RNA-Seq Based Identification of Candidate Parasitism Genes of Cereal Cyst Nematode (Heterodera avenae) during Incompatible Infection to Aegilops variabilis

Chromosome-level genome assembly of the cereal cyst nematode Heterodera flipjevi

As an economically important plant parasitic nematode (PPN), Heterodera filipjevi causes great damage on wheat, and now it was widely recorded in many countries. While multiple genomes of PPNs have been published, high-quality genome assembly and annotation on H. filipjevi have yet to be performed. This study presents a chromosome-scale genome assembly and annotation for H. filipjevi, utilizing a combination of Illumina short-read, PacBio long-read, and Hi-C sequencing technologies. The genome consists of 9 pseudo-chromosomes that contain 134.19 Mb of sequence, with a scaffold N50 length of 11.88 Mb. In total, 10,036 genes were annotated, representing 75.20% of the total predicted protein-coding genes. Our study provides the first chromosome-scale genome for H. filipjevi, which is also the inaugural high-quality genome of cereal cyst nematodes (CCNs). It provides a valuable genomic resource for further biological research and pest management of cereal cyst nematodes disease.

Wheat Root Protection From Cereal Cyst Nematode (Heterodera avenae) by Fluopyram Seed Treatment

Cereal cyst nematode (Heterodera avenae), an important plant-parasitic nematode causing yield losses of wheat, has been found in many provinces in China. It is urgent to develop an effective method of protecting wheat from H. avenae damage. Because of its novel mode of action, fluopyram has been registered for controlling root-knot nematodes on cucumber and tomato in China. However, the bioactivity of fluopyram against H. avenae and whether this seed treatment can effectively control H. avenae on wheat remains unknown. In this study, a bioactivity assay revealed that fluopyram increased the mortality of H. avenae second-stage juveniles (J2), with lethal concentrations (LC) required to kill 50% (LC50) and 90% (LC90) of 0.92 mg⋅liter^-1 and 2.92 mg⋅liter^-1_, respectively. Hatching tests showed that the H. avenae egg hatching percent was reduced by 35.2 to 69.2% with fluopyram at rates of 1.6 to 6.4 mg⋅liter^-1, and that the egg hatching period was delayed by 3 to 9 days compared with the control. During pot and field trials, fluopyram seed treatment significantly reduced the H. avenae population density and increased wheat yield by 3.0 to 13.7%. Therefore, fluopyram seed treatment is an effective approach for the management of H. avenae on wheat in China.

Signatures of adaptation to a monocot host in the plant-parasitic cyst nematode Heterodera sacchari

Interactions between plant-parasitic nematodes and their hosts are mediated by effectors, i.e. secreted proteins that manipulate the plant to the benefit of the pathogen. To understand the role of effectors in host adaptation in nematodes, we analysed the transcriptome of Heterodera sacchari, a cyst nematode parasite of rice (Oryza sativa) and sugarcane (Saccharum officinarum). A multi-gene phylogenetic analysis showed that H. sacchari and the cereal cyst nematode Heterodera avenae share a common evolutionary origin and that they evolved to parasitise monocot plants from a common dicot-parasitic ancestor. We compared the effector repertoires of H. sacchari with those of the dicot parasites Heterodera glycines and Globodera rostochiensis to understand the consequences of this transition. While, in general, effector repertoires are similar between the species, comparing effectors and non-effectors of H. sacchari and G. rostochiensis shows that effectors have accumulated more mutations than non-effectors. Although most effectors show conserved spatiotemporal expression profiles and likely function, some H. sacchari effectors are adapted to monocots. This is exemplified by the plant-peptide hormone mimics, the CLAVATA3/EMBRYO SURROUNDING REGION-like (CLE) effectors. Peptide hormones encoded by H. sacchari CLE effectors are more similar to those from rice than those from other plants, or those from other plant-parasitic nematodes. We experimentally validated the functional significance of these observations by demonstrating that CLE peptides encoded by H. sacchari induce a short root phenotype in rice, whereas those from a related dicot parasite do not. These data provide a functional example of effector evolution that co-occurred with the transition from a dicot-parasitic to a monocot-parasitic lifestyle.

