Comparative genomics of two inbred lines of the potato cyst nematode Globodera rostochiensis reveals disparate effector family-specific diversification patterns

Background Potato cyst nematodes belong to the most harmful pathogens in potato, and durable management of these parasites largely depends on host-plant resistances. These resistances are pathotype specific. The current Globodera rostochiensis pathotype scheme that defines five pathotypes (Ro1 - Ro5) is both fundamentally and practically of limited value. Hence, resistant potato varieties are used worldwide in a poorly informed manner. Results We generated two novel reference genomes of G. rostochiensis inbred lines derived from a Ro1 and a Ro5 population. These genome sequences comprise 173 and 189 scaffolds respectively, marking a ≈ 24-fold reduction in fragmentation as compared to the current reference genome. We provide copy number variations for 19 effector families. Four dorsal gland effector families were investigated in more detail. SPRYSECs, known to be implicated in plant defence suppression, constitute by far the most diversified family studied herein with 60 and 99 variants in Ro1 and Ro5 distributed over 18 and 26 scaffolds. In contrast, CLEs, effectors involved in feeding site induction, show strong physical clustering. The 10 and 16 variants cluster on respectively 2 and 1 scaffolds. Given that pathotypes are defined by their effectoromes, we pinpoint the disparate nature of the contributing effector families in terms of sequence diversification and loss and gain of variants. Conclusions Two novel reference genomes allow for nearly complete inventories of effector diversification and physical organisation within and between pathotypes. Combined with insights we provide on effector family-specific diversification patterns, this constitutes a basis for an effectorome-based virulence scheme for this notorious pathogen.

Comparative Genomics of two Inbred Lines of the Potato Cyst Nematode Globodera rostochiensis reveals disparate Effector Family-specific Diversification Patterns

Background: Potato cyst nematodes belong to the most harmful pathogens in potato, and durable management of these soil-borne parasites largely depends on host-plant resistances. These resistances are pathotype specific. The current Globodera rostochiensis pathotype scheme that defines five pathotypes (Ro1 - Ro5) is for fundamental and practical reasons barely useful. As a result, resistant potato varieties are used worldwide in a non-informed manner. Results: We generated two novel reference genomes of G. rostochiensis inbred lines derived from a Ro1 and a Ro5 population. These genome sequences comprise 173 and 189 scaffolds respectively, marking a » 24-fold reduction in fragmentation as compared to the current reference genome. We provide copy number variations for 18 effector families. Four dorsal gland effector families were investigated in more detail. SPRYSECs, known to be implicated in plant defence suppression, constitute by far the most diversified family with 60 and 99 variants in Ro1 and Ro5 distributed over 18 and 26 scaffolds. In contrast, CLEs, effectors involved in feeding site induction, show strong physical clustering. The 10 and 16 variants cluster on respectively 2 and 1 scaffolds. Given that pathotypes are defined by their effectoromes, we pinpoint the disparate nature of the contributing effector families in terms of sequence diversification and loss and gain of variants.Conclusion: Two novel reference genomes allow for nearly complete inventories of effector diversification and physical organisation within and between pathotypes. Combined with insights we provide on effector family-specific diversification patterns, this constitutes a solid basis for an effectorome-based virulence scheme for this notorious pathogen.

Comparative Genomics of two Inbred Lines of the Potato Cyst Nematode Globodera rostochiensis reveals disparate Effector Family-specific Diversification Patterns

BackgroundPotato cyst nematodes belong to the most harmful pathogens in potato, and durable management of these soil-borne parasites largely depends on host-plant resistances. These resistances are pathotype specific. The current Globodera rostochiensis pathotype scheme that defines five pathotypes (Ro1 - Ro5) is for fundamental and practical reasons barely useful. As a result, resistant potato varieties are worldwide used in a non-informed manner.ResultsWe generated two novel reference genomes of G. rostochiensis inbred lines derived from a Ro1 and a Ro5 population. These genome sequences comprise 173 and 189 scaffolds respectively, marking a ≈ 24-fold reduction in fragmentation as compared to the current reference genome. We provide copy number variations for 18 effector families. Four dorsal gland effector families were investigated in more detail. SPRYSECs, known to be implicated in immune suppression, constitute by far the most diversified family with 60 and 99 variants in Ro1 and Ro5 distributed over 18 and 26 scaffolds. In contrast, CLEs, effectors involved in feeding site induction, show strong physical clustering. The 10 and 16 variants cluster on respectively 2 and 1 scaffolds. Given that pathotypes are defined by their effectoromes, we pinpoint the disparate nature of the contributing effector families in terms of sequence diversification and loss and gain of variants.ConclusionTwo novel reference genomes allow for nearly complete inventories of effector diversification and physical organisation within and between pathotypes. Combined with insights we provide on effector family-specific diversification patterns, this constitutes a solid basis for an effectorome-based virulence scheme for this notorious pathogen.

