利用EST序列构建Mascot本地数据库

对蛋白质质谱数据进行数据库比对和鉴定是蛋白质组学研究技术中的一个重要步骤。由于公共数据库蛋白质数据信息不全,有些蛋白质质谱数据无法得到有效的鉴定。而利用相关物种的EST序列构建专门的质谱数据库则可以增加鉴定未知蛋白的几率。本文介绍了利用EST序列构建Mascot本地数据库的具体方法和步骤,扩展了Mascot检索引擎对蛋白质质谱数据的鉴定范围,从数据库层面提高了对未知蛋白的鉴别几率,为蛋白质组学研究提供了一种较为实用的生物信息学分析技术。     

基于Linux平台的林木EST序列分析系统的构建及应用

利用Phred/Phrap/Consed、cross.match、RepeatMasker、Blast等软件和自主开发程序,基于Linux操作系统,构建了林木EST序列分析系统,完成了从测序峰图向核酸序列的转化、载体序列的去除、重复序列鉴定、EST序列分类和组装、EST序列功能注释与功能分类以及SSR、SNP的发掘。并通过使用Perl语言结合bioperl模块写的脚本程序使分析过程自动化,从而可以快速地对大批林木EST数据进行分析,为林木的功能基因组学研究提供有用的信息。     

结构基因组学研究概述

随着蛋白质数据库、基因组序列数据库和自动化技术的迅速发展,结构基因组学作为新的预测蛋白质结构的技术显得越发重要。本文对结构基因组学的产生发展进行概述,分别介绍结构基因组技术的功能、实验流程、蛋白质功能的预测方法,并对该学科发展进行了展望。     

应用生物信息学技术对植物表达序列标签(EST)的大规模分析

目前 ,一些基因组较小的植物 (如拟南芥 ,水稻等 )的全基因组已经基本完成测序 ,较大基因组的测序工作则主要集中在基因组中表达基因的测序上 ,表达序列标签 (EST)计划由此产生。研究表明 ,对EST进行大规模研究已成为功能基因组学研究的最佳途经之一。本文着重介绍和讨论应用生物信息学技术对植物EST数据的大规模分析。     

环境微生物宏基因组学数据库利用

宏基因组学技术产生的数据是研究环境微生物的宝贵资源,国际上已有微生物计划、海洋计划、生命普查等大项目,采集和测序的样本量数以百万计,产生了海量的环境宏基因组学数据,并以此建立了几十个相关宏基因组数据库和平台。主要从以下几个方面综述环境宏基因组学的研究进展和已有资源:环境宏基因组学国际合作大项目、宏基因组学数据库和宏基因组学数据在线分析平台。将结合相应的数据库网站介绍其项目详情、样本来源、数据类型、使用方式和分析结果等,以便研究者全面了解此类数据并能快速找到和利用相关资源。     

林木基因组学研究进展

林木基因组学研究进展迅速。结构基因组学方面,已构建了近40个主要造林树种的遗传连锁图谱,在不同树种中定位了30余个重要的数量性状位点,在部分树种中开展了基因组比较和综合图谱构建研究,杨树的全基因组测序已经完成,桉树的全基因组测序正在进行。功能基因组学方面,已分析了主要造林树种多种组织的转录组EST序列,对林木次生生长与木材形成、开花和抗寒性的形成等过程开展了功能基因组学研究。另外,探讨了林木基因组学研究的发展趋势,以期为我国林木基因组学研究提供有益的参考。     

Unix下EST数据库本地化更新及序列预处理分析

利用FreeBSD操作系统的文本过滤命令将NCBI的Genbank数据库的EST序列实现本地化导入到MySQL数据库中并能够进行更新,这利于对不同物种不同组织器官基因表达的分析。以水稻EST数据为例,对EST序列两端出现的polyA/T和载体序列亦进行了鉴别及去除,经过预处理的EST序列数据将为进一步进行EST聚类及基因表达分析提供可靠的保证。     

禾本科植物EST的研究进展

禾本科作物与人类密切相关,对其分子水平上的研究具有重要的理论和实践意义。EST技术的产生和不断完善为禾本科植物的研究带来了新的思路,迅速推动禾本科植物研究工作的进行。本文综述了EST技术在禾本科植物研究中的应用,包括EST分子标记、构建遗传学图谱、比较基因组学、发现与克隆新基因、基因表达研究以及DNA芯片技术等,并对EST在禾本科植物研究中存在的问题及应用前景进行了分析。     

植物表达序列标签(EST)标记及其应用研究进展

简要介绍了植物表达序列标签(EST)标记的研究现状,并对几种植物中利用EST建立分子标记的几种策略和EST标记在绘制遗传图谱、资源分析、品种鉴定及比较基因组学研究方面的应用等进行了综合评述。     

球毛壳菌(Chaetomium globosum)EST生物信息分析数据库的建立

用基因本体论（Cene Ontology,GO）中的相关的规范术语和BLAST分析结果来对球毛壳菌EST及CONTIG序列信息进行注释,利用GO的语义模型构建不同物种数据库之间的语义联接,在此基础上建立球毛壳菌EST生物信息分析数据库,在概念和联系层面上有效地解决了不同物种生物信息的整合问题,实现了对球毛壳菌生物信息学数据智能化的多重、复合和交叉检索。为球毛壳菌生物信息学的进一步研究奠定了坚实的基础。文中详细论述了基于GO的球毛壳菌EST生物信息学数据库的研究背景、建立过程、查询功能及其维护。     

花生抗病基因分离克隆研究进展

花生是重要的油料作物和经济作物。近年来多种病害严重威胁着花生产业的发展,筛选花生抗病基因并对其进行研究成为花生抗性育种的新热点。结合抗病基因分离克隆在花生育种工作和遗传研究等领域逐渐显现的广阔前景,我们简要综述了国内外花生抗病基因分离克隆的研究现状,介绍了抗病基因分离克隆的类型及特点,并探讨了今后的研究方向。     

Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species

Background  

Lack of sufficient molecular markers hinders current genetic research in peanuts (Arachis hypogaea L.). It is necessary to develop more molecular markers for potential use in peanut genetic research. With the development of peanut EST projects, a vast amount of available EST sequence data has been generated. These data offered an opportunity to identify SSR in ESTs by data mining.     

