Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis.

The burrowing nematode, Radopholus similis, is an economically important plant-parasitic nematode that inflicts damage and yield loss to a wide range of crops. This migratory endoparasite is widely distributed in warmer regions and causes extensive destruction to the root systems of important food crops (e.g., citrus, banana). Despite the economic importance of this nematode, little is known about the repertoire of effectors owned by this species. Here we combined spatially and temporally resolved next-generation sequencing datasets of R. similis to select a list of candidates for the identification of effector genes for this species. We confirmed spatial expression of transcripts of 30 new candidate effectors within the esophageal glands of R. similis by in situ hybridization, revealing a large number of pioneer genes specific to this nematode. We identify a gland promoter motif specifically associated with the subventral glands (named Rs-SUG box), a putative hallmark of spatial and concerted regulation of these effectors. Nematode transcriptome analyses confirmed the expression of these effectors during the interaction with the host, with a large number of pioneer genes being especially abundant. Our data revealed that R. similis holds a diverse and emergent repertoire of effectors, which has been shaped by various evolutionary events, including neofunctionalization, horizontal gene transfer, and possibly by de novo gene birth. In addition, we also report the first GH62 gene so far discovered for any metazoan and putatively acquired by lateral gene transfer from a bacterial donor. Considering the economic damage caused by R. similis, this information provides valuable data to elucidate the mode of parasitism of this nematode

Different Conformations of Phosphatase and Tensin Homolog, Deleted on Chromosome 10 (PTEN) Protein within the Nucleus and Cytoplasm of Neurons

PTEN is a critical gene involved in the regulation of many cellular processes. The product of this gene has dual phosphatase activity and is able to dephosphorylate the 5′ end of the phosphatidylinositol (3,4,5)-trisphosphate. Within the cellular nucleus, this protein has been associated with regulation of the expression of many genes, although the mechanism of this regulation remains unclear. In this paper, two specific oligonucleotide aptamers were developed and selected, using the SELEX procedure, according to their ability to detect the PTEN protein in different subcellular compartments of neurons. While one aptamer was able to detect PTEN in the nucleus, the other recognized PTEN in the cytoplasm. The recognition pattern of PTEN by both aptamers was confirmed using antibodies in western blots of the proteins purified from mouse cerebellar homogenates and subcellular fractions. Additionally, we demonstrated that the two aptamers recognized different epitopes of the target peptide. The results presented here could not be fully explained by the canonical phosphatase structure of PTEN, suggesting the existence of different conformations of phosphatase in the nucleus and the cytoplasm

Six RNA Viruses and Forty-One Hosts: Viral Small RNAs and Modulation of Small RNA Repertoires in Vertebrate and Invertebrate Systems

We have used multiplexed high-throughput sequencing to characterize changes in small RNA populations that occur during viral infection in animal cells. Small RNA-based mechanisms such as RNA interference (RNAi) have been shown in plant and invertebrate systems to play a key role in host responses to viral infection. Although homologs of the key RNAi effector pathways are present in mammalian cells, and can launch an RNAi-mediated degradation of experimentally targeted mRNAs, any role for such responses in mammalian host-virus interactions remains to be characterized. Six different viruses were examined in 41 experimentally susceptible and resistant host systems. We identified virus-derived small RNAs (vsRNAs) from all six viruses, with total abundance varying from “vanishingly rare” (less than 0.1% of cellular small RNA) to highly abundant (comparable to abundant micro-RNAs “miRNAs”). In addition to the appearance of vsRNAs during infection, we saw a number of specific changes in host miRNA profiles. For several infection models investigated in more detail, the RNAi and Interferon pathways modulated the abundance of vsRNAs. We also found evidence for populations of vsRNAs that exist as duplexed siRNAs with zero to three nucleotide 3′ overhangs. Using populations of cells carrying a Hepatitis C replicon, we observed strand-selective loading of siRNAs onto Argonaute complexes. These experiments define vsRNAs as one possible component of the interplay between animal viruses and their hosts

Evaluation of <i>Coffea arabica</i> Cultivars for Resistance to <i>Meloidogyne konaensis</i>

Coffee is an important agricultural crop for the State of Hawaii. Developing new coffee cultivars with resistance to damaging pests and diseases is crucial for improving production and maintaining the profitability of the industry. With the recent discovery of Hemileia vastatrix, coffee leaf rust (CLR), to Hawaii there is a strong interest in replanting with CLR-resistant germplasm. However, when selecting an appropriate cultivar for replanting, susceptibility to other pathogens, such as plant-parasitic nematodes, should be taken into consideration. Meloidogyne konaensis, the Kona coffee root-knot nematode, causes severe destruction of the root system, reducing the yield and causing the mortality of susceptible Coffea arabica cv. Typica trees. Fortunately, resistance to root-knot nematodes has been found in some C. arabica germplasm. In this study, accessions of wild Ethiopian C. arabica and two CLR-resistant C. arabica cultivars, Tupi-HI and Obata, were evaluated for resistance to M. konaensis in a greenhouse bioassay. All Ethiopian accessions retained high levels of resistance, resulting in reproductive factors (Rfs) lower than 1.0, and low root-rot ratings. Tupi-HI was highly susceptible to M. konanensis, with an Rf value of 7.12, whereas Obata was slightly susceptible, with an Rf value of 2.33. Both cultivars had high root-rot ratings, suggesting intolerance to the nematode. Hybridizing Ethiopian C. arabica with Tupi-HI or Obata may result in new elite cultivars, resistant to both H. vastatrix and M. konaensis