A new reptant species of Leandra (Melastomataceae, Miconieae) from the Atlantic Forest, southeastern Brazil

Leandra reptans is a new species from montane Atlantic Forest at the state of Espírito Santo, southeastern Brazil. It can be recognized by its reptant habit, leaves purple beneath and with a perpendicular, peltate-like insertion of the petiole into the strongly cordate blade base, calyx lobes with a basal constriction and antepetalous stamens with dorsal gland-like appendages.

Activation of hatching in diapaused and quiescent Globodera pallida

SUMMARYThe potato cyst nematodes (PCN) Globodera pallida and G. rostochiensis are major pests of potatoes. The G. pallida (and G. rostochiensis) life cycle includes both diapause and quiescent stages. Nematodes in dormancy (diapause or quiescent) are adapted for long-term survival and are more resistant to nematicides. This study analysed the mechanisms underlying diapause and quiescence. The effects of several compounds (8Br-cGMP, oxotremorine and atropine) on the activation of hatching were studied. The measurements of some morphometric parameters in diapaused and quiescent eggs after exposure to PRD revealed differences in dorsal gland length, subventral gland length and dorsal gland nucleolus. In addition, the expression of 2 effectors (IVg9 and cellulase) was not induced in diapaused eggs in water or PRD, while expression was slightly induced in quiescent eggs. Finally, we performed a comparative study to identify orthologues of C. elegans diapause related genes in plant-parasitic nematodes (G. pallida, Meloidogyne incognita, M. hapla and Bursaphelenchus xylophilus). This analysis suggested that it was not possible to identify G. pallida orthologues of the majority of C. elegans genes involved in the control of dauer formation. All these data suggest that G. pallida may use different mechanisms to C. elegans in regulating the survival stage.

Changes in the pre-parasitic developmental stage of Globodera rostochiensis in response to green manures

The sequence of events during the pre-parasitic and parasitic stages of the life cycle of Globodera rostochiensis, starting from hatching until host invasion and infection, is of major importance. Many of the physiological changes are initiated in the pre-parasitic stage in response to the influences exerted by the root diffusates of the host plant. The objectives of this study were to investigate whether root diffusates and extracts of green manures from Brassicaceae, in particular yellow mustard, fodder radish and rapeseed, have a direct effect on the pre-parasitic stage of G. rostochiensis. Unhatched second-stage juveniles (J2) were exposed to root diffusates and extracts from roots or above-ground parts of the green manures to assess: i) changes in eggshell permeability; ii) changes in diameter of the dorsal gland nucleolus; and iii) the activation of transcription in the dorsal and subventral pharyngeal glands. The 24 h exposure of unhatched J2 to the green manures did not indicate an alteration in eggshell permeability. The diameter of the dorsal gland nucleolus increased significantly after exposure to diffusates but not to extracts of the green manures, although the size in that case still did not exceed the measurements in J2 exposed to tomato root diffusates. The expression of the gene IVg9 in the dorsal gland was not detected after any treatment. However, transcriptional activation in the subventral pharyngeal glands was observed. Although the maximum expression of the cellulase gene was found in J2 exposed to tomato root diffusates, the expression in J2 exposed to root extracts of green manures was higher than in J2 exposed to root diffusates and extracts of above-ground plant parts. The potential of the investigated brassicaceous green manures to influence the pre-parasitic stage of G. rostochiensis is discussed.

