稻瘟病菌株的DNA指纹分析及小种鉴别

基于对稻瘟病菌(Pyricularia oryzae)基因文库的分析,我们找到了一套含重复顺序的克隆。其中POR6和POR7被证实具有高度的多态性并随机散布于稻瘟病菌生理小种的致病性时,可以获得可分辨的基因组特异的杂交带型。我们还分析了致病性与8个稻瘟病菌株DNA指纹图谱之间的关系,结果表明各个小种组合间的百分相似率S_xy,值与该小种组合间共同侵染的鉴别品种数目有正相关性。     

基于比较基因组学方法的丝状子囊菌同源序列分析

为探讨丝状子囊菌基因组的同源保守序列作为标记基因,利用Standalone BLASTN方法将构巢曲霉全基因组基因分别与30种丝状子囊菌基因组比较.构巢曲霉与每个丝状子囊菌基因组之间的同源匹配基因数量似乎可反映子囊菌之间的进化关系,构巢曲霉（10,560个基因）与15种散囊菌纲其他真菌间的匹配基因数量为5,179-7,747个,其中与另外7个同属的种匹配的基因数量为7,434-7,747个,而与亲缘关系较远的2种锤舌菌纲真菌灰葡萄孢和核盘菌的匹配基因数量分别仅有4,318个和4,242个.构巢曲霉的10,560个基因与20余种子囊菌基因组同时匹配的基因数为3,509个,占33.2％,构巢曲霉基因与30种子囊菌共同匹配的基因仅924个.此外,E值大小在10-30_0.1范围的同源序列变异性大,而在0-10-100范围的同源序列高度保守.随着基因组序列数据的增加,比较基因组方法将会在真菌系统学研究领域发挥更大的作用.     

Probenazole-induced accumulation of salicylic acid confers resistance to Magnaporthe grisea in adult rice plants

Probenazole (PBZ) is the active ingredient of Oryzemate, an agrochemical which is used for the protection of rice plants from Magnaporthe grisea (blast fungus). While PBZ was reported to function upstream of salicylic acid (SA) in Arabidopsis, little is known about the mechanism of PBZ-induced resistance in rice. The role of SA in blast fungus resistance is also unclear. The recommended application period for Oryzemate is just before the Japanese rainy season, at which time rice plants in the field have reached the 8-leaf stage with adult traits. Thus, the involvement of SA in PBZ-induced resistance was studied in compatible and incompatible blast fungus-rice interactions at two developmentally different leaf morphology stages. Pre-treatment of inoculated fourth leaves of young wild-type rice plants at the 4-leaf stage with PBZ did not influence the development of whitish expanding lesions (ELs) in the susceptible interaction without the accumulation of SA and pathogenesis-related (PR) proteins. However, PBZ pre-treatment increased accumulation of SA and PR proteins in the eighth leaves of adult plants at the 8-leaf stage, resulting in the formation of hypersensitive reaction (HR) lesions (HRLs). Exogenous SA induced resistance in adult but not young plants. SA concentrations in blast fungus-inoculated young leaves were essentially the same in compatible and incompatible interactions, suggesting that PBZ-induced resistance in rice is age-dependently regulated via SA accumulation.     

Microsatellite and minisatellite markers based DNA fingerprinting and genetic diversity of blast and ufra resistant genotypes

A total of 78 alleles and 29 loci were detected from nine microsatellite and three minisatellite markers, respectively across 26 blast and ufra disease resistant genotypes. For blast resistant genotypes, the Polymorphic Information Content (PIC) values ranged from 0.280 to 0.726 and RM21 was considered as the best marker. PIC values ranged from 0.5953 to 0.8296 for ufra resistant genotypes and RM23 was the best marker for characterization of ufra resistant genotypes. The genetic similarity analysis using UPGMA clustering generated nine clusters with coefficient of 0.66 for blast resistant genotypes while five genetic clusters with similarity coefficient of 0.42 for ufra resistant genotypes. In order to develop resistant varieties of two major diseases of rice, hybridisation should be made using the parents, BR29 and NJ70507, BR36 and NJ70507 for blast, while BR11 and Aokazi, BR3 and Aokazi, Rayda and BR3 and Rayda and BR11 for ufra.     