RNAi-Based Biocontrol of Wheat Nematodes Using Natural Poly-Component Biostimulants

With the growing global demands on sustainable food production, one of the biggest challenges to agriculture is associated with crop losses due to parasitic nematodes. While chemical pesticides have been quite successful in crop protection and mitigation of damage from parasites, their potential harm to humans and environment, as well as the emergence of nematode resistance, have necessitated the development of viable alternatives to chemical pesticides. One of the most promising and targeted approaches to biocontrol of parasitic nematodes in crops is that of RNA interference (RNAi). In this study we explore the possibility of using biostimulants obtained from metabolites of soil streptomycetes to protect wheat (Triticum aestivum L.) against the cereal cyst nematode Heterodera avenae by means of inducing RNAi in wheat plants. Theoretical models of uptake of organic compounds by plants, and within-plant RNAi dynamics, have provided us with useful insights regarding the choice of routes for delivery of RNAi-inducing biostimulants into plants. We then conducted in planta experiments with several streptomycete-derived biostimulants, which have demonstrated the efficiency of these biostimulants at improving plant growth and development, as well as in providing resistance against the cereal cyst nematode. Using dot blot hybridization we demonstrate that biostimulants trigger a significant increase of the production in plant cells of si/miRNA complementary with plant and nematode mRNA. Wheat germ cell-free experiments show that these si/miRNAs are indeed very effective at silencing the translation of nematode mRNA having complementary sequences, thus reducing the level of nematode infestation and improving plant resistance to nematodes. Thus, we conclude that natural biostimulants produced from metabolites of soil streptomycetes provide an effective tool for biocontrol of wheat nematode.

Cereal Root Interactions with Soilborne Pathogens—From Trait to Gene and Back

Realizing the yield potential of crop plants in the presence of shifting pathogen populations, soil quality, rainfall, and other agro-environmental variables remains a challenge for growers and breeders worldwide. In this review, we discuss current approaches for combatting the soilborne phytopathogenic nematodes, Pratylenchus and Heterodera of wheat and barley, and Meloidogyne graminicola Golden and Birchfield, 1965 of rice. The necrotrophic fungal pathogens, Rhizoctonia solani Kühn 1858 AG-8 and Fusarium spp. of wheat and barley, also are discussed. These pathogens constitute major causes of yield loss in small-grain cereals of the Pacific Northwest, USA and throughout the world. Current topics include new sources of genetic resistance, molecular leads from whole genome sequencing and genome-wide patterns of hosts, nematode or fungal gene expression during root-pathogen interactions, host-induced gene silencing, and building a molecular toolbox of genes and regulatory sequences for deployment of resistance genes. In conclusion, improvement of wheat, barley, and rice will require multiple approaches.

Two venom allergen-like proteins, HaVAP1 and HaVAP2, are involved in the parasitism of Heterodera avenae

Despite the fact that venom allergen-like proteins (VAPs) have been identified in many animal- and plant-parasitic nematodes, studies on VAPs in Heterodera avenae, which is an important phytonematode, are still in their infancy. Here, we isolated, cloned and characterized two VAPs, named HaVAP1 and HaVAP2, from H. avenae. The two encoded proteins, HaVAP1 and HaVAP2, harbour an SCP-like domain each, but share only 38% identity with each other. HaVAP1 and HaVAP2 are expressed in subventral and dorsal oesophageal glands, respectively. HaVAP1 is expressed mainly at the early stages, whereas HaVAP2 accumulates principally at the late stages. Both HaVAP1 and HaVAP2 are secreted when expressed in Nicotiana benthamiana leaves, but HaVAP1 is delivered into chloroplasts, whereas HaVAP2 is translocated to the nucleus without signal peptides. Knocking down HaVAP1 increased the virulence of H. avenae. In contrast, silencing of HaVAP2 hampered the parasitism of H. avenae. Both HaVAP1 and HaVAP2 suppressed the cell death induced by BAX in N. benthamiana leaves. Moreover, HaVAP2 physically interacted with a CYPRO4-like protein (HvCLP) of Hordeum vulgare in the nucleus of the plant. It is reasonable to speculate that the changes in the transcript of HvCLP are associated with HaVAP2 during the parasitism of H. avenae. All results obtained in this study show that both HaVAP1 and HaVAP2 are involved in the parasitism of H. avenae, but they possess different functions, broadening our understanding of the parasitic mechanism of H. avenae.