Nonlethal ectoparasitism of the mycophagous nematode Filenchus discrepans (Nematoda: Tylenchidae)

Filenchus discrepans ingested hyphal contents of Botrytis cinerea without killing the hyphal cells that they fed on. Individuals of this nematode penetrated B. cinerea hyphae with their stylets, after which intense pulsation of the median bulb and dorsal gland duct followed (indicating salivation). In addition, light pumping of the median bulb (indicating food ingestion) was also observed. Fungal cells continued to show cytoplasmic streaming while the nematode ingested hyphal contents. Moreover, actively growing tips of the hyphae usually continued their growth during and after cytoplasm ingestion by the nematode. In less active, older hyphae the penetrated tip cells stopped growing during nematode feeding. However, the majority of the tip cells resumed growth after feeding by the nematode. The hyphal tips often exhibited an abnormal shape during nematode feeding and gradually regained normal shape and growth afterwards. The growth rate of hyphal tip cells decreased to less than 10% compared with the growth of intact hyphal tip cells during attack by F. discrepans, which often fed on a hyphal cell for up to 3 h. Filenchus discrepans propagated well in B. cinerea cultures and their population growth rate ranged between six- and 11-fold 1 month after incubation. This is the first report of nonlethal ectoparasitism by a mycophagous nematode, showing that the nematode does not kill fungal cells during and after feeding.

Volatile Components in Dorsal Gland Secretions of the Chacoan Peccary, Catagonus wagneri

The dorsal gland secretions of captive-reared male and female Chacoan peccaries (Catagonus wagneri) were analyzed by gas chromatography-mass spectrometry. C8-C19 carboxylic acids, squalene, cholesterol, cholestanol, and cholest-7-en-3-ol were present in both males and females. Heptylbenzene, C14-C18 methyl esters, and an isomer of springene were observed in males. C15-C19 aldehydes were observed in females. The composition of the dorsal gland secretions of C. wagneri is compared to what has been reported for other peccaries (Tayassu spp.).

First Report of Meloidogyne arenaria Parasitizing Lettuce in Southern Spain

During the 2005-2006 autumn to winter lettuce-growing (Lactuca sativa cv. Iceberg) season, severely stunted and yellowing lettuce plants with disease incidence ranging from 80 to100% were observed in four commercial, fall-sown fields at Almodóvar del Río (Córdoba Province) in southern Spain. Early symptoms consisted of severely reduced growth of the plants that continued with extensive leaf yellowing and the absence of tight-head formation. Attacks by the disease were estimated to cause near complete loss of the crop yields since the lettuce head produced in affected fields were unmarketable. Observations of affected lettuce plants revealed high parasitism of the root system by a root-knot nematode (Meloidogyne sp.) in the main and feeder roots as well as heavy soil infestations by the nematode. The nematode was identified by the female perineal pattern, esterases phenotype, and a sequence-characterized amplified region polymerase chain reaction (SCAR-PCR) technique (1,2,4). Measurements and morphological observations of 20 second-stage juveniles (J2s) (body length = 463 ± 28 μm, dorsal gland orifice from stylet base = 2.8 ± 0.6 μm, stylet length = 10.4 ± 0.5 μm, tail length = 54.4 ± 0.6 μm; hyaline tail terminus = 9.4 ± 0.6 μm) and 10 adult females (stylet length = 14.5 ± 0.7 μm, dorsal gland orifice from stylet base = 4.7 ± 0.5 μm, and perineal pattern with low and rounded dorsal arch with coarse striae) conformed to the description of Meloidogyne arenaria (3). On the basis of the characteristics of the perineal pattern, the 2-band esterase phenotype, and the 420-bp SCAR fragment, the causal agent was identified as the peanut root-knot nematode M. arenaria. Nematodes were extracted from soil and root samples by standard procedures and their populations quantified. M. arenaria was detected in nearly all soil and root samples assessed, with nematode population densities ranging from 206 to 1,072 eggs and J2s per 5 g of fresh roots. Different Meloidogyne spp. have been reported parasitizing lettuce roots, especially M. hapla in northern areas (2); however, to our knowledge this is the first time that M. arenaria is reported parasitizing lettuce roots in Spain and elsewhere. References: (1) P. R. Esbenshade and A. C. Triantaphyllou. J. Nematol. 22:10, 1990. (2) N. A. Mitkowski et al. Plant Dis. 86:840, 2002. (3) K. J. Orton Williams. Meloidogyne arenaria. CIH Descriptions of Plant-Parasitic Nematodes. Set 5, No. 62. Commonwealth Institute of Helminthology, St. Albans, 1975. (4) C. Zijlstra et al. Nematology 2:847, 2000.