tuber yield on logPi for Russet Burbank, 30.5 to 40.9% yield loss was predicted at a Pi of 40 and 80 eggs/g soil, respectively, and for Ranger Russet, 16.5 and 19.7% yield loss was predicted at a Pi of 40 and 80 eggs/g soil, respectively. None of the potato cultivars inoculated with 80 G. ellingtonae eggs/g soil had significantly reduced yields compared to non-inoculated plants. Reproduction factor values across trials ranged from 4.0 to 8.3 when inoculated with Pi of 40 eggs/g soil, demonstrating that the nematode successfully invaded and reproduced on potato in all trials. Care should be taken in extrapolating the results from these experiments conducted in Oregon to probable effects of G. ellingtonae on potato in other environments.KeywordsPotato, Damage, Globodera, Regression.

The Draft Genome of Globodera ellingtonae.

Globodera ellingtonae is a newly described potato cyst nematode (PCN) found in Idaho, Oregon, and Argentina. Here, we present a genome assembly for G. ellingtonae, a relative of the quarantine nematodes G. pallida and G. rostochiensis, produced using data from Illumina and Pacific Biosciences DNA sequencing technologies.

Draft Transcriptome of Globodera ellingtonae.

Globodera ellingtonae is a newly described cyst nematode found in Idaho, Oregon, and Argentina. Here we present the first transcriptome assembly of G. ellingtonae, providing a valuable resource for comparing the evolution of expressed genes between potato cyst nematode species.

Control of Globodera spp. Using Brassica juncea Seed Meal and Seed Meal Extract.

The eradication program for the potato cyst nematode (PCN), Globodera pallida, in the Northwest of the United States revolves around the use of soil fumigation. Alternative, integrated strategies are needed to continue to battle this invasive nematode. Laboratory, greenhouse, and field experiments were conducted with G. pallida and another cyst nematode found in the United States, Globodera ellingtonae, to evaluate the efficacy of a new formulated Brassica juncea seed meal extract, as well as a traditional B. juncea seed meal, as alternate eradication strategies. This is the first report on the efficacy of B. juncea seed meal extract against plant-parasitic nematodes. Rates of B. juncea seed meal greater than 2.2 t/ha and 4.5 t/ha for G. pallida and G. ellingtonae, respectively, were required for egg hatch suppression, as determined by a potato root diffusate (PRD) bioassay. Reproduction of G. pallida on potato after exposure to B. juncea seed meal at a rate of 2.2 t/ha was also significantly reduced. In the field, 8.9 t/ha B. juncea seed meal almost eliminated egg hatch of G. ellingtonae. Rates needed for Globodera spp. suppression were greatly reduced when using the B. juncea seed meal extract. When compared side-by-side, half as much B. juncea seed meal extract, 1.1 t/ha, was required to suppress G. ellingtonae egg hatch to the same extent as B. juncea seed meal. Exposure of G. pallida to B. juncea seed meal extract at 4.5 t/ha reduced egg hatch by 90% compared with a nonamended control. The ability to reduce the amount of material being applied to soil by using an extract has the potential for integration into a G. pallida eradication program.

Developmental Dynamics of Globodera ellingtonae in Field-Grown Potato.

Globodera ellingtonae is a recently described nematode parasite of potato, which is closely related to the economically significant potato cyst nematodes G. rostochiensis and G. pallida. Because of the close relationship of G. ellingtonae to the potato cyst nematodes, a greater understanding of its biology is critical. Two experiments were conducted in Oregon to explore the developmental biology of G. ellingtonae in field-grown potato. The first experiment was conducted in 2013 and 2014 to determine the developmental timing of G. ellingtonae life stages and reproduction by inoculating potato with soil containing cysts followed by weekly collection of soil and root samples. Life stages; second-stage juveniles (J2) in soil and roots, third-stage juveniles (J3) and fourth-stage (J4) females and males in roots, males and females or cysts in soil, and egg number and developmental state were quantified. Normalizing across years using accumulated developmental degree days above 6°C (DD6), J2 of G. ellingtonae were found in soil from 41 to 588 DD6; two peaks of J2 invasion of roots were observed. The first adult females were observed at 387 and 449 DD6 in 2013 and 2014, respectively. The next generation of eggs was first observed from 675 to 854 DD6 and 50% egg development (containing a vermiform juvenile) occurred at approximately 920 DD6. A second J2 hatch was observed in both years at 927 to 1,073 DD6. The developmental dynamics of G. ellingtonae observed here are similar to those reported for G. rostochiensis and G. pallida from several geographical locations. In the second experiment, the effect of potato and bare soil on G. ellingtonae egg hatch was evaluated; in 2014 and 2015, packages containing cysts in soil were buried under potato or in bare soil at the time of planting and eggs per cyst determined weekly. Across years, a significant reduction in eggs per cysts under potato (>50%) was observed 35 days after planting (DAP) and, at 63 DAP, eggs per cyst were reduced by 76 to 96% compared with initial egg per cyst densities. In bare soil, the maximum reduction in densities of eggs per cyst was 55 to 73%. This annual reduction in egg numbers of G. ellingtonae in bare soil is similar to that reported for G. pallida and G. rostochiensis.

The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers.

BACKGROUND: The evolution of animal mitochondrial (mt) genomes has resulted in a highly conserved structure: a single compact circular chromosome approximately 14 to 20 kb long. Within the last two decades exceptions to this conserved structure, such as the division of the genome into multiple chromosomes, have been reported in a diverse set of metazoans. We report on the two circle multipartite mt genome of a newly described cyst nematode, Globodera ellingtonae. RESULTS: The G. ellingtonae mt genome was found to be comprised of two circles, each larger than any other multipartite circular mt chromosome yet reported, and both were larger than the single mt circle of the model nematode Caenorhabditis elegans. The genetic content of the genome was disproportionately divided between the two circles, although they shared a ~6.5 kb non-coding region. The 17.8 kb circle (mtDNA-I) contained ten protein-coding genes and two tRNA genes, whereas the 14.4 kb circle (mtDNA-II) contained two protein-coding genes, 20 tRNA genes and both rRNA genes. Perhaps correlated with this division of genetic content, the copy number of mtDNA-II was more than four-fold that of mtDNA-I in individual nematodes. The difference in copy number increased between second-stage and fourth-stage juveniles. CONCLUSIONS: The segregation of gene types to different mt circles in G. ellingtonae could provide benefit by localizing gene functional types to independent transcriptional units. This is the first report of both two-circle and several-circle mt genomes within a single genus. The differential copy number associated with this multipartite mt organization could provide a model system for deconstructing mechanisms regulating mtDNA copy number both in somatic cells and during germline development.

Selfish Mitochondrial DNA Proliferates and Diversifies in Small, but not Large, Experimental Populations of Caenorhabditis briggsae.

Evolutionary interactions across levels of biological organization contribute to a variety of fundamental processes including genome evolution, reproductive mode transitions, species diversification, and extinction. Evolutionary theory predicts that so-called "selfish" genetic elements will proliferate when the host effective population size (Ne) is small, but direct tests of this prediction remain few. We analyzed the evolutionary dynamics of deletion-containing mitochondrial DNA (ΔmtDNA) molecules, previously characterized as selfish elements, in six different natural strains of the nematode Caenorhabditis briggsae allowed to undergo experimental evolution in a range of population sizes (N = 1, 10, 100, and 1,000) for a maximum of 50 generations. Mitochondrial DNA (mtDNA) was analyzed for replicate lineages at each five-generation time point. Ten different ΔmtDNA molecule types were observed and characterized across generations in the experimental populations. Consistent with predictions from evolutionary theory, lab lines evolved in small-population sizes (e.g., nematode N = 1) were more susceptible to accumulation of high levels of preexisting ΔmtDNA compared with those evolved in larger populations. New ΔmtDNA elements were observed to increase in frequency and persist across time points, but almost exclusively at small population sizes. In some cases, ΔmtDNA levels decreased across generations when population size was large (nematode N = 1,000). Different natural strains of C. briggsae varied in their susceptibilities to ΔmtDNA accumulation, owing in part to preexisting compensatory mtDNA alleles in some strains that prevent deletion formation. This analysis directly demonstrates that the evolutionary trajectories of ΔmtDNA elements depend upon the population-genetic environments and molecular-genetic features of their hosts.