The Tryptophan decarboxylase 1 Gene From Aegilops variabilis No.1 Regulate the Resistance Against Cereal Cyst Nematode by Altering the Downstream Secondary Metabolite Contents Rather Than Auxin Synthesis

Cereal cyst nematode (CCN, Heterodera avenae) is a most important pathogen of wheat and causes tremendous yield loss annually over the world. Since the lack of resistance materials among wheat cultivars, identification and characterization of the resistance-related genes from the relatives of wheat is a necessary and efficient way. As a close relative of wheat with high resistance against CCN, Aegilops variabilis No.1 is believed to be a valuable source for wheat breeding against this devastating disease. However so far, very few resistance-associated genes have been characterized from this species. In this study, we present that the tryptophan decarboxylase genes from Ae. variabilis No.1 (AeVTDC1 and AeVTDC2) were both induced by CCN juveniles at the early stage of resistance response (30 h post-inoculation), with AeVTDC1 more sensitive to CCN infection than AeVTDC2. Silencing of AeVTDC1 led to compromised immunity to CCN with more CCN intrusion into roots; while overexpression AeVTDC1 in Nicotiana tabacum dramatically enhanced the resistance of plants by reducing the knots formed on roots. Metabolism analysis showed that the contents of secondary metabolites with activity of resistance to varied pathogens correlated with the expression level of AeVTDC1 in both Ae. variabilis No.1 and the transgenic tobacco plants. In addition, the content of IAA was not affected by either silencing or overexpressing of AeVTDC1. Hence, our research provided AeVTDC1 a valuable target that mediates resistance to CCN and root knot nematode (RKN, Meloidogyne naasi) without influencing the auxin biosynthesis.

Characterization of Putative Effectors from the Cereal Cyst Nematode Heterodera avenae

Few molecular details of effectors of Heterodera avenae parasitism are known. We performed a high-throughput sequencing analysis of the H. avenae transcriptome at five developmental stages. A total of 82,549 unigenes were ultimately obtained, and 747 transcripts showed best hits to genes putatively encoding carbohydrate-active enzymes in plant-parasitic nematodes that play an important role in the invasion process. A total of 1,480 unigenes were homologous to known phytonematode effectors, and 63 putative novel effectors were identified in the H. avenae transcriptomes. Twenty-three unigenes were analyzed by qRT-PCR and confirmed to be highly expressed during at least one developmental stage. For in situ hybridization, 17 of the 22 tested putative effectors were specifically expressed and located in the subventral gland cells, and five putative novel effectors were specifically expressed in the dorsal gland. Furthermore, 115 transcripts were found to have putative lethal RNA interference (RNAi) phenotypes. Three target genes with lethal RNAi phenotypes and two of the four tested putative effectors were associated with a decrease in the number of cysts through in vitro RNAi technology. These transcriptomic data lay a foundation for further studies of interactions of H. avenae with cereal and H. avenae parasitic control.

