de novo analysis and functional classification of the transcriptome of the root lesion nematode, Pratylenchus thornei, after 454 GS FLX sequencing

Advances in Migratory Plant Endoparasitic Nematode Effectors

Unlike sedentary plant-parasitic nematodes, migratory plant endoparasitic nematodes (MPENs) are unable to establish permanent feeding sites, and all developmental stages (except eggs) can invade and feed on plant tissues and can be easily overlooked because of the unspecific symptoms. They cause numerous economic losses in agriculture, forestry, and horticulture. In order to understand the pathogenetic mechanism of MPENs, here we describe research on functions and host targets focused on currently identified effectors from six MPENs, namely Radopholus similis, Pratylenchus spp., Ditylenchus destructor, Bursaphelenchus xylophilus, Aphelenchoides besseyi, and Hirschmanniella oryzae. This information will provide valuable insights into understanding MPEN effectors and for future fostering advancements in plant protection.

Chorismate mutase and isochorismatase, two potential effectors of the migratory nematode Hirschmanniella oryzae, increase host susceptibility by manipulating secondary metabolite content of rice

Hirschmanniella oryzae is one of the most devastating nematodes on rice, leading to substantial yield losses. Effector proteins aid the nematode during the infection process by subduing plant defence responses. In this research we characterized two potential H. oryzae effector proteins, chorismate mutase (HoCM) and isochorismatase (HoICM), and investigated their enzymatic activity and their role in plant immunity. Both HoCM and HoICM proved to be enzymatically active in complementation tests in mutant Escherichia coli strains. Infection success by the migratory nematode H. oryzae was significantly higher in transgenic rice lines constitutively expressing HoCM or HoICM. Expression of HoCM, but not HoICM, increased rice susceptibility against the sedentary nematode Meloidogyne graminicola also. Transcriptome and metabolome analyses indicated reductions in secondary metabolites in the transgenic rice plants expressing the potential nematode effectors. The results presented here demonstrate that both HoCM and HoICM suppress the host immune system and that this may be accomplished by lowering secondary metabolite levels in the plant.

Bacterial Community Structure Dynamics in Meloidogyne incognita-Infected Roots and Its Role in Worm-Microbiome Interactions

Plant parasitic nematodes such as Meloidogyne incognita have a complex life cycle, occurring sequentially in various niches of the root and rhizosphere. They are known to form a range of interactions with bacteria and other microorganisms that can affect their densities and virulence. High-throughput sequencing can reveal these interactions in high temporal and geographic resolutions, although thus far we have only scratched the surface. In this study, we have carried out a longitudinal sampling scheme, repeatedly collecting rhizosphere soil, roots, galls, and second-stage juveniles from 20 plants to provide a high-resolution view of bacterial succession in these niches, using 16S rRNA metabarcoding. Our findings indicate that a structured community develops in the root, in which gall communities diverge from root segments lacking a gall, and that this structure is maintained throughout the crop season. We describe the successional process leading toward this structure, which is driven by interactions with the nematode and later by an increase in bacteria often found in hypoxic and anaerobic environments. We present evidence that this structure may play a role in the nematode's chemotaxis toward uninfected root segments. Finally, we describe the J2 epibiotic microenvironment as ecologically deterministic, in part, due to the active bacterial attraction of second-stage juveniles.IMPORTANCE The study of high-resolution successional processes within tightly linked microniches is rare. Using the power and relatively low cost of metabarcoding, we describe the bacterial succession and community structure in roots infected with root-knot nematodes and in the nematodes themselves. We reveal separate successional processes in galls and adjacent non-gall root sections, which are driven by the nematode's life cycle and the progression of the crop season. With their relatively low genetic diversity, large geographic range, spatially complex life cycle, and the simplified agricultural ecosystems they occupy, root-knot nematodes can serve as a model organism for terrestrial holobiont ecology. This perspective can improve our understanding of the temporal and spatial aspects of biological control efficacy.

An Expansin-Like Candidate Effector Protein from Pratylenchus penetrans Modulates Immune Responses in Nicotiana benthamiana

The root lesion nematode (RLN) Pratylenchus penetrans is a migratory species that attacks a broad range of crops. After the RLN is initially attracted to host roots by root exudates and compounds, it releases secretions that are critical for successful parasitism. Among those secretions are nematode virulence factors or effectors that facilitate the entry and migration of nematodes through the roots and modulate plant immune defenses. The recognition of the effectors by host resistance proteins leads to effector-triggered immunity and incompatible plant-nematode interactions. Although many candidate effectors of the RLN and other plant-parasitic nematodes have been identified, the detailed mechanisms of their functions and particularly, their host targets remain largely unexplored. In this study, we sequenced and annotated genes encoding expansin-like proteins, which are major candidate effectors of P. penetrans. One of the genes, Pp-EXPB1, which was the most highly expressed during nematode infection in different plant species, was further functionally characterized via transient expression in the model plant Nicotiana benthamiana and global transcriptome profiling of gene expression changes triggered by this candidate effector in plants. As a result of this investigation, the biological roles of Pp-EXPB1 in nematode parasitism were proposed, the putative cellular targets of the proteins were identified, and the molecular mechanisms of plant responses to the nematode-secreted proteins were outlined.