The Relationship between Temperature and Development in Globodera ellingtonae.

A new cyst nematode species, Globodera ellingtonae, was recently described from populations in Oregon and Idaho. This nematode has been shown to reproduce on potato. Because of this nematode's close relationship to the potato cyst nematodes, G. rostochiensis and G. pallida, an understanding of the risk of its potential spread, including prediction of potential geographical distribution, is required. To determine the development of G. ellingtonae under different temperatures, we conducted growth chamber experiments over a range of temperatures (10.0°C to 26.5°C) and tracked length of time to various developmental stages, including adult females bearing the next generation of eggs. Both the time to peak population densities of G. ellingtonae life stages and their duration in roots generally increased with decreasing temperature. Regression of growth rate to second-stage (J2) and third-stage (J3) juveniles on temperature yielded different base temperatures: 6.3°C and 4.4°C for J2 and J3, respectively. Setting a base temperature of 6°C allowed calculation of the degree-days (DD6) over which different life stages occurred. The largest population densities of J2 were found in roots between 50 and 200 DD6. Population densities of J3 peaked between 200 and 300 DD6. Adult males were detected in soil starting at 300 to 400 DD6 and remained detectable for approximately 500 DD6. By 784 to 884 DD6, half of the eggs in adult females contained vermiform juveniles. Given the similarity in temperature ranges for successful development between G. ellingtonae and G. rostochiensis, G. ellingtonae populations likely could survive in the same geographic range in which G. rostochiensis now occurs.

Analytical approach for selecting normalizing genes from a cDNA microarray platform to be used in q-RT-PCR assays: a cnidarian case study.

Research in gene function using Quantitative Reverse Transcription PCR (q-RT-PCR) and microarray approaches are emerging and just about to explode in the field of coral and cnidarian biology. These approaches are showing the great potential to significantly advance our understanding of how corals respond to abiotic and biotic stresses, and how host cnidarians/dinoflagellates symbioses are maintained and regulated. With these genomic advances, however, new analytical challenges are also emerging, such as the normalization of gene expression data derived from q-RT-PCR. In this study, an effective analytical method is introduced to identify candidate housekeeping genes (HKG) from a sea anemone (Anthopleura elegantissima) cDNA microarray platform that can be used as internal control genes to normalize q-RT-PCR gene expression data. It is shown that the identified HKGs were stable among the experimental conditions tested in this study. The three most stables genes identified, in term of gene expression, were beta-actin, ribosomal protein L12, and a Poly(a) binding protein. The applications of these HKGs in other cnidarian systems are further discussed.

Knockdown of actin and caspase gene expression by RNA interference in the symbiotic anemone Aiptasia pallida.

Since the discovery of the ancient eukaryotic process of RNA-mediated gene silencing, the reverse-genetics technique RNA interference (RNAi) has increasingly been used to examine gene function in vertebrate and invertebrate systems. In this study, we report on the use of RNAi, adapted from studies on animal model systems, to manipulate gene expression in a symbiotic marine cnidarian. We describe gene knockdown of actin and of acasp--a cysteine protease, or caspase--in the symbiotic sea anemone Aiptasia pallida. Knockdown was assessed qualitatively with in situ hybridizations for both genes. Quantitative PCR and caspase activity assays were used as a quantitative measure of knockdown for acasp.

Characterization of a novel EF-hand homologue, CnidEF, in the sea anemone Anthopleura elegantissima.