Transcriptional responses of wheat and the cereal cyst nematode Heterodera avenae during their early contact stage

Cereal cyst nematode (Heterodera avenae) is attracted to and aggregated around wheat roots to initiate infection, but this interaction between wheat and the nematode is not fully understood. The transcriptional responses of both wheat and H. avenae were examined during their early contact stage by mRNA sequencing analysis; certain numbers of the differentially expressed genes (DEGs) were validated using quantitative real-time PCR. The immobile host wheat root only had 93 DEGs (27 up-regulated and 66 down-regulated), while the mobile plant parasitic nematode reacted much more actively with 879 DEGs (867 up-regulated and 12 down-regulated). Among them, a number of wheat DEGs (mostly down-regulated) were involved in biotic stress pathways, while several putative effector genes were up-regulated in the nematode DEGs. One putative chitinase-like effector gene of H. avenae was able to suppress BAX-triggered programmed cell death in Nicotiana benthamiana. Results of these experiments demonstrated that nematode responded more actively than wheat during the contact stage of parasitism. The parasite's responses mainly involved up-regulation of genes including at least one anti-plant-defence effector gene, whereas the host responses mainly involved down-regulation of certain defence-related genes.

Cereal Cyst Nematodes: A Complex and Destructive Group of Heterodera Species

Small grain cereals have served as the basis for staple foods, beverages, and animal feed for thousands of years. Wheat, barley, oats, rye, triticale, rice, and others are rich in calories, proteins, carbohydrates, vitamins, and minerals. These cereals supply 20% of the calories consumed by people worldwide and are therefore a primary source of energy for humans and play a vital role in global food and nutrition security. Global production of small grains increased linearly from 1960 to 2005, and then began to decline. Further decline in production is projected to continue through 2050 while global demand for these grains is projected to increase by 1% per annum. Currently, wheat, barley, and oat production exceeds consumption in developed countries, while in developing countries the consumption rate is higher than production. An increasing demand for meat and livestock products is likely to compound the demand for cereals in developing countries. Current production levels and trends will not be sufficient to fulfill the projected global demand generated by increased populations. For wheat, global production will need to be increased by 60% to fulfill the estimated demand in 2050. Until recently, global wheat production increased mostly in response to development of improved cultivars and farming practices and technologies. Production is now limited by biotic and abiotic constraints, including diseases, nematodes, insect pests, weeds, and climate. Among these constraints, plant-parasitic nematodes alone are estimated to reduce production of all world crops by 10%. Cereal cyst nematodes (CCNs) are among the most important nematode pests that limit production of small grain cereals. Heavily invaded young plants are stunted and their lower leaves are often chlorotic, forming pale green patches in the field. Mature plants are also stunted, have a reduced number of tillers, and the roots are shallow and have a "bushy-knotted" appearance. CCNs comprise a number of closely-related species and are found in most regions where cereals are produced.

Comparative analysis of pre- and post-parasitic transcriptomes and mining pioneer effectors of Heterodera avenae

BACKGROUND

The cereal cyst nematode (CCN, Heterodera avenae) is a devastating pathogen of wheat and barley crops in many countries. We aimed to prioritize genetic and molecular targets for H. avenae control via the powerful and integrative bioinformatics platform.

RESULTS

Here, we sequenced mRNA isolated from Chinese H. avenae at pre-parasitic (consisting of egg, J1 and hatched-J2) stages and post-parasitic (consisting of parasitic-J2, J3, J4 and adults) stages. Total 1,066,719 reads of whole life cycle transcriptomes were assembled into 10,811 contigs with N50 length of 1754 bp and 71,401 singletons. Comparative analyses of orthologous among H. avenae and 7 other nematodes with various life-styles revealed the significance and peculiarity of neurological system for sedentary phytonematode. KEGG pathway enrichment demonstrated active crosstalk events of nervous system at pre-parasitic stages, and 6 FMRFamide-like neuropeptides were verified to display an expression peak at the hatched-J2 stage in H. avenae. Furthermore, multiple approaches were undertaken to mine putative effectors and parasitism-specific genes. Notably, H. avenae might represent the first phytonematode reported to possess the pioneer effectors with RxLR motif and potential effectors with homologies to Ant-5/Ant-34.

CONCLUSION

Our work provides valuable resources for in-depth understanding the parasitism and pathogenicity of H. avenae, as well as developing new targets-oriented strategies on effective managements.