Serendipitous identification of Pratylenchus curvicauda from the grainbelt of Western Australia

A Pratylenchus species identified during a survey of Pratylenchus quasitereoides incidence at four locations of the grainbelt of Western Australia is described. Morphological and morphometric features indicated the previously undescribed morphotypes in nematode mixtures encountered were conspecific to P. curvicauda, and were clearly distinguishable from nine common Pratylenchus spp. Typical features of P. curvicauda were its body length (415-540 µm), which was curved to a c-shaped with a maximum body diameter of 20 µm, and the nature of its tail; 34 µm long, 2.8 µm wide at the anus and a typical ventrally arcuate with a round terminus. Sequenced for the first time, the sequences of the partial 18S-ITS1-5.8S-ITS2-partial 28S (80 clones, 14 individual nematodes) and the 28S-D3 (17 clones) regions of the rDNA of P. curvicauda had overall mean distances of 0.013 and 0.085, respectively. Phylogenetic analyses with sequences of both segments of the rDNA clearly showed the P. curvicauda isolates as monophyletic, distinct from ca 40 Pratylenchus species. Notably, it was distinct from Pratylenchus species present in Australia including P. quasitereoides and a Western Australia isolate of P. thornei. Further research into the biology of P. curvicauda is needed to facilitate development of strategies for its management, if it is an important pest.

Life-stage specific transcriptomes of a migratory endoparasitic plant nematode, Radopholus similis elucidate a different parasitic and life strategy of plant parasitic nematodes

Radopholus similis is an important migratory endoparasitic nematode, severely harms banana, citrus and many other commercial crops. Little is known about the molecular mechanism of infection and pathogenesis of R. similis. In this study, 64761 unigenes were generated from eggs, juveniles, females and males of R. similis. 11443 unigenes showed significant expression difference among these four life stages. Genes involved in host parasitism, anti-host defense and other biological processes were predicted. There were 86 and 102 putative genes coding for cell wall degrading enzymes and antioxidase respectively. The amount and type of putative parasitic-related genes reported in sedentary endoparasitic plant nematodes are variable from those of migratory parasitic nematodes on plant aerial portion. There were no sequences annotated to effectors in R. similis, involved in feeding site formation of sedentary endoparasites nematodes. This transcriptome data provides a new insight into the parasitic and pathogenic molecular mechanisms of the migratory endoparasitic nematodes. It also provides a broad idea for further research on R. similis.

Interactions of endoparasitic and ectoparasitic nematodes within the plant root system

Root-knot and cyst nematodes have sophisticated mechanisms to invade their plant hosts to reprogram the plant developmental program to induce feeding structures essential for nematode survival and reproduction. This has a detrimental effect on the plant as this sedentary endoparasitic interaction affects the growth and yields of many crop plants. However, other migratory endoparasitic nematodes that do not establish root feeding sites are as aggressive on many crop plants. With new information gained from the genome and transcriptomes of the migratory endoparasitic nematode, Pratylenchus spp., this review compares the different lifestyles and the pathogenic interactions these nematodes have with their plant host. Pratylenchus spp. utilises a common arsenal of effectors involved in plant cell wall degradation and the manipulation of plant host innate immunity. The absence of specific cell reprogramming effector genes may explain its migratory endoparasitic lifestyle, making it relevant to pest management approaches in Australia.

Identification of candidate effector genes of Pratylenchus penetrans

Pratylenchus penetrans is one of the most important species of root lesion nematodes (RLNs) because of its detrimental and economic impact in a wide range of crops. Similar to other plant-parasitic nematodes (PPNs), P. penetrans harbours a significant number of secreted proteins that play key roles during parasitism. Here, we combined spatially and temporally resolved next-generation sequencing datasets of P. penetrans to select a list of candidate genes aimed at the identification of a panel of effector genes for this species. We determined the spatial expression of transcripts of 22 candidate effectors within the oesophageal glands of P. penetrans by in situ hybridization. These comprised homologues of known effectors of other PPNs with diverse putative functions, as well as novel pioneer effectors specific to RLNs. It is noteworthy that five of the pioneer effectors encode extremely proline-rich proteins. We then combined in situ localization of effectors with available genomic data to identify a non-coding motif enriched in promoter regions of a subset of P. penetrans effectors, and thus a putative hallmark of spatial expression. Expression profiling analyses of a subset of candidate effectors confirmed their expression during plant infection. Our current results provide the most comprehensive panel of effectors found for RLNs. Considering the damage caused by P. penetrans, this information provides valuable data to elucidate the mode of parasitism of this nematode and offers useful suggestions regarding the potential use of P. penetrans-specific target effector genes to control this important pathogen.

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.

Signatures of adaptation to plant parasitism in nematode genomes

Plant-parasitic nematodes cause considerable damage to global agriculture. The ability to parasitize plants is a derived character that appears to have independently emerged several times in the phylum Nematoda. Morphological convergence to feeding style has been observed, but whether this is emergent from molecular convergence is less obvious. To address this, we assess whether genomic signatures can be associated with plant parasitism by nematodes. In this review, we report genomic features and characteristics that appear to be common in plant-parasitic nematodes while absent or rare in animal parasites, predators or free-living species. Candidate horizontal acquisitions of parasitism genes have systematically been found in all plant-parasitic species investigated at the sequence level. Presence of peptides that mimic plant hormones also appears to be a trait of plant-parasitic species. Annotations of the few genomes of plant-parasitic nematodes available to date have revealed a set of apparently species-specific genes on every occasion. Effector genes, important for parasitism are frequently found among those species-specific genes, indicating poor overlap. Overall, nematodes appear to have developed convergent genomic solutions to adapt to plant parasitism.

Characterization of Lilium longiflorum cv. 'Nellie White' Infection with Root-lesion Nematode Pratylenchus penetrans by Bright-field and Transmission Electron Microscopy

Lilium longiflorum cv. Nellie White, commonly known as Easter lily, is an important floral crop with an annual wholesale value of over $26 million in the United States. The root-lesion nematode, Pratylenchus penetrans, is a major pest of lily due to the significant root damage it causes. In this study, we investigated the cytological aspects of this plant-nematode interaction using bright-field and transmission electron microscopy. We took advantage of an in vitro culture method to multiply lilies and follow the nematode infection over time. Phenotypic reactions of roots inoculated with P. penetrans were evaluated from 0 to 60 d after nematode infection. Symptom development progressed from initial randomly distributed discrete necrotic areas to advanced necrosis along entire roots of each inoculated plant. A major feature characterizing this susceptible host response to nematode infection was the formation of necrosis, browning, and tissue death involving both root epidermis and cortical cells. Degradation of consecutive cell walls resulted in loss of cell pressure, lack of cytoplasmic integrity, followed by cell death along the intracellular path of the nematode's migration. Pratylenchus penetrans was never seen in the vascular cylinder as the layer of collapsed endodermal cells presumably blocked the progression of nematodes into this area of the roots. This study presents the first detailed cytological characterization of P. penetrans infection of Easter lily plants.

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.

The Distribution of Lectins across the Phylum Nematoda: A Genome-Wide Search

Nematodes are a very diverse phylum that has adapted to nearly every ecosystem. They have developed specialized lifestyles, dividing the phylum into free-living, animal, and plant parasitic species. Their sheer abundance in numbers and presence in nearly every ecosystem make them the most prevalent animals on earth. In this research nematode-specific profiles were designed to retrieve predicted lectin-like domains from the sequence data of nematode genomes and transcriptomes. Lectins are carbohydrate-binding proteins that play numerous roles inside and outside the cell depending on their sugar specificity and associated protein domains. The sugar-binding properties of the retrieved lectin-like proteins were predicted in silico. Although most research has focused on C-type lectin-like, galectin-like, and calreticulin-like proteins in nematodes, we show that the lectin-like repertoire in nematodes is far more diverse. We focused on C-type lectins, which are abundantly present in all investigated nematode species, but seem to be far more abundant in free-living species. Although C-type lectin-like proteins are omnipresent in nematodes, we have shown that only a small part possesses the residues that are thought to be essential for carbohydrate binding. Curiously, hevein, a typical plant lectin domain not reported in animals before, was found in some nematode species.

Transcriptome Analysis of the Chrysanthemum Foliar Nematode, Aphelenchoides ritzemabosi (Aphelenchida: Aphelenchoididae)

The chrysanthemum foliar nematode (CFN), Aphelenchoides ritzemabosi, is a plant parasitic nematode that attacks many plants. In this study, a transcriptomes of mixed-stage population of CFN was sequenced on the Illumina HiSeq 2000 platform. 68.10 million Illumina high quality paired end reads were obtained which generated 26,817 transcripts with a mean length of 1,032 bp and an N50 of 1,672 bp, of which 16,467 transcripts were annotated against six databases. In total, 20,311 coding region sequences (CDS), 495 simple sequence repeats (SSRs) and 8,353 single-nucleotide polymorphisms (SNPs) were predicted, respectively. The CFN with the most shared sequences was B. xylophilus with 16,846 (62.82%) common transcripts and 10,543 (39.31%) CFN transcripts matched sequences of all of four plant parasitic nematodes compared. A total of 111 CFN transcripts were predicted as homologues of 7 types of carbohydrate-active enzymes (CAZymes) with plant/fungal cell wall-degrading activities, fewer transcripts were predicted as homologues of plant cell wall-degrading enzymes than fungal cell wall-degrading enzymes. The phylogenetic analysis of GH5, GH16, GH43 and GH45 proteins between CFN and other organisms showed CFN and other nematodes have a closer phylogenetic relationship. In the CFN transcriptome, sixteen types of genes orthologues with seven classes of protein families involved in the RNAi pathway in C. elegans were predicted. This research provides comprehensive gene expression information at the transcriptional level, which will facilitate the elucidation of the molecular mechanisms of CFN and the distribution of gene functions at the macro level, potentially revealing improved methods for controlling CFN.

De Novo Analysis of the Transcriptome of Meloidogyne enterolobii to Uncover Potential Target Genes for Biological Control

Meloidogyne enterolobii is one of the obligate biotrophic root-knot nematodes that has the ability to reproduce on many economically-important crops. We carried out de novo sequencing of the transcriptome of M. enterolobii using Roche GS FLX and obtained 408,663 good quality reads that were assembled into 8193 contigs and 31,860 singletons. We compared the transcripts in different nematodes that were potential targets for biological control. These included the transcripts that putatively coded for CAZymes, kinases, neuropeptide genes and secretory proteins and those that were involved in the RNAi pathway and immune signaling. Typically, 75 non-membrane secretory proteins with signal peptides secreted from esophageal gland cells were identified as putative effectors, three of which were preliminarily examined using a PVX (pGR107)-based high-throughput transient plant expression system in Nicotiana benthamiana (N. benthamiana). Results showed that these candidate proteins suppressed the programmed cell death (PCD) triggered by the pro-apoptosis protein BAX, and one protein also caused necrosis, suggesting that they might suppress plant immune responses to promote pathogenicity. In conclusion, the current study provides comprehensive insight into the transcriptome of M. enterolobii for the first time and lays a foundation for further investigation and biological control strategies.

Advances in Understanding the Molecular Mechanisms of Root Lesion Nematode Host Interactions

Root lesion nematodes (RLNs) are one of the most economically important groups of plant nematodes. As migratory endoparasites, their presence in roots is less obvious than infestations of sedentary endoparasites; nevertheless, in many instances, they are the major crop pests. With increasing molecular information on nematode parasitism, available data now reflect the differences and, in particular, similarities in lifestyle between migratory and sedentary endoparasites. Far from being unsophisticated compared with sedentary endoparasites, migratory endoparasites are exquisitely suited to their parasitic lifestyle. What they lack in effectors required for induction of permanent feeding sites, they make up for with their versatile host range and their ability to move and feed from new host roots and survive adverse conditions. In this review, we summarize the current molecular data available for RLNs and highlight differences and similarities in effectors and molecular mechanisms between migratory and sedentary endoparasitic nematodes.

De novo analysis of the transcriptome of Pratylenchus zeae to identify transcripts for proteins required for structural integrity, sensation, locomotion and parasitism

The root lesion nematode Pratylenchus zeae, a migratory endoparasite, is an economically important pest of major crop plants (e.g. cereals, sugarcane). It enters host roots, migrates through root tissues and feeds from cortical cells, and defends itself against biotic and abiotic stresses in the soil and in host tissues. We report de novo sequencing of the P. zeae transcriptome using 454 FLX, and the identification of putative transcripts encoding proteins required for movement, response to stimuli, feeding and parasitism. Sequencing generated 347,443 good quality reads which were assembled into 10,163 contigs and 139,104 singletons: 65% of contigs and 28% of singletons matched sequences of free-living and parasitic nematodes. Three-quarters of the annotated transcripts were common to reference nematodes, mainly representing genes encoding proteins for structural integrity and fundamental biochemical processes. Over 15,000 transcripts were similar to Caenorhabditis elegans genes encoding proteins with roles in mechanical and neural control of movement, responses to chemicals, mechanical and thermal stresses. Notably, 766 transcripts matched parasitism genes employed by both migratory and sedentary endoparasites in host interactions, three of which hybridized to the gland cell region, suggesting that they might be secreted. Conversely, transcripts for effectors reported to be involved in feeding site formation by sedentary endoparasites were conspicuously absent. Transcripts similar to those encoding some secretory-excretory products at the host interface of Brugia malayi, the secretome of Meloidogyne incognita and products of gland cells of Heterodera glycines were also identified. This P. zeae transcriptome provides new information for genome annotation and functional analysis of possible targets for control of pratylenchid nematodes.

Analysis of the Transcriptome of the Infective Stage of the Beet Cyst Nematode, H. schachtii

The beet cyst nematode, Heterodera schachtii, is a major root pest that significantly impacts the yield of sugar beet, brassicas and related species. There has been limited molecular characterisation of this important plant pathogen: to identify target genes for its control the transcriptome of the pre-parasitic J2 stage of H. schachtii was sequenced using Roche GS FLX. Ninety seven percent of reads (i.e., 387,668) with an average PHRED score > 22 were assembled with CAP3 and CLC Genomics Workbench into 37,345 and 47,263 contigs, respectively. The transcripts were annotated by comparing with gene and genomic sequences of other nematodes and annotated proteins on public databases. The annotated transcripts were much more similar to sequences of Heterodera glycines than to those of Globodera pallida and root knot nematodes (Meloidogyne spp.). Analysis of these transcripts showed that a subset of 2,918 transcripts was common to free-living and plant parasitic nematodes suggesting that this subset is involved in general nematode metabolism and development. A set of 148 contigs and 183 singletons encoding putative homologues of effectors previously characterised for plant parasitic nematodes were also identified: these are known to be important for parasitism of host plants during migration through tissues or feeding from cells or are thought to be involved in evasion or modulation of host defences. In addition, the presence of sequences from a nematode virus is suggested. The sequencing and annotation of this transcriptome significantly adds to the genetic data available for H. schachtii, and identifies genes primed to undertake required roles in the critical pre-parasitic and early post-parasitic J2 stages. These data provide new information for identifying potential gene targets for future protection of susceptible crops against H. schachtii.

The Pratylenchus penetrans Transcriptome as a Source for the Development of Alternative Control Strategies: Mining for Putative Genes Involved in Parasitism and Evaluation of in planta RNAi

The root lesion nematode Pratylenchus penetrans is considered one of the most economically important species within the genus. Host range studies have shown that nearly 400 plant species can be parasitized by this species. To obtain insight into the transcriptome of this migratory plant-parasitic nematode, we used Illumina mRNA sequencing analysis of a mixed population, as well as nematode reads detected in infected soybean roots 3 and 7 days after nematode infection. Over 140 million paired end reads were obtained for this species, and de novo assembly resulted in a total of 23,715 transcripts. Homology searches showed significant hit matches to 58% of the total number of transcripts using different protein and EST databases. In general, the transcriptome of P. penetrans follows common features reported for other root lesion nematode species. We also explored the efficacy of RNAi, delivered from the host, as a strategy to control P. penetrans, by targeted knock-down of selected nematode genes. Different comparisons were performed to identify putative nematode genes with a role in parasitism, resulting in the identification of transcripts with similarities to other nematode parasitism genes. Focusing on the predicted nematode secreted proteins found in this transcriptome, we observed specific members to be up-regulated at the early time points of infection. In the present study, we observed an enrichment of predicted secreted proteins along the early time points of parasitism by this species, with a significant number being pioneer candidate genes. A representative set of genes examined using RT-PCR confirms their expression during the host infection. The expression patterns of the different candidate genes raise the possibility that they might be involved in critical steps of P. penetrans parasitism. This analysis sheds light on the transcriptional changes that accompany plant infection by P. penetrans, and will aid in identifying potential gene targets for selection and use to design effective control strategies against root lesion nematodes.

Identification of Ramie Genes in Response to Pratylenchus coffeae Infection Challenge by Digital Gene Expression Analysis

Root lesion disease, caused by Pratylenchus coffeae, seriously impairs the growth and yield of ramie, an important natural fiber crop. The ramie defense mechanism against P. coffeae infection is poorly understood, which hinders efforts to improve resistance via breeding programs. In this study, the transcriptome of the resistant ramie cultivar Qingdaye was characterized using Illumina sequence technology. About 46.3 million clean pair end (PE) reads were generated and assembled into 40,826 unigenes with a mean length of 830 bp. Digital gene expression (DGE) analysis was performed on both the control roots (CK) and P. coffeae-challenged roots (CH), and the differentially expressed genes (DEGs) were identified. Approximately 10.16 and 8.07 million cDNA reads in the CK and CH cDNA libraries were sequenced, respectively. A total of 137 genes exhibited different transcript abundances between the two libraries. Among them, the expressions of 117 and 20 DEGs were up- and down-regulated in P. coffeae-challenged ramie, respectively. The expression patterns of 15 candidate genes determined by qRT-PCR confirmed the results of DGE analysis. Time-course expression profiles of eight defense-related genes in susceptible and resistant ramie cultivars were different after P. coffeae inoculation. The differential expression of protease inhibitors, pathogenesis-related proteins (PRs), and transcription factors in resistant and susceptible ramie during P. coffeae infection indicated that cystatin likely plays an important role in nematode resistance.

Qualitative de novo analysis of full length cDNA and quantitative analysis of gene expression for common marmoset (Callithrix jacchus) transcriptomes using parallel long-read technology and short-read sequencing

The common marmoset (Callithrix jacchus) is a non-human primate that could prove useful as human pharmacokinetic and biomedical research models. The cytochromes P450 (P450s) are a superfamily of enzymes that have critical roles in drug metabolism and disposition via monooxygenation of a broad range of xenobiotics; however, information on some marmoset P450s is currently limited. Therefore, identification and quantitative analysis of tissue-specific mRNA transcripts, including those of P450s and flavin-containing monooxygenases (FMO, another monooxygenase family), need to be carried out in detail before the marmoset can be used as an animal model in drug development. De novo assembly and expression analysis of marmoset transcripts were conducted with pooled liver, intestine, kidney, and brain samples from three male and three female marmosets. After unique sequences were automatically aligned by assembling software, the mean contig length was 718 bp (with a standard deviation of 457 bp) among a total of 47,883 transcripts. Approximately 30% of the total transcripts were matched to known marmoset sequences. Gene expression in 18 marmoset P450- and 4 FMO-like genes displayed some tissue-specific patterns. Of these, the three most highly expressed in marmoset liver were P450 2D-, 2E-, and 3A-like genes. In extrahepatic tissues, including brain, gene expressions of these monooxygenases were lower than those in liver, although P450 3A4 (previously P450 3A21) in intestine and P450 4A11- and FMO1-like genes in kidney were relatively highly expressed. By means of massive parallel long-read sequencing and short-read technology applied to marmoset liver, intestine, kidney, and brain, the combined next-generation sequencing analyses reported here were able to identify novel marmoset drug-metabolizing P450 transcripts that have until now been little reported. These results provide a foundation for mechanistic studies and pave the way for the use of marmosets as model animals for drug development in the future.

De novo transcriptome sequencing and analysis of the cereal cyst nematode, Heterodera avenae

The cereal cyst nematode (CCN, Heterodera avenae) is a major pest of wheat (Triticum spp) that reduces crop yields in many countries. Cyst nematodes are obligate sedentary endoparasites that reproduce by amphimixis. Here, we report the first transcriptome analysis of two stages of H. avenae. After sequencing extracted RNA from pre parasitic infective juvenile and adult stages of the life cycle, 131 million Illumina high quality paired end reads were obtained which generated 27,765 contigs with N50 of 1,028 base pairs, of which 10,452 were annotated. Comparative analyses were undertaken to evaluate H. avenae sequences with those of other plant, animal and free living nematodes to identify differences in expressed genes. There were 4,431 transcripts common to H. avenae and the free living nematode Caenorhabditis elegans, and 9,462 in common with more closely related potato cyst nematode, Globodera pallida. Annotation of H. avenae carbohydrate active enzymes (CAZy) revealed fewer glycoside hydrolases (GHs) but more glycosyl transferases (GTs) and carbohydrate esterases (CEs) when compared to M. incognita. 1,280 transcripts were found to have secretory signature, presence of signal peptide and absence of transmembrane. In a comparison of genes expressed in the pre-parasitic juvenile and feeding female stages, expression levels of 30 genes with high RPKM (reads per base per kilo million) value, were analysed by qRT-PCR which confirmed the observed differences in their levels of expression levels. In addition, we have also developed a user-friendly resource, Heterodera transcriptome database (HATdb) for public access of the data generated in this study. The new data provided on the transcriptome of H. avenae adds to the genetic resources available to study plant parasitic nematodes and provides an opportunity to seek new effectors that are specifically involved in the H. avenae-cereal host interaction.

Analysis of the transcriptome of Hirschmanniella oryzae to explore potential survival strategies and host-nematode interactions

The rice root nematode Hirschmanniella oryzae is the most abundant plant-parasitic nematode in flooded rice fields and is distributed world-wide. Although it is economically less important than sedentary nematodes, it can cause severe yield reductions and economic losses in specific environmental conditions. No transcriptome data for this genus were available until now. We have performed 454 sequencing on a mixed life stages population to gain an insight into nematode-plant interactions and nematode survival strategies. The results of two assembly strategies were combined to reduce the redundancy of the data, generating a final dataset of 21 360 contigs. The data were screened for putative plant cell wall-modifying proteins, which facilitate nematode migration through host roots. A β-mannanase, previously not reported in nematodes, was detected in the dataset. The data were screened for putative effector proteins that may alter the host defence mechanism. Two enzymes, chorismate mutase and isochorismatase, thought to be involved in the salicyclic acid pathway, were identified. Experimental treatments of H. oryzae with artificial seawater showed that late embryogenesis abundant (LEA) proteins and SXP/RAL-2 are induced, suggesting that these proteins are involved in the process of anhydrobiosis. The newly generated data can highlight potential differences between sedentary and migratory nematodes, and will be useful in the further study of host-nematode interactions and the developmental biology of this nematode.

Transcriptomic analysis of the rice white tip nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)

Background

The rice white tip nematode Aphelenchoides besseyi, a devastating nematode whose genome has not been sequenced, is distributed widely throughout almost all the rice-growing regions of the world. The aims of the present study were to define the transcriptome of A. besseyi and to identify parasite-related, mortality-related or host resistance-overcoming genes in this nematode.

Methodology and Principal Findings

Using Solexa/Illumina sequencing, we profiled the transcriptome of mixed-stage populations of A. besseyi. A total of 51,270 transcripts without gaps were produced based on high-quality clean reads. Of all the A. besseyi transcripts, 9,132 KEGG Orthology assignments were annotated. Carbohydrate-active enzymes of glycoside hydrolases (GHs), glycosyltransferases (GTs), carbohydrate esterases (CEs) and carbohydrate-binding modules (CBMs) were identified. The presence of the A. besseyi GH45 cellulase gene was verified by in situ hybridization. Given that 13 unique A. besseyi potential effector genes were identified from 41 candidate effector homologs, further studies of these homologs are merited. Finally, comparative analyses were conducted between A. besseyi contigs and Caenorhabditis elegans genes to look for orthologs of RNAi phenotypes, neuropeptides and peptidases.

Conclusions and Significance

The present results provide comprehensive insight into the genetic makeup of A. besseyi. Many of this species' genes are parasite related, nematode mortality-related or necessary to overcome host resistance. The generated transcriptome dataset of A. besseyi reported here lays the foundation for further studies of the molecular mechanisms related to parasitism and facilitates the development of new control strategies for this species.

Characterisation of the transcriptome of Aphelenchoides besseyi and identification of a GHF 45 cellulase

While the majority of Aphelenchoides species are fungivorous, some species are plant parasites that have retained the ability to feed on fungi. Aphelenchoides besseyi is an important and widespread pathogen that causes ‘white tip’ disease on rice. This migratory endoparasitic nematode makes a significant contribution to the estimated $US 16 billion worth of damage caused by nematodes to rice crops. Here we describe a small-scale analysis of the transcriptome of A. besseyi. After sequencing, QC and assembly, approximately 5000 contigs were analysed. Bioinformatic analysis allowed 375 secreted proteins to be identified, including orthologues of proteins known to be secreted by other nematodes. One contig could encode an A. besseyi orthologue of a GHF45 cellulase, similar to those present in Bursaphelenchus xylophilus. No transcripts similar to GHF5 cellulases were present in this dataset.

Assessment of the geographic origins of pinewood nematode isolates via single nucleotide polymorphism in effector genes

The pinewood nematode, Bursaphelenchus xylophilus, is native to North America but it only causes damaging pine wilt disease in those regions of the world where it has been introduced. The accurate detection of the species and its dispersal routes are thus essential to define effective control measures. The main goals of this study were to analyse the genetic diversity among B. xylophilus isolates from different geographic locations and identify single nucleotide polymorphism (SNPs) markers for geographic origin, through a comparative transcriptomic approach. The transcriptomes of seven B. xylophilus isolates, from Continental Portugal (4), China (1), Japan (1) and USA (1), were sequenced in the next generation platform Roche 454. Analysis of effector gene transcripts revealed inter-isolate nucleotide diversity that was validated by Sanger sequencing in the genomic DNA of the seven isolates and eight additional isolates from different geographic locations: Madeira Island (2), China (1), USA (1), Japan (2) and South Korea (2). The analysis identified 136 polymorphic positions in 10 effector transcripts. Pairwise comparison of the 136 SNPs through Neighbor-Joining and the Maximum Likelihood methods and 5-mer frequency analysis with the alignment-independent bilinear multivariate modelling approach correlated the SNPs with the isolates geographic origin. Furthermore, the SNP analysis indicated a closer proximity of the Portuguese isolates to the Korean and Chinese isolates than to the Japanese or American isolates. Each geographic cluster carried exclusive alleles that can be used as SNP markers for B. xylophilus isolate identification.