The superfamily of EF-hand proteins is comprised of a large and diverse group of proteins that contain one or more characteristic EF-hand calcium-binding domains. This study describes and characterizes a novel EF-hand cDNA, CnidEF, from the sea anemone Anthopleura elegantissima (Phylum Cnidaria, Class Anthozoa). CnidEF was found to contain two EF-hand motifs near the C-terminus of the deduced amino acid sequence and two regions near the N-terminus that could represent degenerate EF-hand motifs. CnidEF homologues were also identified from two other sea anemone species. A combination of bioinformatic and molecular phylogenetic analyses was used to compare CnidEF to EF-hand proteins in other organisms. The closest homologues identified from these analyses were a luciferin binding protein (LBP) involved in the bioluminescence of the anthozoan Renilla reniformis, and a sarcoplasmic calcium-binding protein (SARC) involved in fluorescence of the annelid worm Nereis diversicolor. Predicted structure and folding analysis revealed a close association with bioluminescent aequorin (AEQ) proteins from the hydrozoan cnidarian Aequorea aequorea. Neighbor-joining analyses grouped CnidEF within the SARC lineage along with AEQ and other cnidarian bioluminescent proteins rather than in the lineage containing calmodulin (CAM) and troponin-C (TNC).

Highly conserved caspase and Bcl-2 homologues from the sea anemone Aiptasia pallida: lower metazoans as models for the study of apoptosis evolution.

Key insight into the complexities of apoptosis may be gained from the study of its evolution in lower metazoans. In this study we describe two genes from a cnidarian, Aiptasia pallida, that are homologous to key genes in the apoptotic pathway from vertebrates. The first is a novel ancient caspase, acasp, that displays attributes of both initiator and executioner caspases and includes a caspase recruitment domain (CARD). The second, a Bcl-2 family member, abhp, contains a BH1 and BH2 domain and shares structural characteristics and phylogenetic affinity with a group of antiapoptotic Bcl-2s including A1 and Bcl-2L10. The breadth of occurrence of other invertebrate homologues across the phylogenetic trees of both genes suggests that the complexity of apoptotic pathways is an ancient trait that predates the evolution of vertebrates and higher invertebrates such as nematodes and flies. This paves the way for establishing new lower metazoan model systems for the study of apoptosis.

Transcriptome analysis of a cnidarian-dinoflagellate mutualism reveals complex modulation of host gene expression.

BACKGROUND: Cnidarian-dinoflagellate intracellular symbioses are one of the most important mutualisms in the marine environment. They form the trophic and structural foundation of coral reef ecosystems, and have played a key role in the evolutionary radiation and biodiversity of cnidarian species. Despite the prevalence of these symbioses, we still know very little about the molecular modulators that initiate, regulate, and maintain the interaction between these two different biological entities. In this study, we conducted a comparative host anemone transcriptome analysis using a cDNA microarray platform to identify genes involved in cnidarian-algal symbiosis. RESULTS: We detected statistically significant differences in host gene expression profiles between sea anemones (Anthopleura elegantissima) in a symbiotic and non-symbiotic state. The group of genes, whose expression is altered, is diverse, suggesting that the molecular regulation of the symbiosis is governed by changes in multiple cellular processes. In the context of cnidarian-dinoflagellate symbioses, we discuss pivotal host gene expression changes involved in lipid metabolism, cell adhesion, cell proliferation, apoptosis, and oxidative stress. CONCLUSION: Our data do not support the existence of symbiosis-specific genes involved in controlling and regulating the symbiosis. Instead, it appears that the symbiosis is maintained by altering expression of existing genes involved in vital cellular processes. Specifically, the finding of key genes involved in cell cycle progression and apoptosis have led us to hypothesize that a suppression of apoptosis, together with a deregulation of the host cell cycle, create a platform that might be necessary for symbiont and/or symbiont-containing host cell survival. This first comprehensive molecular examination of the cnidarian-dinoflagellate associations provides critical insights into the maintenance and regulation of the symbiosis.