Large-Scale Identification and Characterization of Heterodera avenae Putative Effectors Suppressing or Inducing Cell Death in Nicotiana benthamiana

Heterodera avenae is one of the most important plant pathogens and causes vast losses in cereal crops. As a sedentary endoparasitic nematode, H. avenae secretes effectors that modify plant defenses and promote its biotrophic infection of its hosts. However, the number of effectors involved in the interaction between H. avenae and host defenses remains unclear. Here, we report the identification of putative effectors in H. avenae that regulate plant defenses on a large scale. Our results showed that 78 of the 95 putative effectors suppressed programmed cell death (PCD) triggered by BAX and that 7 of the putative effectors themselves caused cell death in Nicotiana benthamiana. Among the cell-death-inducing effectors, three were found to be dependent on their specific domains to trigger cell death and to be expressed in esophageal gland cells by in situ hybridization. Ten candidate effectors that suppressed BAX-triggered PCD also suppressed PCD triggered by the elicitor PsojNIP and at least one R-protein/cognate effector pair, suggesting that they are active in suppressing both pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Notably, with the exception of isotig16060, these putative effectors could also suppress PCD triggered by cell-death-inducing effectors from H. avenae, indicating that those effectors may cooperate to promote nematode parasitism. Collectively, our results indicate that the majority of the tested effectors of H. avenae may play important roles in suppressing cell death induced by different elicitors in N. benthamiana.

Molecular Characterization of A Novel Effector Expansin-like Protein from Heterodera avenae that Induces Cell Death in Nicotiana benthamiana

Cereal cyst nematodes are sedentary biotrophic endoparasites that maintain a complex interaction with their host plants. Nematode effector proteins are synthesized in the oesophageal glands and are secreted into plant tissues through the stylet. To understand the function of nematode effectors in parasitic plants, we cloned predicted effectors genes from Heterodera avenae and transiently expressed them in Nicotiana benthamiana. Infiltration assays showed that HaEXPB2, a predicted expansin-like protein, caused cell death in N. benthamiana. In situ hybridization showed that HaEXPB2 transcripts were localised within the subventral gland cells of the pre-parasitic second-stage nematode. HaEXPB2 had the highest expression levels in parasitic second-stage juveniles. Subcellular localization assays revealed that HaEXPB2 could be localized in the plant cell wall after H. avenae infection.This The cell wall localization was likely affected by its N-terminal and C-terminal regions. In addition, we found that HaEXPB2 bound to cellulose and its carbohydrate-binding domain was required for this binding. The infectivity of H. avenae was significantly reduced when HaEXPB2 was knocked down by RNA interference in vitro. This study indicates that HaEXPB2 may play an important role in the parasitism of H. avenae through targeting the host cell wall.

Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages

The sweet potato weevil, Cylas formicarius (F.) (Coleoptera: Brentidae), is an important pest of sweet potato worldwide. However, there is limited knowledge on the molecular mechanisms underlying growth and differentiation of C. formicarius The transcriptomes of the eggs, second instar larvae, third instar larvae (L3), pupae, females, and males of C. formicarius were sequenced using Illumina sequencing technology for obtaining global insights into developing transcriptome characteristics and elucidating the relative functional genes. A total of 54,255,544 high-quality reads were produced, trimmed, and de novo assembled into 115,281 contigs. 61,686 unigenes were obtained, with an average length of 1,009 nt. Among these unigenes, 17,348 were annotated into 59 Gene Ontology (GO) terms and 12,660 were assigned to 25 Cluster of Orthologous Groups classes, whereas 24,796 unigenes were mapped to 258 pathways. Differentially expressed unigenes between various developmental stages of C. formicarius were detected. Higher numbers of differentially expressed genes (DEGs) were recorded in the eggs versus L3 and eggs versus male samples (2,141 and 2,058 unigenes, respectively) than the others. Genes preferentially expressed in each stage were also identified. GO and pathway-based enrichment analysis were used to further investigate the functions of the DEGs. In addition, the expression profiles of ten DEGs were validated by quantitative real-time PCR. The transcriptome profiles presented in this study and these DEGs detected by comparative analysis of different developed stages of C. formicarius will facilitate the understanding of the molecular mechanism of various living process and will contribute to further genome-wide research.