The architecture of the High Performance Storage System (HPSS)

The rapid growth in the size of datasets has caused a serious imbalance in I/O and storage system performance and functionality relative to application requirements and the capabilities of other system components. The High Performance Storage System (HPSS) is a scalable, next-generation storage system that will meet the functionality and performance requirements or large-scale scientific and commercial computing environments. Our goal is to improve the performance and capacity of storage by two orders of magnitude or more over what is available in the general or mass marketplace today. We are also providing corresponding improvements in architecture and functionality. This paper describes the architecture and functionality of HPSS

Morphological and molecular characterisation of Scutellonema species from yam (Dioscorea spp.) and a key to the species of the genus

The yam nematode, Scutellonema bradys, is a major threat to yam (Dioscorea spp.) production across yam-growing regions. In West Africa, this species cohabits with many morphologically similar congeners and, consequently, its accurate diagnosis is essential for control and for monitoring its movement. In the present study, 46 Scutellonema populations collected from yam rhizosphere and yam tubers in different agro-ecological zones in Ghana and Nigeria were characterised by their morphological features and by sequencing of the D2-D3 region of the 28S rDNA gene and the mitochondrial COI genes. Molecular phylogeny, molecular species delimitation and morphology revealed S. bradys, S. cavenessi, S. clathricaudatum and three undescribed species from yam rhizosphere. Only S. bradys was identified from yam tuber tissue, however. For barcoding and identifying Scutellonema spp., the most suitable marker used was the COI gene. Additionally, 99 new Scutellonema sequences were generated using populations obtained also from banana, carrot, maize and tomato, including the first for S. paralabiatum and S. clathricaudatum, enabling the development of a dichotomous key for identification of Scutellonema spp. The implications of these results are discussed

Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution

The polyphagous parthenogenetic root-knot nematodes of the genus Meloidogyne are considered to be the most significant nematode pest in sub-tropical and tropical agriculture. Despite the crucial need for correct diagnosis, identification of these pathogens remains problematic. The traditionally used diagnostic strategies, including morphometrics, host-range tests, biochemical and molecular techniques, now appear to be unreliable due to the recently-suggested hybrid origin of root-knot nematodes. In order to determine a suitable barcode region for these pathogens nine quickly-evolving mitochondrial coding genes were screened. Resulting haplotype networks revealed closely related lineages indicating a recent speciation, an anthropogenic-aided distribution through agricultural practices, and evidence for reticulate evolution within M. arenaria. Nonetheless, nucleotide polymorphisms harbor enough variation to distinguish these closely-related lineages. Furthermore, completeness of lineage sorting was verified by screening 80 populations from widespread geographical origins and variable hosts. Importantly, our results indicate that mitochondrial haplotypes are strongly linked and consistent with traditional esterase isozyme patterns, suggesting that different parthenogenetic lineages can be reliably identified using mitochondrial haplotypes. The study indicates that the barcode region Nad5 can reliably identify the major lineages of tropical root-knot nematodes

Integrative taxonomy of root-knot nematodes reveals multiple independent origins of mitotic parthenogenesis

Open Access JournalDuring sampling of several Coffea arabica plantations in Tanzania severe root galling, caused by a root-knot nematode was observed. From pure cultures, morphology and morphometrics of juveniles and females matched perfectly with Meloidogyne africana, whereas morphology of the males matched identically with those of Meloidogyne decalineata. Based on their Cox1 sequence, however, the recovered juveniles, females and males were confirmed to belong to the same species, creating a taxonomic conundrum. Adding further to this puzzle, re-examination of M. oteifae type material showed insufficient morphological evidence to maintain its status as a separate species. Consequently, M. decalineata and M. oteifae are synonymized with M. africana, which is herewith redescribed based on results of light and scanning electron microscopy, ribosomal and mitochondrial DNA sequences, isozyme electrophoresis, along with bionomic and cytogenetic features. Multi-gene phylogenetic analysis placed M. africana outside of the three major clades, together with M. coffeicola, M. ichinohei and M. camelliae. This phylogenetic position was confirmed by several morphological features, including cellular structure of the spermatheca, egg mass position, perineal pattern and head shape. Moreover, M. africana was found to be a polyphagous species, demonstrating that "early-branching" Meloidogyne spp. are not as oligophagous as had previously been assumed. Cytogenetic information indicates M. africana (2n = 21) and M. ardenensis (2n = 51-54) to be a triploid mitotic parthenogenetic species, revealing at least four independent origins of mitotic parthenogenesis within the genus Meloidogyne. Furthermore, M. mali (n = 12) was found to reproduce by amphimixis, indicating that amphimictic species with a limited number of chromosomes are widespread in the genus, potentially reflecting the ancestral state of the genus. The wide variation in chromosome numbers and associated changes in reproduction modes indicate that cytogenetic evolution played a crucial role in the speciation of root-knot nematodes and plant-parasitic nematodes in general