Integrating Trap Cropping and Entomopathogenic Nematode Foliar Sprays to Manage Diamondback Moth and Imported Cabbage Worm

Diamondback moth (DBM), Plutella xylostella, and imported cabbage worm (ICW), Pieris rapae, are destructive pests of crucifers worldwide. Although several insecticides are effective against ICW, pesticide management against DBM is challenged by insecticide resistant populations. The objective of this study was to explore the potential of integrating foliar sprays of the entomopathogenic nematode (EPN) Steinernema feltiae with trap cropping using kai choi (Brassica juncea) planted as an intercrop for the management of DBM and ICW. Four 2 &times; 2 (trap crop &times; EPN) factorial designed field trials were conducted with 2 trials on head cabbage (Brassica oleraceae var capitata) and 2 on kale (Brassica oleraceae var acephala). In the first head cabbage trial, trap cropping reduced DBM abundance by 46% and ICW abundance by 73%. Leaf damage by DBM and ICW were reduced by 45% and 33%, respectively. In the second head cabbage trial, DBM populations were reduced by 19% whereas ICW was reduced by 65%. No effects were observed on leaf damage. Trap cropping suppressed DBM abundance by 50% and DBM leaf damage by 19% in the first kale trial. No significant effects were observed on ICW. In the second kale trial, trap cropping reduced ICW leaf damage by 13%. In the first head cabbage trial, adding EPN foliar sprays further reduced DBM populations in plots with trap crops and ICW in plots without trap crops. In the second kale trial, EPNs suppressed DBM populations entirely. No effects from EPNs were observed in the second head cabbage trial or the first kale trial. It is concluded that trap cropping with kai choi did not improve the efficacy of EPN foliar sprays consistently. EPNs were most successful at suppressing DBM and ICW populations when the average pest pressure was below 0.5/plant whereas trap crops worked more effectively at insect populations above 0.5/plant. Although the use of trap cropping reduced pest abundance and leaf damage, the weight of head cabbage and kale was lower when planted 30 cm or closer to kai choi plants. This was resolved by leaving a distance of 60 cm between cash and trap crops. With further optimization, the use of trap cropping and EPN foliar sprays can be beneficial to an integrated pest management program to control DBM and ICW in cruciferous crops

Integrated Pest Management of Coffee Berry Borer in Hawaii and Puerto Rico: Current Status and Prospects

The coffee berry borer (CBB), Hypothenemus hampei, is the most significant insect pest of coffee worldwide. Since CBB was detected in Puerto Rico in 2007 and Hawaii in 2010, coffee growers from these islands are facing increased costs, reduced coffee quality, and increased pest management challenges. Here, we outline the CBB situation, and summarize the findings of growers, researchers, and extension professionals working with CBB in Hawaii. Recommendations for the Integrated Pest Management (IPM) program for CBB in Hawaiian Islands and Puerto Rico include: (1) establish a CBB monitoring program, (2) synchronize applications of insecticides with peak flight activity of CBB especially during the early coffee season, (3) conduct efficient strip-picking as soon as possible after harvest and perform pre-harvest sanitation picks in CBB hotspots if needed, (4) establish protocols to prevent the escape of CBB from processing areas and when transporting berries during harvest, and (5) stump prune by blocks. Progress achieved includes the introduction of the mycoinsecticide Beauveria bassiana to coffee plantations, the coordination of area-wide CBB surveys, the establishment and augmentation of native beetle predators, and an observed reduction of CBB populations and increased coffee quality where IPM programs were established. However, CBB remains a challenge for coffee growers due to regional variability in CBB pressures, high costs, and labor issues, including a lack of training and awareness of CBB management practices among growers

Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis

The burrowing nematode, Radopholus similis, is an economically important plant-parasitic nematode that inflicts damage and yield loss to a wide range of crops. This migratory endoparasite is widely distributed in warmer regions and causes extensive destruction to the root systems of important food crops (e.g., citrus, banana). Despite the economic importance of this nematode, little is known about the repertoire of effectors owned by this species. Here we combined spatially and temporally resolved next-generation sequencing datasets of R. similis to select a list of candidates for the identification of effector genes for this species. We confirmed spatial expression of transcripts of 30 new candidate effectors within the esophageal glands of R. similis by in situ hybridization, revealing a large number of pioneer genes specific to this nematode. We identify a gland promoter motif specifically associated with the subventral glands (named Rs-SUG box), a putative hallmark of spatial and concerted regulation of these effectors. Nematode transcriptome analyses confirmed the expression of these effectors during the interaction with the host, with a large number of pioneer genes being especially abundant. Our data revealed that R. similis holds a diverse and emergent repertoire of effectors, which has been shaped by various evolutionary events, including neofunctionalization, horizontal gene transfer, and possibly by de novo gene birth. In addition, we also report the first GH62 gene so far discovered for any metazoan and putatively acquired by lateral gene transfer from a bacterial donor. Considering the economic damage caused by R. similis, this information provides valuable data to elucidate the mode of parasitism of this nematode.This article is published as Vieira P, Myers RY, Pellegrin C, Wram C, Hesse C, Maier TR, et al. (2021) Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis. PLoS Pathog 17(11): e1010036. https://doi.org/10.1371/journal.ppat.1010036. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication