Characterization of the reniform nematode genome by shotgun sequencing

Nematode Genome Announcement: A Draft Genome of Seed Gall Nematode, Anguina tritici

Anguina tritici is the first plant-parasitic nematode described in literature, dating back to the year 1743. It is responsible for causing earcockle (seed gall) and tundu diseases in wheat and rye. Notably, this nematode has been observed to survive in an anhydrobiotic state for up to 32 years within wheat seed galls. These exceptional characteristics have inspired the sequencing of the A. tritici genome. In this study, we present the initial draft genome of A. tritici, obtained using the Illumina MiSeq platform with coverage of 60-fold. The genome is estimated to have a size of 164 Mb and comprises 39,965 protein-coding genes, exhibiting a GC content of 39.1%. The availability of this genome data will serve as a foundation for future functional biological investigations, particularly for genes whose functions remain unknown to this day.

New Distribution and Molecular Diversity of the Reniform Nematode Rotylenchulus macrosoma (Nematoda: Rotylenchulinae) in Europe

Reniform nematodes of the genus Rotylenchulus are semi-endoparasites of numerous herbaceous and woody plant species roots and occur largely in regions with temperate, subtropical, and tropical climates. In this study, we provide new records of the nematode Rotylenchulus macrosoma in eight European countries (Czech Republic, France, Germany, Hungary, Italy, Romania, Serbia, and Portugal), in addition to the six Mediterranean countries (Greece, Israel, Jordan, Spain, Syria, and Turkey) where the nematode was previously reported. Four new host species (corn, pea, wheat, and an almond-peach hybrid rootstock) are added to the recorded host species (bean, chickpea, hazelnut, peanut, soybean, and wild and cultivated olive). Molecular analyses based on the cytochrome c oxidase subunit coxI and D2-D3 segments of 28S RNA markers showed high diversity and pronounced genetic structure among populations of Rotylenchulus macrosoma. However, the complexity of phylogeographic patterns in plant-parasitic nematodes may be related to the intrinsic heterogeneity in the distribution of soil organisms, a rare occurrence of a species, or the potential human impact associated with agricultural practices.

Characterizing Repeats in Two Whole-Genome Amplification Methods in the Reniform Nematode Genome

One of the major problems in the U.S. and global cotton production is the damage caused by the reniform nematode, Rotylenchulus reniformis. Amplification of DNA from single nematodes for further molecular analysis can be challenging sometimes. In this research, two whole-genome amplification (WGA) methods were evaluated for their efficiencies in DNA amplification from a single reniform nematode. The WGA was carried out using both REPLI-g Mini and Midi kits, and the GenomePlex single cell whole-genome amplification kit. Sequence analysis produced 4 Mb and 12 Mb of genomic sequences for the reniform nematode using REPLI-g and SIGMA libraries. These sequences were assembled into 28,784 and 24,508 contigs, respectively, for REPLI-g and SIGMA libraries. The highest repeats in both libraries were of low complexity, and the lowest for the REPLI-g library were for satellites and for the SIGMA library, RTE/BOV-B. The same kind of repeats were observed for both libraries; however, the SIGMA library had four other repeat elements (Penelope (long interspersed nucleotide element (LINE)), RTE/BOV-B (LINE), PiggyBac, and Mirage/P-element/Transib), which were not seen in the REPLI-g library. DNA transposons were also found in both libraries. Both reniform nematode 18S rRNA variants (RN_VAR1 and RN_VAR2) could easily be identified in both libraries. This research has therefore demonstrated the ability of using both WGA methods, in amplification of gDNA isolated from single reniform nematodes.

Anatomical Alterations in Plant Tissues Induced by Plant-Parasitic Nematodes

Plant-parasitic nematodes (PPNs) interact with plants in different ways, for example, through subtle feeding behavior, migrating destructively through infected tissues, or acting as virus-vectors for nepoviruses. They are all obligate biotrophic parasites as they derive their nutrients from living cells which they modify using pharyngeal gland secretions prior to food ingestion. Some of them can also shield themselves against plant defenses to sustain a relatively long lasting interaction while feeding. This paper is centered on cell types or organs that are newly induced in plants during PPN parasitism, including recent approaches to their study based on molecular biology combined with cell biology-histopathology. This issue has already been reviewed extensively for major PPNs (i.e., root-knot or cyst nematodes), but not for other genera (viz. Nacobbus aberrans, Rotylenchulus spp.). PPNs have evolved with plants and this co-evolution process has allowed the induction of new types of plant cells necessary for their parasitism. There are four basic types of feeding cells: (i) non-hypertrophied nurse cells; (ii) single giant cells; (iii) syncytia; and (iv) coenocytes. Variations in the structure of these cells within each group are also present between some genera depending on the nematode species viz. Meloidogyne or Rotylenchulus. This variability of feeding sites may be related in some way to PPN life style (migratory ectoparasites, sedentary ectoparasites, migratory ecto-endoparasites, migratory endoparasites, or sedentary endoparasites). Apart from their co-evolution with plants, the response of plant cells and roots are closely related to feeding behavior, the anatomy of the nematode (mainly stylet size, which could reach different types of cells in the plant), and the secretory fluids produced in the pharyngeal glands. These secretory fluids are injected through the stylet into perforated cells where they modify plant cytoplasm prior to food removal. Some species do not produce specialized feeding sites (viz. Ditylenchus, Subanguina), but may develop a specialized modification of the root system (e.g., unspecialized root galls or a profusion of roots). This review introduces new data on cell types and plant organs stimulated by PPNs using sources varying from traditional histopathology to new holistic methodologies.

Smart Parasitic Nematodes Use Multifaceted Strategies to Parasitize Plants

Nematodes are omnipresent in nature including many species which are parasitic to plants and cause enormous economic losses in various crops. During the process of parasitism, sedentary phytonematodes use their stylet to secrete effector proteins into the plant cells to induce the development of specialized feeding structures. These effectors are used by the nematodes to develop compatible interactions with plants, partly by mimicking the expression of host genes. Intensive research is going on to investigate the molecular function of these effector proteins in the plants. In this review, we have summarized which physiological and molecular changes occur when endoparasitic nematodes invade the plant roots and how they develop a successful interaction with plants using the effector proteins. We have also mentioned the host genes which are induced by the nematodes for a compatible interaction. Additionally, we discuss how nematodes modulate the reactive oxygen species (ROS) and RNA silencing pathways in addition to post-translational modifications in their own favor for successful parasitism in plants.

Morphological and molecular characterisation of one new and several known species of the reniform nematode, Rotylenchulus Linford & Oliveira, 1940 (Hoplolaimidae: Rotylenchulinae), and a phylogeny of the genus

The reniform nematodes of the genusRotylenchulusare semi-endoparasites of numerous herbaceous and woody plant roots and are mainly distributed in tropical and subtropical regions. In this study, we provide morphological and molecular characterisation of six out of ten presently known valid species ofRotylenchulus:R. clavicaudatus,R. leptus,R. macrodoratus,R. macrosoma,R. reniformisandR. saccharifrom South Africa, USA, Italy and Spain.Rotylenchulus parvuswas only studied morphologically. A new species,R. macrosomoidessp. n., isolated from soil and roots of sugarcane in South Africa, is described. The phylogeny ofRotylenchulus, as inferred from the analyses of D2-D3 of 28S rRNA, ITS rRNA,coxImtDNA andhsp90gene sequences, is presented. The study revealed thatR. reniformisandR. macrosomahave a sister relationship, but that relationships between otherRotylenchulusspecies remain unresolved. The phylogenetic analysis also confirmed the hypothesis that this genus originated from the Afrotropical zoogeographical region. Our study revealed thatR. reniformisandR. macrosomoidessp. n. have two distinct rRNA gene types andR. macrosomahave three rRNA gene types in their genomes. PCR with species-specific primers was developed for rapid diagnostics ofR. reniformis.