Potato cyst nematodes Globodera rostochiensis and G. pallida

Innovate UK. Grant Number: 105653 (RESOLVE) Rural and Environment Science and Analytical Services Division. Grant Number: WP2.1 Scottish Funding Council. Grant Number: ODA GCRF XFC105Taxonomy: Phylum Nematoda; class Chromadorea; order Rhabditida; suborder Tylenchina; infraorder Tylenchomorpha; superfamily Tylenchoidea; family Heteroderidae; subfamily Heteroderinae; Genus Globodera. Biology: Potato cyst nematodes (PCN) are biotrophic, sedentary endoparasitic nematodes. Invasive (second) stage juveniles (J2) hatch from eggs in response to the presence of host root exudates and subsequently locate and invade the host. The nematodes induce the formation of a large, multinucleate syncytium in host roots, formed by fusion of up to 300 root cell protoplasts. The nematodes rely on this single syncytium for the nutrients required to develop through a further three moults to the adult male or female stage. This extended period of biotrophy?between 4 and 6 weeks in total?is almost unparalleled in plant?pathogen interactions. Females remain at the root while adult males revert to the vermiform body plan of the J2 and leave the root to locate and fertilize the female nematodes. The female body forms a cyst that contains the next generation of eggs. Host range: The host range of PCN is limited to plants of the Solanaceae family. While the most economically important hosts are potato (Solanum tuberosum), tomato (Solanum lycopersicum), and aubergine (Solanum melongena), over 170 species of Solanaceae are thought to be potential hosts for PCN (Sullivan et al., 2007). Disease symptoms: Symptoms are similar to those associated with nutrient deficiency, such as stunted growth, yellowing of leaves and reduced yields. This absence of specific symptoms reduces awareness of the disease among growers. Disease control: Resistance genes (where available in suitable cultivars), application of nematicides, crop rotation. Great effort is put into reducing the spread of PCN through quarantine measures and use of certified seed stocks. Useful websites: Genomic information for PCN is accessible through WormBase ParaSite.Publisher PDFPeer reviewe

Arbuscular mycorrhizal fungal communities in sub-Saharan Savannas of Benin, West Africa, as affected by agricultural land use intensity and ecological zone

The rapid decline of soil fertility of cultivated lands in the sub-Saharan savannas of West Africa is considered to be the main cause of the increasingly severe constraints of food production. The soils in this tropical area are highly fragile, and crop yields are limited by characteristically low levels of available phosphorus. Under such preconditions, the multiple benefits of the arbuscular mycorrhizal (AM) symbiosis are likely to play a pivotal role for maintaining natural soil fertility by enhancing plant nutrient use efficiency, plant health, and stabilization of a favorable soil structure. Thus, it is important to explore the impact of the commonly applied farming practices on the native AM fungal community. In the present study, we determined the AM fungal species composition in three ecological zones differing by an increasingly prolonged dry season from South to North, from the Southern Guinea Savanna (SG), to the Northern Guinea Savanna (NG), to the Sudan Savanna (SU). In each zone, four "natural” and four "cultivated” sites were selected. "Natural” sites were three natural forest savannas (at least 25-30years old) and a long-term fallow (6-7years old). "Cultivated” sites comprised a field with yam (Dioscorea spp.) established during the first year after forest clearance, a field under mixed cropping with maize (Zea mays) and peanut (Arachis hypogaea), a field under peanut, and a field under cotton (Gossypium hirsutum) which was the most intensively managed crop. Soil samples were collected towards the end of the wet season in each zone. AM fungal spores were extracted and morphologically identified. Soil subsamples were used to inoculate AM fungal trap cultures using Stylosanthes guianensis and Brachiaria humidicola as host plants to monitor AM root colonization and spore formation over 10 and 24months, respectively. A total of 60 AM fungal species were detected, with only seven species sporulating in the trap cultures. Spore density and species richness were generally higher in the natural savannas and under yam than at the other cultivated sites and lowest under the intensively managed cotton. In the fallows, species richness was intermediate, indicating that the high richness of the natural savannas was not restored. Surprisingly, higher species richness was observed in the SU than in the SG and NG, mainly due to a high proportion of species in the Gigasporaceae, Acaulosporaceae, and Glomeraceae. We conclude that the West African savannas contain a high natural AM fungal species richness, but that this natural richness is significantly affected by the common agricultural land use practices and appears not to be quickly restored by fallo

Parasitic nematode Meloidogyne incognita interactions with different Capsicum annum cultivars reveal the chemical constituents modulating root herbivory

