A global surveillance system for crop diseases

To satisfy a growing demand for food, global agricultural production must increase by 70% by 2050. However, pests and crop diseases put global food supplies at risk. Worldwide, yield losses caused by pests and diseases are estimated to average 21.5% in wheat, 30.0% in rice, 22.6% in maize, 17.2% in potato, and 21.4% in soybean (1); these crops account for half of the global human calorie intake (2). Climate change and global trade drive the distribution, host range, and impact of plant diseases (3), many of which can spread or reemerge after having been under control (4). Though many national and regional plant protection organizations (NPPOs and RPPOs) work to monitor and contain crop disease outbreaks, many countries, particularly low-income countries (LICs), do not efficiently exchange information, delaying coordinated responses to prevent disease establishment and spread. To improve responses to unexpected crop disease spread, we propose a Global Surveillance System (GSS) that will extend and adapt established biosecurity practices and networking facilities into LICs, enabling countries and regions to quickly respond to emerging disease outbreaks to stabilize food supplies, enhancing global food protection

Next generation transcriptomes for next generation genomes using est2assembly

<p>Abstract</p> <p>Background</p> <p>The decreasing costs of capillary-based Sanger sequencing and next generation technologies, such as 454 pyrosequencing, have prompted an explosion of transcriptome projects in non-model species, where even shallow sequencing of transcriptomes can now be used to examine a range of research questions. This rapid growth in data has outstripped the ability of researchers working on non-model species to analyze and mine transcriptome data efficiently.</p> <p>Results</p> <p>Here we present a semi-automated platform '<it>est2assembly</it>' that processes raw sequence data from Sanger or 454 sequencing into a hybrid <it>de-novo </it>assembly, annotates it and produces GMOD compatible output, including a SeqFeature database suitable for GBrowse. Users are able to parameterize assembler variables, judge assembly quality and determine the optimal assembly for their specific needs. We used <it>est2assembly </it>to process <it>Drosophila </it>and <it>Bicyclus </it>public Sanger EST data and then compared them to published 454 data as well as eight new insect transcriptome collections.</p> <p>Conclusions</p> <p>Analysis of such a wide variety of data allows us to understand how these new technologies can assist EST project design. We determine that assembler parameterization is as essential as standardized methods to judge the output of ESTs projects. Further, even shallow sequencing using 454 produces sufficient data to be of wide use to the community. <it>est2assembly </it>is an important tool to assist manual curation for gene models, an important resource in their own right but especially for species which are due to acquire a genome project using Next Generation Sequencing.</p

Pyrosequencing the Bemisia tabaci Transcriptome Reveals a Highly Diverse Bacterial Community and a Robust System for Insecticide Resistance

BACKGROUND: Bemisia tabaci (Gennadius) is a phloem-feeding insect poised to become one of the major insect pests in open field and greenhouse production systems throughout the world. The high level of resistance to insecticides is a main factor that hinders continued use of insecticides for suppression of B. tabaci. Despite its prevalence, little is known about B. tabaci at the genome level. To fill this gap, an invasive B. tabaci B biotype was subjected to pyrosequencing-based transcriptome analysis to identify genes and gene networks putatively involved in various physiological and toxicological processes. METHODOLOGY AND PRINCIPAL FINDINGS: Using Roche 454 pyrosequencing, 857,205 reads containing approximately 340 megabases were obtained from the B. tabaci transcriptome. De novo assembly generated 178,669 unigenes including 30,980 from insects, 17,881 from bacteria, and 129,808 from the nohit. A total of 50,835 (28.45%) unigenes showed similarity to the non-redundant database in GenBank with a cut-off E-value of 10-5. Among them, 40,611 unigenes were assigned to one or more GO terms and 6,917 unigenes were assigned to 288 known pathways. De novo metatranscriptome analysis revealed highly diverse bacterial symbionts in B. tabaci, and demonstrated the host-symbiont cooperation in amino acid production. In-depth transcriptome analysis indentified putative molecular markers, and genes potentially involved in insecticide resistance and nutrient digestion. The utility of this transcriptome was validated by a thiamethoxam resistance study, in which annotated cytochrome P450 genes were significantly overexpressed in the resistant B. tabaci in comparison to its susceptible counterparts. CONCLUSIONS: This transcriptome/metatranscriptome analysis sheds light on the molecular understanding of symbiosis and insecticide resistance in an agriculturally important phloem-feeding insect pest, and lays the foundation for future functional genomics research of the B. tabaci complex. Moreover, current pyrosequencing effort greatly enriched the existing whitefly EST database, and makes RNAseq a viable option for future genomic analysis

Maintenance of primary cell cultures of immunocytes from Cacopsylla spp. psyllids: a new in vitro tool for the study of crop pest insects

Primary cell cultures of immunocytes have been developed from the three psyllid species Cacopsylla melanoneura, Cacopsylla pyri (vectors of ‘Candidatus Phytoplasma mali’ and ‘Candidatus Phytoplasma pyri’, respectively) and Cacopsylla crataegi. The medium most suitable of those evaluated was Hert-Hunter 70 (HH70) psyllid medium. In fact, good survival and proliferation of the Cacopsylla immunocytes for over 60 d were observed, with mitosis activities starting at 15-d post culture. Moreover, adhesion and phagocytosis activities were confirmed for all the psyllid cell cultures by functionality tests. Morphological examination of cultured immunocytes revealed the presence of different cell types in all the three psyllid species in accordance to published data about insect immunocytes. The in vitro maintenance of psyllid immunocytes represents a powerful tool for a wide range of applications, especially for psyllid cell biology. In particular, in-depth studies on the biology of psyllids as vector insects as well as analyses to understand the mechanisms behind the interactions with pathogens and symbionts are now possible. These cultures can be used as an in vitro model to study psyllid humoral immune responses, which also will allow in-depth investigations on the abilities of psyllids as vectors of phytoplasmas. All these applications provide new opportunities to develop more focused and specific pest control strategies

A global surveillance system for crop diseases: Global preparedness minimizes the risk to food supplies

To satisfy growing demand for food, global agricultural production must in-crease by 70% by 2050. However, pests and crop diseases put global food supplies at risk. Worldwide, yield losses caused by pests and diseases are estimated to aver-age 21.5% in wheat, 30.0% in rice, 22.6% in maize, 17.2% in potato, and 21.4% in soybean [1]; these crops account for half of the global human calorie intake [2]. Climate change and global trade drive the distribution, host range, and impact of plant diseases [3], many of which can spread or re-emerge after having been under control [4] (see photo). Though many national and regional plant protec-tion organizations (NPPOs and RPPOs) work to monitor and contain crop disease outbreaks, many countries, particularly low-income countries (LIC) do not effi-ciently exchange information, delaying coordinated responses to prevent disease establishment and spread. To improve re-sponses to unexpected crop disease spread, we propose a Global Surveillance System (GSS) that will extend and adapt established biosecurity practices and networking facilities into LIC, enabling countries and regions to quickly respond to emerging disease outbreaks to stabilize food supplies, enhancing global food pro-tection