Top 10 plant-parasitic nematodes in molecular plant pathology

The aim of this review was to undertake a survey of researchers working with plant-parasitic nematodes in order to determine a 'top 10' list of these pathogens based on scientific and economic importance. Any such list will not be definitive as economic importance will vary depending on the region of the world in which a researcher is based. However, care was taken to include researchers from as many parts of the world as possible when carrying out the survey. The top 10 list emerging from the survey is composed of: (1) root-knot nematodes (Meloidogyne spp.); (2) cyst nematodes (Heterodera and Globodera spp.); (3) root lesion nematodes (Pratylenchus spp.); (4) the burrowing nematode Radopholus similis; (5) Ditylenchus dipsaci; (6) the pine wilt nematode Bursaphelenchus xylophilus; (7) the reniform nematode Rotylenchulus reniformis; (8) Xiphinema index (the only virus vector nematode to make the list); (9) Nacobbus aberrans; and (10) Aphelenchoides besseyi. The biology of each nematode (or nematode group) is reviewed briefly.

Stacking resistance to crown gall and nematodes in walnut rootstocks

Background

Crown gall (CG) (Agrobacterium tumefaciens) and the root lesion nematodes (RLNs) (Pratylenchus vulnus) are major challenges faced by the California walnut industry, reducing productivity and increasing the cost of establishing and maintaining orchards. Current nematode control strategies include nematicides, crop rotation, and tolerant cultivars, but these methods have limits. Developing genetic resistance through novel approaches like RNA interference (RNAi) can address these problems. RNAi-mediated silencing of CG disease in walnut (Juglans regia L.) has been achieved previously. We sought to place both CG and nematode resistance into a single walnut rootstock genotype using co-transformation to stack the resistance genes. A. tumefaciens, carrying self-complimentary iaaM and ipt transgenes, and Agrobacterium rhizogenes, carrying a self-complimentary Pv010 gene from P. vulnus, were used as co-transformation vectors. RolABC genes were introduced by the resident T-DNA in the A. rhizogenes Ri-plasmid used as a vector for plant transformation. Pv010 and Pv194 (transgenic control) genes were also transferred separately using A. tumefaciens. To test for resistance, transformed walnut roots were challenged with P. vulnus and microshoots were challenged with a virulent strain of A. tumefaciens.

Results

Combining the two bacterial strains at a 1:1 rather than 1:3 ratio increased the co-transformation efficiency. Although complete immunity to nematode infection was not observed, transgenic lines yielded up to 79% fewer nematodes per root following in vitro co-culture than untransformed controls. Transgenic line 33-3-1 exhibited complete crown gall control and 32% fewer nematodes. The transgenic plants had thicker, longer roots than untransformed controls possibly due to insertion of rolABC genes. When the Pv010 gene was present in roots with or without rolABC genes there was partial or complete control of RLNs. Transformation using only one vector showed 100% control in some lines.

Conclusions

CG and nematode resistance gene stacking controlled CG and RLNs simultaneously in walnuts. Silencing genes encoding iaaM, ipt, and Pv010 decrease CG formation and RLNs populations in walnut. Beneficial plant genotype and phenotype changes are caused by co-transformation using A. tumefaciens and A. rhizogenes strains. Viable resistance against root lesion nematodes in walnut plants may be accomplished in the future using this gene stacking technology.

Exploring the host parasitism of the migratory plant-parasitic nematode Ditylenchus destuctor by expressed sequence tags analysis

The potato rot nematode, Ditylenchus destructor, is a very destructive nematode pest on many agriculturally important crops worldwide, but the molecular characterization of its parasitism of plant has been limited. The effectors involved in nematode parasitism of plant for several sedentary endo-parasitic nematodes such as Heterodera glycines, Globodera rostochiensis and Meloidogyne incognita have been identified and extensively studied over the past two decades. Ditylenchus destructor, as a migratory plant parasitic nematode, has different feeding behavior, life cycle and host response. Comparing the transcriptome and parasitome among different types of plant-parasitic nematodes is the way to understand more fully the parasitic mechanism of plant nematodes. We undertook the approach of sequencing expressed sequence tags (ESTs) derived from a mixed stage cDNA library of D. destructor. This is the first study of D. destructor ESTs. A total of 9800 ESTs were grouped into 5008 clusters including 3606 singletons and 1402 multi-member contigs, representing a catalog of D. destructor genes. Implementing a bioinformatics' workflow, we found 1391 clusters have no match in the available gene database; 31 clusters only have similarities to genes identified from D. africanus, the most closely related species to D. destructor; 1991 clusters were annotated using Gene Ontology (GO); 1550 clusters were assigned enzyme commission (EC) numbers; and 1211 clusters were mapped to 181 KEGG biochemical pathways. 22 ESTs had similarities to reported nematode effectors. Interestedly, most of the effectors identified in this study are involved in host cell wall degradation or modification, such as 1,4-beta-glucanse, 1,3-beta-glucanse, pectate lyase, chitinases and expansin, or host defense suppression such as calreticulin, annexin and venom allergen-like protein. This result implies that the migratory plant-parasitic nematode D. destructor secrets similar effectors to those of sedentary plant nematodes. Finally we further characterized the two D. destructor expansin proteins.