A comparative analysis of dynamic grids vs. virtual grids using the A3pviGrid framework

With the proliferation of Quad/Multi-core micro-processors in mainstream platforms such as desktops and workstations; a large number of unused CPU cycles can be utilized for running virtual machines (VMs) as dynamic nodes in distributed environments. Grid services and its service oriented business broker now termed cloud computing could deploy image based virtualization platforms enabling agent based resource management and dynamic fault management. In this paper we present an efficient way of utilizing heterogeneous virtual machines on idle desktops as an environment for consumption of high performance grid services. Spurious and exponential increases in the size of the datasets are constant concerns in medical and pharmaceutical industries due to the constant discovery and publication of large sequence databases. Traditional algorithms are not modeled at handing large data sizes under sudden and dynamic changes in the execution environment as previously discussed. This research was undertaken to compare our previous results with running the same test dataset with that of a virtual Grid platform using virtual machines (Virtualization). The implemented architecture, A3pviGrid utilizes game theoretic optimization and agent based team formation (Coalition) algorithms to improve upon scalability with respect to team formation. Due to the dynamic nature of distributed systems (as discussed in our previous work) all interactions were made local within a team transparently. This paper is a proof of concept of an experimental mini-Grid test-bed compared to running the platform on local virtual machines on a local test cluster. This was done to give every agent its own execution platform enabling anonymity and better control of the dynamic environmental parameters. We also analyze performance and scalability of Blast in a multiple virtual node setup and present our findings. This paper is an extension of our previous research on improving the BLAST application framework using dynamic Grids on virtualization platforms such as the virtual box.     

Control of blast and sheath blight diseases of rice using antifungal metabolites produced by Streptomyces sp. PM5

Two antifungal aliphatic compounds, SPM5C-1 and SPM5C-2 with a lactone and ketone carbonyl unit, respectively obtained from Streptomyces sp. PM5 were evaluated under in vitro and in vivo conditions against major rice pathogens, Pyricularia oryzae and Rhizoctonia solani. These compounds were dissolved in distilled water/medium to get the required concentrations. The well diffusion bioassay indicated that the of SPM5C-1 remarkably inhibited the mycelial growth of P. oryzae and R. solani in comparison to SPM5C-2. Though SPM5C-2 showed low antifungal activity against P. oryzae, it was not active against R. solani. Further, SPM5C-1 completely inhibited the growth of P. oryzae and R. solani at concentrations of 25, 50, 75 and 100 μg/ml. Greenhouse experiments revealed that spraying of SPM5C-1 at 500 μg/ml on rice significantly decreased blast and sheath blight development by 76.1% and 82.3%, respectively, as compared to the control with a corresponding increase in rice grain yield.     

Secretome analysis of Magnaporthe oryzae using in vitro systems

Magnaporthe oryzae is a devastating blast fungal pathogen of rice (Oryza sativa L.) that causes dramatic decreases in seed yield and quality. During the early stages of infection by this pathogen, the fungal spore senses the rice leaf surface, germinates, and penetrates the cell via an infectious structure known as an appressorium. During this process, M. oryzae secretes several proteins; however, these proteins are largely unknown mainly due to the lack of a suitable method for isolating secreted proteins during germination and appressoria formation. We examined the secretome of M. oryzae by mimicking the early stages of infection in vitro using a glass plate (GP), PVDF membrane, and liquid culture medium (LCM). Microscopic observation of M. oryzae growth revealed appressorium formation on the GP and PVDF membrane resembling natural M. oryzae-rice interactions; however, appresorium formation was not observed in the LCM. Secreted proteins were collected from the GP (3, 8, and 24 h), PVDF membrane (24 h), and LCM (48 h) and identified by two-dimensional gel electrophoresis (2DE) followed by tandem mass spectrometry. The GP, PVDF membrane, and LCM-derived 2D gels showed distinct protein patterns, indicating that they are complementary approaches. Collectively, 53 nonredundant proteins including previously known and novel secreted proteins were identified. Six biological functions were assigned to the proteins, with the predominant functional classes being cell wall modification, reactive oxygen species detoxification, lipid modification, metabolism, and protein modification. The in vitro system using GPs and PVDF membranes applied in this study to survey the M. oryzae secretome, can be used to further our understanding of the early interactions between M. oryzae and rice leaves.     