Transcriptomic and Proteomic Analyses of Resistant Host Responses in Arachis diogoi Challenged with Late Leaf Spot Pathogen,Phaeoisariopsis personata

Late leaf spot is a serious disease of peanut caused by the imperfect fungus, Phaeoisariopsis personata. Wild diploid species, Arachis diogoi. is reported to be highly resistant to this disease and asymptomatic. The objective of this study is to investigate the molecular responses of the wild peanut challenged with the late leaf spot pathogen using cDNA-AFLP and 2D proteomic study. A total of 233 reliable, differentially expressed genes were identified in Arachis diogoi. About one third of the TDFs exhibit no significant similarity with the known sequences in the data bases. Expressed sequence tag data showed that the characterized genes are involved in conferring resistance in the wild peanut to the pathogen challenge. Several genes for proteins involved in cell wall strengthening, hypersensitive cell death and resistance related proteins have been identified. Genes identified for other proteins appear to function in metabolism, signal transduction and defence. Nineteen TDFs based on the homology analysis of genes associated with defence, signal transduction and metabolism were further validated by quantitative real time PCR (qRT-PCR) analyses in resistant wild species in comparison with a susceptible peanut genotype in time course experiments. The proteins corresponding to six TDFs were differentially expressed at protein level also. Differentially expressed TDFs and proteins in wild peanut indicate its defence mechanism upon pathogen challenge and provide initial breakthrough of genes possibly involved in recognition events and early signalling responses to combat the pathogen through subsequent development of resistivity. This is the first attempt to elucidate the molecular basis of the response of the resistant genotype to the late leaf spot pathogen, and its defence mechanism.     

可转化大片段DNA载体系统及其在花生育种中的应用前景

可转化大片段DNA载体系统主要包括双元细菌人工染色体BIBAC(binary bacterial artificial chromosome)和可转化人工染色体TAC(transformation-competent artificial chromosome)系统,它们能够高效克隆大片段DNA,在获取目的基因相关信息的同时转化植物得到转基因植株。本文综述了BIBAC和TAC载体的特点、种类、发展现状以及近年来在植物种质创新中的应用。同时,根据我国花生育种的现状,展望了可转化大片段DNA载体系统在利用野生花生资源改良栽培花生品种中的应用前景。     

花生黄曲霉侵染抗性的SCAR标记

利用与花生黄曲霉侵染抗性基因紧密连锁的AFLP标记 “E45/M53-440”, 经PAGE凝胶电泳后回收、克隆、测序, 并根据测序结果设计PCR特异引物, 通过对PCR条件的优化, 成功地将AFLP标记“E45/M53-440”转化为实验结果稳定, 操作更简单的SCAR标记“AFs-412”, 标记与花生黄曲霉侵染抗性间的遗传距离为6.5 cM。利用获得的SCAR标记对抗、感黄曲霉的花生种质资源进行了分子鉴定, 结果表明标记与抗性鉴定结果具有较高的一致性, 证实了该标记应用于研究群体之外的育种潜力。SCAR标记的建立为开展花生黄曲霉侵染抗性的标记辅助选择育种提供了简便实用的鉴定技术。     

LOCALIZATION OF PHYTOCHROME DURING PEANUT (ARACHIS HYPOGAEA) GYNOPHORE AND OVULE DEVELOPMENT

Previous studies indirectly indicated that phytochrome plays a role in peanut (Arachis hypogaea L. cv. Virginia) gynophore elongation and in ovule and embryo development. Recent advances in the use of monoclonal antibody procedures used in this study have allowed precise localization of phytochrome in the developing peanut gynophore and ovular tissues. Peanut phytochrome from etiolated tissues was found to have a molecular weight of 124 kD as determined by immunoblotting procedures using a monoclonal antibody to pea (Pisum sativum L. cv. Alaska) phytochrome. Immunoblotting procedures revealed that no detectable phytochrome was present in the gynophore tissues or immature ovules during the elongation of the peanut gynophores. After the gynophores penetrated the soil for 8–12 d, phytochrome was detected in increasing amounts in the ovular tissues but not the gynophore tissues. Immunohistological analysis revealed that phytochrome was localized in the developing embryo and adjacent integument tissues. These findings contradict earlier reports that suggested phytochrome was initially present in the gynophore tissues after fertilization where it was believed to inhibit ovular development and stimulate gynophore elongation.     

Advances in Arachis genomics for peanut improvement

Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to the tetraploid; cultivated peanut, recent polyploidization combined with self pollination, and the narrow genetic base of the primary genepool have resulted in low genetic diversity that has remained a major bottleneck for genetic improvement of peanut. Harnessing the rich source of wild relatives has been negligible due to differences in ploidy level as well as genetic drag and undesirable alleles for low yield. Lack of appropriate genomic resources has severely hampered molecular breeding activities, and this crop remains among the less-studied crops. The last five years, however, have witnessed accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding has been initiated for several traits for development of superior genotypes. The genome or at least gene space sequence is expected to be available in near future and this will further accelerate use of biotechnological approaches for peanut improvement.