The map-based sequence of the rice genome

Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.     

The genome sequence of the filamentous fungus Neurospora crassa

Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes--more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.     

The genome sequence and structure of rice chromosome 1

The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequence indicates the importance of a high-quality finished sequence.     

Functional genomics in the rice blast fungus to unravel the fungal pathogenicity

A rapidly growing number of successful genome sequencing projects in plant pathogenic fungi greatly increase the demands for tools and methodologies to study fungal pathogenicity at genomic scale. Magnaporthe oryzae is an economically important plant pathogenic fungus whose genome is fully sequenced. Recently we have reported the development and application of functional genomics platform technologies in M. oryzae. This model approach would have many practical ramifications in design and implementation of upcoming functional genomics studies of filamentous fungi aimed at understanding fungal pathogenicity.     

稻瘟菌侵染对水稻细胞骨架排列方式的影响

采用免疫荧光技术成功检测到水稻叶鞘内表皮细胞中微管和微丝的分布情况.稻瘟病菌的侵染使水稻叶鞘内表皮细胞中微管、微丝排列方式发生明显的改变,这种排列方式的改变非常灵敏,且在亲和性互作和非亲和性互作之间差异明显.非亲和性互作反应中,病菌侵染早期微管、微丝均放射状向病菌侵染点分布,至寄主细胞产生过敏性坏死时,逐渐受到破坏而降解.亲和性互作反应中,微管、微丝在病菌侵染的早期则已开始降解,形成短棒状或点状结构,比较均匀地分布于整个细胞,病原菌侵染菌丝在寄主细胞中扩展时,难以观察到完整的微管、微丝.     

贵州省稻瘟病菌对春雷霉素和稻瘟灵的抗药性监测

采用生长速率法分别测定2013年从贵州省不同3个稻区分离的30个稻瘟病菌株,并测定分离出的菌株对稻瘟灵与春雷霉素的敏感性及抗药性水平。实验结果表明:春雷霉素、稻瘟灵对供试30个稻瘟病菌株的EC50值范围分别为1.60⁶.42μg/mL,1.936.42μg/mL,1.93⁶.26μg/mL,其平均值分别为3.69μg/mL,3.54μg/mL,且敏感菌株都为30个,都没有抗性菌株,表明贵州省稻瘟病菌株对春雷霉素与稻瘟灵的抗性均表现为较低水平。从菌株对春雷霉素与稻瘟灵的抗性分析表明贵州省稻瘟病菌对春雷霉素与稻瘟灵未产生交互抗药性或多抗性。     

A draft sequence of the rice (Oryza sativa ssp. indicd) genome

The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a “whole genome shotgun” approach, we have produced a draft rice genome sequence ofOryza sativa ssp.indica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from anindica variant cultivar93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEMBLER, a custom-designed software package used for the initial assembly, were verified rigorously by comparisons against finished BAC clone sequences from bothindica andjapanica strains, available from the public databases. Over all, 96.3% of full-length cDNAs, 96.4% of STS, STR, RFLP markers, 94.0% of ESTs and 94.9% unigene clusters were identified from the draft sequence. Our preliminary analysis on the data set shows that our rice draft sequence is consistent with the comman standard accepted by the genome sequencing community. The unconditional release of the draft to the public also undoubtedly provides a fundamental resource to the international scientific communities to facilitate genomic and genetic studies on rice biology. These authors contributed equally to this work.     

The genome sequence of Schizosaccharomyces pombe

We have sequenced and annotated the genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.     

稻瘟菌侵染后水稻抗氧化酶类的变化与抗病性的关系

以对稻瘟菌70-15小种表现抗病和感病反应的近等位基因系两水稻品种(C101和C039)为材料,对其接种稻瘟菌,结果表明:POD酶活性与抗稻瘟病正相关;而水稻抗瘟性与病害早期的SOD和CAT活性呈负相关;同时还发现,在不亲和反应的水稻中膜脂过氧化产物-丙二醛(MDA)的含量上升,并显著高于亲和反应水稻的MDA的含量,这表明水稻叶片中有膜脂过氧化的发生.     