Open Access Journal; Published online: 06 June 2017Plant volatile signatures are often used as cues by herbivores to locate their preferred hosts. Here, we report on the volatile organic compounds used by the subterranean root-knot nematode (RKN) Meloidogyne incognita for host location. We compared responses of infective second stage juveniles (J2s) to root volatiles of three cultivars and one accession of the solanaceous plant, Capsicum annum against moist sand in dual choice assays. J2s were more attracted to the three cultivars than to the accession, relative to controls. GC/MS analysis of the volatiles identified common constituents in each plant, five of which were identified as α-pinene, limonene, 2-methoxy-3-(1-methylpropyl)-pyrazine, methyl salicylate and tridecane. We additionally identified thymol as being specific to the accession. In dose-response assays, a blend of the five components elicited positive chemotaxis (71–88%), whereas individual components elicited varying responses; Methyl salicylate (MeSA) elicited the highest positive chemotaxis (70–80%), α-pinene, limonene and tridecane were intermediate (54–60%), and 2-methoxy- 3-(1-methylpropyl)-pyrazine the lowest (49–55%). In contrast, thymol alone or thymol combined with either the preferred natural plant root volatiles or the five-component synthetic blend induced negative chemotaxis. Our results provide insights into RKN-host plant interactions, creating new opportunities for plant breeding programmes towards management of RKNs

Effect of two species of arbuscular mycorrhizal fungi inoculation on development of micro-propagated yam plantlets and suppression of Scutellonema bradys (Tylenchideae)

Using two commercially available arbuscular mycorrhizal fungal (AMF) products, one based on Funneliformis mosseae and the other on Glomus dussii, an experiment was conducted to assess their effect on yam growth and ability to suppress nematode damage in pots. Four yam cultivars (cvs) were used: two Dioscorea alata cvs (TDa98-01183 and TDa98-165), and two Dioscorea rotundata cvs (TDr97- 00551 and TDr 745). Micropropagated yam plantlets were inoculated either with F. mosseae or with G. dussii at the stage of transplanting into 2L pots and - one month later - with 500 vermiform Scutellonema bradys. The plantlets were grown for further six months in the greenhouse at IITA-Ibadan. The results showed that the presence of AMF tended to lead to improved growth of yam, especially D. alata cvs, as compared with the non-arbuscular mycorrhizal control plants. When challenged with the yam nematode S. bradys, plantlets of the two D. alata cultivars pre-inoculated with F. mosseae and cv TDr97-00551 pre-inoculated with G. dussii yielded significantly higher tuber weights compared to non- AMF control plantlets. S. bradys densities on yam plantlets pre-inoculated with AMF were generally suppressed, although no differences were observed in visible damage scores, which remained low or absent across treatments

Morphological and molecular characterization of Pratylenchus species from Yam (Dioscorea spp.) in West Africa

The root-lesion nematodes (RLN), Pratylenchus spp., are among the major plant-parasitic nematodes affecting yam (Dioscorea spp.) production in West Africa. The distribution and diversity of RLN species associated with yam was investigated through a soil and tuber survey of the main producing areas in Nigeria and Ghana. Pratylenchus spp. were detected in the yam rhizosphere in 59% of 81 soil samples from Ghana and 39% of 114 soil samples from Nigeria. Pratylenchus spp. were detected in 24 of 400 tubers examined, in combination with root-knot nematodes (Meloidogyne spp.) and their associated damage of galls and crazy roots (79%), and with yam nematode (Scutellonema bradys) and their associated damage of dry rot (17%), although no specific additional symptoms were observed for Pratylenchus spp. Species of Pratylenchus were identified by their morphological features and by sequences of the D2-D3 region of the 28 S rDNA gene and the mitochondrial cytochrome oxidase I gene (COI). Pratylenchus brachyurus was the most frequent RLN species in both the rhizosphere and tubers of yam. Pratylenchus hexincisus was recovered from one tuber collected in Nigeria. While further investigations are required to establish the host status of yam for this nematode, this appears to be the first record of P. hexincisus on yam. The present taxonomical status of P. scribneri and P. hexincisus is discussed

A pathogen complex between the root knot nematode Meloidogyne incognita and Fusarium verticillioides results in extreme mortality of the inka nut (Plukenetia volubilis)

The combined infection of the root knot nematode Meloidogyne incognita and two Fusarium species led to high plant mortality of inka nut (Plukenetia volubilis) seedlings in pots after 80 days growth in two independent inoculation experiments. Inoculation of M. incognita juveniles and conidia of F. solani or F. verticillioides, simultaneously, increased plant mortality by 25-30%, compared with M. incognita alone (5-10% mortality). When inoculated with F. verticillioides at 20 days post nematode inoculation, plant mortality increased to 55%. Either of the Fusarium spp. alone caused some plant mortality, but less than when combined with M. incognita. The synergistic interaction of M. incognita and especially F. verticillioides demonstrates a lethal outcome for inka nuts. It appears that M. incognita creates favorable conditions that lead to enhanced effect and damage by the Fusarium species, especially F. verticillioides, leading to devastating levels of plant death