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.

Effects of fluopyram and azadirachtin integration with sunn hemp on nematode communities in zucchini, tomato and sweet potato in Hawaii.

Fluopyram (Velum® One) is a synthetic nematicide and azadirachtin (Molt-X®) is a biological nematicide. Both have shown promise against plant-parasitic nematodes on several agriculturally important crops. There is a lack of information on integration of pre-plant sunn hemp (Crotalaria juncea) cover crop with these post-plant nematicides, aiming to improve plant-parasitic nematodes management and mitigate any detrimental effects on free-living nematodes. Three field trials were conducted to investigate the effects of fluopyram alone or in combination with pre-plant sunn hemp cover crop, and azadirachtin combined with pre-plant sunn hemp on Rotylenchulus reniformis and Meloidogyne spp., and free-living nematodes. Zucchini (Cucurbita pepo) and tomato (Solanum lycopersicum) were grown in Trials I and II, and sweet potato (Ipomoea batatas) only was grown in Trial III. In all three trials, early applications of fluopyram at crop planting were effective in suppressing the abundance of Meloidogyne spp. (M. incognita and M. javanica) but it was not effective in reducing R. reniformis in the soil. Combining sunn hemp with fluopyram was suppressive to R. reniformis on short-term zucchini crop, but not on longer term tomato and sweet potato crops. In addition, application of fluopyram at transplanting was the key to successful suppression of Meloidogyne spp. as later fluopyram chemigation (at 2 weeks after planting in Trial II or 1 month after planting in Trial III) had no effect against Meloidogyne spp. On the other hand, planting of sunn hemp followed by monthly post-plant azadirachtin application consistently suppressed R. reniformis, but this treatment did not suppress Meloidogyne spp. Integrating sunn hemp with fluopyram increased zucchini yield by >2.3 folds and that with azadirachtin increased the zucchini yield by >1.7 folds. Although no yield improvement was observed on tomato in Trial II, integrating sunn hemp with azadirachtin and fluopyram increased tomato yield by 0.23 and 1.12 folds, respectively, in Trial I. Marketable yield of sweet potato was increased by 4.5-6.4 folds in all the fluopyram treatments but was only increased 61.5% by sunn hemp plus azadirachtin treatment. While fluopyram alone often reduced the abundance of free-living nematodes, integrating with sunn hemp mitigated the negative impacts of fluopyram on soil health.

Reduced Emergence of Cylas formicarius elegantulus (Coleoptera: Curculionidae) from Sweet Potato Roots by Heterorhabditis indica.

Okinawan sweet potato, Ipomoea batatas, is an important food staple and export crop for the Island of Hawaii. Cylas formicarius elegantulus, sweet potato weevil, is a major quarantine pest that causes severe destruction to the crop. Root malformation and a bitter taste occur when larvae feed and tunnel within the storage root. Off-grade roots are often left in the field after harvest and serve as a reservoir for the weevils. Current management involves the unsustainable practice of moving to virgin land for the next cropping cycle. Strains of Heterorhabditis indica isolated from the Hawaiian Islands were tested for their efficacy at causing mortality of C. formicarius and reducing the emergence of adults from infested roots. In well plate assays, H. indica caused mortality of 88% larvae, 96% pupae, and 4% adults after 48 h. When applied to infested roots, the nematodes caused an average mortality of 78% larvae, 66% pupae, and 32% adults. Greater mortality was observed at the highest inoculum levels (10,000 infective juveniles per storage tuber) but a reduction of 90% inoculum density was still effective at weevil management. In simulated field trials, infestation of storage roots was reduced by 42-99.6% when planted among infested roots that had been inoculated with H. indica. Rates of 2.5 billion IJs/hectare were just as effective as 5 billion IJs/hectare. Application of local H. indica strains in sweet potato production has the potential to manage C. formicarius populations and allow for consecutive cropping seasons.

Organ-specific transcriptome profiling of metabolic and pigment biosynthesis pathways in the floral ornamental progenitor species Anthurium amnicola Dressler.

Anthurium amnicola Dressler possesses a number of desirable and novel ornamental traits such as a purple-colored upright spathe, profuse flowering, and floral scent, some of which have been introgressed into modern Anthurium cultivars. As a first step in identifying genes associated with these traits, the transcriptome from root, leaf, spathe, and spadix from an accession of A. amnicola was assembled, resulting in 28,019 putative transcripts representing 19,458 unigenes. Genes involved in pigmentation, including those for the metabolism of chlorophyll and the biosynthesis of carotenoids, phenylpropanoids, and flavonoids were identified. The expression levels of one MYB transcription factor was highly correlated with naringenin 3-dioxygenase (F3H) and dihydroflavonol-4-reductase (DFR) in leaves, whereas a bHLH transcription factor was highly correlated with flavonoid 3'-monooxygenase (F3'H) and a DFR in spathes, suggesting that these two transcription factors might regulate flavonoid and anthocyanin synthesis in A. amnicola. Gene sequence and expression data from four major organs of A. amnicola provide novel basal information for understanding the genetic bases of ornamental traits and the determinants and evolution of form and function in the Araceae.