L. M. Quesada-Ocampo

BACKGROUND: Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). RESULTS: The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. CONCLUSIONS: A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.

Since L. H. Leonian's first description of Phytophthora capsici as a pathogen of chile pepper in 1922, we have made many advances in our understanding of this pathogen's biology, host range, dissemination, and management. P. capsici causes foliar blighting, damping-off, wilting, and root, stem, and fruit rot of susceptible hosts, and economic losses are experienced annually in vegetable crops including cucurbits and peppers. Symptoms of P. capsici infection may manifest as stunting, girdling, or cankers for some cultivars or crops that are less susceptible. P. capsici continues to be a constraint on production, and implementation of an aggressive integrated management scheme can still result in insufficient control when weather is favorable for disease. Management of diseases caused by P. capsici is currently limited by the long-term survival of the pathogen as oospores in the soil, a wide host range, long-distance movement of the pathogen in surface water used for irrigation, the presence of fungicide-resistant pathogen populations, and a lack of commercially acceptable resistant host varieties. P. capsici can infect a wide range of hosts under laboratory and greenhouse conditions including cultivated crops, ornamentals, and native plants belonging to diverse plant families. As our understanding of P. capsici continues to grow, future research should focus on developing novel and effective solutions to manage this pathogen and prevent economic losses due to the diseases it causes.

Pseudoperonospora cubensis[(Berkeley & M. A. Curtis) Rostovzev], the causal agent of cucurbit downy mildew, is responsible for devastating losses worldwide of cucumber, cantaloupe, pumpkin, watermelon and squash. Although downy mildew has been a major issue in Europe since the mid-1980s, in the USA, downy mildew on cucumber has been successfully controlled for many years through host resistance. However, since the 2004 growing season, host resistance has been effective no longer and, as a result, the control of downy mildew on cucurbits now requires an intensive fungicide programme. Chemical control is not always feasible because of the high costs associated with fungicides and their application. Moreover, the presence of pathogen populations resistant to commonly used fungicides limits the long-term viability of chemical control. This review summarizes the current knowledge of taxonomy, disease development, virulence, pathogenicity and control of Ps. cubensis. In addition, topics for future research that aim to develop both short- and long-term control measures of cucurbit downy mildew are discussed. TAXONOMY: Kingdom Straminipila; Phylum Oomycota; Class Oomycetes; Order Peronosporales; Family Peronosporaceae; Genus Pseudoperonospora; Species Pseudoperonospora cubensis. DISEASE SYMPTOMS: Angular chlorotic lesions bound by leaf veins on the foliage of cucumber. Symptoms vary on different cucurbit species and varieties, specifically in terms of lesion development, shape and size. Infection of cucurbits by Ps. cubensis impacts fruit yield and overall plant health. INFECTION PROCESS: Sporulation on the underside of leaves results in the production of sporangia that are dispersed by wind. On arrival on a susceptible host, sporangia germinate in free water on the leaf surface, producing biflagellate zoospores that swim to and encyst on stomata, where they form germ tubes. An appressorium is produced and forms a penetration hypha, which enters the leaf tissue through the stomata. Hyphae grow through the mesophyll and establish haustoria, specialized structures for the transfer of nutrients and signals between host and pathogen. CONTROL: Management of downy mildew in Europe requires the use of tolerant cucurbit cultivars in conjunction with fungicide applications. In the USA, an aggressive fungicide programme, with sprays every 5-7 days for cucumber and every 7-10 days for other cucurbits, has been necessary to control outbreaks and to prevent crop loss. USEFUL WEBSITES: http://www.daylab.plp.msu.edu/pseudoperonospora-cubensis/ (Day Laboratory website with research advances in downy mildew); http://veggies.msu.edu/ (Hausbeck Laboratory website with downy mildew news for growers); http://cdm.ipmpipe.org/ (Cucurbit downy mildew forecasting homepage); http://ipm.msu.edu/downymildew.htm (Downy mildew information for Michigan's vegetable growers).

In 2004, an outbreak of cucurbit downy mildew (CDM) caused by the oomycete Pseudoperonospora cubensis (Berk. & M. A. Curtis) Rostovzev resulted in an epidemic that stunned the cucumber (Cucumis sativus L.) industry in the eastern United States. The disease affects all major cucurbit crops, including cucumber, muskmelon, squashes, and watermelon. Although the 2004 epidemic began in North Carolina, the cucumber crop from Florida to the northern growing regions in the United States was devastated, resulting in complete crop loss in several areas. Many cucumber fields were abandoned prior to harvest. The rapid spread of the disease coupled with the failure of fungicide control programs surprised growers, crop consultants, and extension specialists. The epidemic raised several fundamental questions about the potential causes for the resurgence of the disease. Some of these questions revolved around whether the epidemic would recur in subsequent years and the possible roles that changes in the host, pathogen, and environment may have played in the epidemic.

The AVR3a protein of Phytophthora infestans is a polymorphic member of the RXLR class of cytoplasmic effectors with dual functions. AVR3a(KI) but not AVR3a(EM) activates innate immunity triggered by the potato resistance protein R3a and is a strong suppressor of the cell-death response induced by INF1 elicitin, a secreted P. infestans protein that has features of pathogen-associated molecular patterns. To gain insights into the molecular basis of AVR3a activities, we performed structure-function analyses of both AVR3a forms. We utilized saturated high-throughput mutant screens to identify amino acids important for R3a activation. Of 6,500 AVR3a(EM) clones tested, we identified 136 AVR3a(EM) mutant clones that gained the ability to induce R3a hypersensitivity. Fifteen amino-acid sites were affected in this set of mutant clones. Most of these mutants did not suppress cell death at a level similar to that of AVR3a(KI). A similar loss-of-function screen of 4,500 AVR3a(KI) clones identified only 13 mutants with altered activity. These results point to models in which AVR3a functions by interacting with one or more host proteins and are not consistent with the recognition of AVR3a through an enzymatic activity. The identification of mutants that gain R3a activation but not cell-death suppression activity suggests that distinct amino acids condition the two AVR3a effector activities.