序列比对程序Blat在转录组数据分析中的应用

随着功能基因组学研究领域的快速发展,人们已经开始系统地研究全基因组的转录以及全部基因发挥功能的动态机制。为实现此目标,需要从海量的转录组数据中提炼出能够揭示基因功能以及表达调控的重要信息。采用高性能的序列比对程序以满足规模化的比对需求是其中的瓶颈环节。通过综合比较目前流行的各种序列比对软件的性能,并针对不同的转录组数据分析任务对Blat进行详细的应用分析,结果发现,Blat能够解决转录组数据分析过程中的序列比对这一瓶颈,可广泛应用于功能基因组相关的数据分析任务。     

水稻品种对美国稻瘟病小种IB-33、IB-45和IE-1的抗性遗传

1995年10月至1997年11月,在美国阿肯色大学水稻研究推广中心,用水稻品种LA110和Jasmine-85与水稻品种Teqing、Katy、Mars、LaGrue和Newbonnet进行不完全双列杂交,对其杂交后代和亲本用美国3个主要稻瘟病菌小种(以下简称小种)IB-33、IB-45和IE-1进行接种鉴定和遗传分析研究.结果表明:亲本LA110、Jasmine-85、Teqing抗所有3个小种.Katy抗小种IB-45和IE-1,感小种IB-33.Mars抗小种IE-1,感小种IB-33和IB-45.LaGrue感所有3个小种.Newbonnet抗小种IB-45,感小种IB-33和IE-1.所有抗病亲本的抗病基因,其F1分别对相应小种呈现显性抗病性.抗病亲本杂交,LA110与Jasmine-85对小种IB-33,LA110与Teqing、Jasmine-85对小种IE-1,及Jasmine-85与Teqing对小种IE-1,是等位的抗病基因.LA110与Teqing对小种IB-33,及Jasmine-85与Teqing对小种IB-33,分别存在三对独立遗传的显性抗病基因.LA110与Teqing、Katy、Newbonnet、Jasmine-85对小种IB-45,Jasmine-85与Teqing、Katy、Newbonnet对小种IB-45,LA110与Katy、Mars对小种IE-1,Jasmine-85与Katy、Mars对小种IE-1,分别存在两对独立遗传的显性抗性基因.抗病亲本LA110或Jasmine-85与感病亲本Mars对小种IB-33,抗病亲本LA110与感病亲本Mars对小种IB-45,具有两对显性互补抗病基因,当两对显性抗病基因同时存在时,表现出抗性.抗病亲本LA110或Jasmine-85与感病亲本Katy、LaGrue、Newbonnet对小种IB-33,抗病亲本LA110与感病亲本LaGrue对小种IB-45,抗病亲本Jasmine-85与感病亲本Mars、LaGrue对小种IB-45,抗病亲本LA110或Jasmine-85与感病亲本LaGrue、Newbonnet对小种IE-1,分别存在一对显性抗病基因.两个亲本正、反交的遗传表现一致.本文也讨论了LA110、Teqing和Jasmine-85三个抗病品种在美国水稻抗病育种中利用的可能性.     

序列同源性分析软件Blast的WEB界面构建及其应用

基于局域网(Intranet)内的PC/Linux服务器, 构建了序列同源性分析软件Blast的WEB界面. 局域网内的所有计算机均可通过WEB方式访问该服务器进行公共数据库和自建数据库的查询,具有保密、高效、免费的优点,能够满足实验室和研究院所的大规模、快速数据分析任务.