Identification of candidate effector genes in the transcriptome of the rice root knot nematode Meloidogyne graminicola

Plant-parasitic nematodes secrete so-called effectors into their host plant which are able to suppress the plant's defence responses, alter plant signalling pathways and, in the case of root knot nematodes, induce the formation of giant cells. Putative effectors have been successfully identified by genomics, transcriptomics and proteomics approaches. In this study, we investigated the transcriptome of the rice root knot nematode Meloidogyne graminicola by 454 sequencing of second-stage juveniles as well as mRNA-seq of rice infected tissue. Over 350 000 reads derived from M. graminicola preparasitic juveniles were assembled, annotated and checked for homologues in different databases. From infected rice tissue, 1.4% of all reads generated were identified as being derived from the nematode. Using multiple strategies, several putative effector genes were identified, both pioneer genes and genes corresponding to already known effectors. To check whether these genes could be involved in the interaction with the plant, in situ hybridization was performed on a selection of genes to localize their expression in the nematode. Most were expressed in the gland cells or amphids of the nematode, confirming possible secretion of the proteins and hence a role in infection. Other putative effectors showed a different expression pattern, potentially linked with the excretory/secretory system. This transcriptome study is a good starting point to functionally investigate novel effectors derived from M. graminicola. This will lead to better insights into the interaction between these nematodes and the model plant rice. Moreover, the transcriptome can be used to identify possible target genes for RNA interference (RNAi)-based control strategies. Four genes proved to be interesting targets by showing up to 40% higher mortality relative to the control treatment when soaked in gene-specific small interfering RNAs (siRNAs).

Identification of candidate effector genes in the transcriptome of the rice root knot nematode Meloidogyne graminicola

Plant-parasitic nematodes secrete so-called effectors into their host plant which are able to suppress the plant's defence responses, alter plant signalling pathways and, in the case of root knot nematodes, induce the formation of giant cells. Putative effectors have been successfully identified by genomics, transcriptomics and proteomics approaches. In this study, we investigated the transcriptome of the rice root knot nematode Meloidogyne graminicola by 454 sequencing of second-stage juveniles as well as mRNA-seq of rice infected tissue. Over 350 000 reads derived from M. graminicola preparasitic juveniles were assembled, annotated and checked for homologues in different databases. From infected rice tissue, 1.4% of all reads generated were identified as being derived from the nematode. Using multiple strategies, several putative effector genes were identified, both pioneer genes and genes corresponding to already known effectors. To check whether these genes could be involved in the interaction with the plant, in situ hybridization was performed on a selection of genes to localize their expression in the nematode. Most were expressed in the gland cells or amphids of the nematode, confirming possible secretion of the proteins and hence a role in infection. Other putative effectors showed a different expression pattern, potentially linked with the excretory/secretory system. This transcriptome study is a good starting point to functionally investigate novel effectors derived from M. graminicola. This will lead to better insights into the interaction between these nematodes and the model plant rice. Moreover, the transcriptome can be used to identify possible target genes for RNA interference (RNAi)-based control strategies. Four genes proved to be interesting targets by showing up to 40% higher mortality relative to the control treatment when soaked in gene-specific small interfering RNAs (siRNAs).

Gene silencing in root lesion nematodes (Pratylenchus spp.) significantly reduces reproduction in a plant host

Root lesion nematodes (RLNs, Pratylenchus species) are a group of economically important migratory endoparasitic plant pathogens that attack host roots of major crops such as wheat and sugarcane, and can reduce crop yields by 7-15%. Pratylenchus thornei and Pratylenchus zeae were treated with double stranded RNA (dsRNA) to study gene silencing, (RNA interference, RNAi), as a potential strategy for their control. Mixed stages of nematodes of both species ingested dsRNA when incubated in a basic soaking solution in the presence of the neurostimulant octopamine. Incubation for up to 16 h in soaking solutions containing 10-50 mM octopamine, 0.1-1.0 mg/mL FITC, and 0.5-6 mM spermidine did not affect vitality. Spermidine phosphate salt hexahydrate rather than spermidine or spermidine trihydrochloride increased uptake of FITC by nematodes, and this resulted in more effective gene silencing. Silencing pat-10 and unc-87 genes of P. thornei and P. zeae resulted in paralysis and uncoordinated movements in both species, although to a higher degree in P. thornei. There was also a greater reduction in transcript of both genes in P. thornei indicating that it may be more susceptible to RNAi. For P. thornei treated with dsRNA of pat-10 and unc-87 there was a significant reduction (77-81%) in nematode reproduction on carrot mini discs over a 5 week period. The results show that RLNs are clearly amenable to gene silencing, and that in planta delivery of dsRNA to target genes in these nematodes should confer host resistance. Moreover, for the two genes, dsRNA derived from either nematode species silenced the corresponding gene in both species. This implies cross-species control of nematodes via RNAi is possible.