稻瘟菌致病性变异突变体的筛选及共分离分析

通过筛选稻瘟菌(Magnaporthe grisea)P131小种的REMI(Restriction Enzyme MediatedIntegration)转化体库获得对水稻品种梅雨明致病性变异的突变体,命名为PX1.与野生型菌株P131相比,该突变体对水稻品种梅雨明致病性丧失,在洋葱表皮上侵染钉形成率显著降低,而孢子萌发率和附着胞形成率差异不显著.遗传分析表明,该突变体的突变表型和潮霉素抗性标记共分离,说明突变是由于外源质粒插入引起的,因此,可以此为标记克隆控制该表型的基因.     

The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum

Thermoplasma acidophilum is a thermoacidophilic archaeon that thrives at 59 degrees C and pH 2, which was isolated from self-heating coal refuse piles and solfatara fields. Species of the genus Thermoplasma do not possess a rigid cell wall, but are only delimited by a plasma membrane. Many macromolecular assemblies from Thermoplasma, primarily proteases and chaperones, have been pivotal in elucidating the structure and function of their more complex eukaryotic homologues. Our interest in protein folding and degradation led us to seek a more complete representation of the proteins involved in these pathways by determining the genome sequence of the organism. Here we have sequenced the 1,564,905-base-pair genome in just 7,855 sequencing reactions by using a new strategy. The 1,509 open reading frames identify Thermoplasma as a typical euryarchaeon with a substantial complement of bacteria-related genes; however, evidence indicates that there has been much lateral gene transfer between Thermoplasma and Sulfolobus solfataricus, a phylogenetically distant crenarchaeon inhabiting the same environment. At least 252 open reading frames, including a complete protein degradation pathway and various transport proteins, resemble Sulfolobus proteins most closely.     

稻瘟病菌限制酶介导整合(REMI)转化的致病性诱变

应用提高直菌转化率的技术－限制酶介质整合（restriction enzyme mediated integration,REMI)技术转化稻瘟病菌株Magnaporthe grisea131原生质体，在限制酶HindIII,KpnI介质下转化效率化效率分别提高6.5,10,3.7倍，通过300μg/mL潮霉素筛选获得1000个以上转化子，用突变体接种水稻鉴别品种，发现其中M25和M36与M131比较其致病性发生了改变，另外还发现产孢缺陷型变体和培养性状发生改变的突变菌株，rep-RCR试验表明REMI突变菌株由于质粒插入而与M131指纹有差异。     

Rapid genome evolution in Pms 1 region of rice revealed by comparative sequence analysis

Pms1, a locus for photoperiod sensitive genic male sterility in rice, was identified and mapped to chromosome 7 in previous studies. Here we report an effort to identify the candidate genes for Pms1 by comparative sequencing of BAC clones from two cultivars Minghui 63 and Nongken 58, the parents for the initial mapping population. Annotation and comparison of the sequences of the two clones resulted in a total of five potential candidates which should be functionally tested. We also conducted com-parative analysis of sequences of these two cultivars with two other cultivars, Nipponbare and 93-11, for which sequence data were available in public databases. The analysis revealed large differences in sequence composition among the four genotypes in the Pms1 region primarily due to retroelement activity leading to rapid recent growth and divergence of the genomes. High levels of polymorphism in the forms of indels and SNPs were found both in intra- and inter-subspecific comparisons. Dating analysis using LTRs of the retroelements in this region showed that the substitution rate of LTRs was much higher than reported in the literature. The results provided strong evidence for rapid genomic evolution of this region as a consequence of natural and artificial selection.     

The diploid genome sequence of an Asian individual

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.     

Initial sequence of the chimpanzee genome and comparison with the human genome

Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.     

Quality assessment of the human genome sequence

As the final sequencing of the human genome has now been completed, we present the results of the largest examination of the quality of the finished DNA sequence. The completed study covers the major contributing sequencing centres and is based on a rigorous combination of laboratory experiments and computational analysis.     

唐古特大黄内生放线菌分离鉴定及生防作用研究

以唐古特大黄为材料,采用匀浆涂布法进行内生放线菌的分离,并运用平板对峙法和生长速率法筛选内生放线菌的抑菌活性;皿内抑菌结果表明,菌株4-21对稻瘟病菌抑制率高达84.12%.通过形态学观察、生理生化特性检测和16SrDNA序列分析将菌株4-21鉴定为Streptomyces albidoflavus.通过盆栽试验证明,菌株4-21对水稻稻瘟病具有良好的防治效果,其相对防治效果为52.73%.结果表明,内生放线菌4-21在水稻稻瘟病的生物防治中具有潜在的应用价值.