芸薹属植物基因组学研究进展

芸薹属是十字花科植物300多个属中最为重要的一个属,是我国栽培面积最大的蔬菜作物。拟南芥和芸薹属在十字花科中两者的亲缘关系最近,通过它们之间的比较作图,两者之间的共线性被大量发现。模式植物拟南芥全基因组测序已经完成,这为芸薹属作物的基因组研究提供了便利条件。芸薹属作物的功能基因组学能够进一步明确不同发育时期基因的功能,为解释芸薹属的进化提供基因证据。就芸薹属植物在比较基因组学、功能基因组学最新进展,特别是芸薹属与模式植物拟南芥在基因组之间的相互关系进行了综述。     

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。     

Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species

Genic microsatellites or simple sequence repeat markers derived from expressed sequence tags (ESTs), referred to as EST–SSRs, are inexpensive to develop, represent transcribed genes, and often have assigned putative function. The large apple (Malus × domestica) EST database (over 300,000 sequences) provides a valuable resource for developing well-characterized DNA molecular markers. In this study, we have investigated the level of transferability of 68 apple EST–SSRs in 50 individual members of the Rosaceae family, representing three genera and 14 species. These representatives included pear (Pyrus communis), apricot (Prunus armeniaca), European plum (P. domestica), Japanese plum (P. salicina), almond (P. dulcis), peach (P. persica), sour cherry (P. cerasus), sweet cherry (P. avium), strawberry (Fragaria vesca, F. moschata, F. virginiana, F. nipponica, and F. pentaphylla), and rose (Rosa hybrida). All 68 primer pairs gave an amplification product when tested on eight apple cultivars, and for most, the genomic DNA-derived amplification product matched the expected size based on EST (in silico) data. When tested across members of the Rosaceae, 75% of these primer pairs produced amplification products. Transferability of apple EST–SSRs across the Rosaceae ranged from 25% in apricot to 59% in the closely related pear. Besides pear, the highest transferability of these apple EST–SSRs, at the genus level, was observed for strawberry and peach/almond, 49 and 38%, respectively. Three markers amplified in at least one genotype within all tested species, while eight additional markers amplified in all species, except for cherry. These 11 markers are deemed good candidates for a widely transferable Rosaceae marker set provided their level of polymorphism is adequate. Overall, these findings suggest that transferability of apple EST–SSRs across Rosaceae is varied, yet valuable, thereby providing additional markers for comparative mapping and for carrying out evolutionary studies.     

白菜的EST标记及其对油菜的通用性

根据白菜的表达序列标签,设计了28对引物。在对引物、dNTP、MgCl2的浓度及退火温度等参数进行测试后,建立了合适的PCR反应体系。在此反应体系下,以构建EST的白菜自交系A的DNA为模板,对设计的引物进行了筛选,发现有18对引物能对白菜DNA扩增出产物。用筛选出来的引物分别对17个白菜类品种进行PCR扩增,用琼脂糖凝胶电泳分析其产物的多态性,发现10对引物有多态性,这占了筛选引物的55.6%。为检测白菜EST标记的通用性,进一步利用设计的引物对不同油菜品种的DNA进行PCR扩增。在检测的28对引物中,共有24对引物能扩增出产物,占引物总数的85.7%,显示多态性的引物为18对,占引物总数的64.3%.。在对白菜DNA能扩增出产物的18对引物中,对油菜完全可用,且有13对引物产生多态性。而在那些对白菜未扩增出产物的10对引物中,也有6对能扩增出产物,其中5对显示多态性。文章研究结果证明,通过EST建立分子标记是可行的,而且这种标记对近缘物种是可通用的。     

Characterization and Genetic Mapping of Simple Sequence Repeats in the Rice Genome

We searched partial sequences of over 22,706 rice cDNA and 1220genomic DNA clones to find and characterize simple sequencerepeats (SSRs) in the rice genome. The most frequently foundrepeated SSR motif in both cDNA and genomic DNA sequences wasd(CCG/CGG)n. The second most frequently found SSR was d(AG/CT)n.In contrast with mammalian genomes, in which d(AC/GT)n sequencesare the most abundant, d(AC/GT)n sequences were not frequentlyobserved in rice. Sequences containing d(CCG/CGG)n, d(AG/CT)nrepeats, and other SSRs were chosen for polymorphism detection.It was predicted that 17 of 20 SSRs in cDNA sequences were locatedin 5'-untranslated regions near initiation codons. Twenty-twoloci can be mapped on our RFLP linkage map by these SSRs. Sixmarkers were tested with 16 japonica rice varieties as templatesfor PCR. Two markers exhibited amplified fragment length polymorphismamong these rice varieties, implying that SSRs are polymorphicamong rice varieties which have similar genetic backgrounds.Even these polymorphic SSRs are located within or around geneswhich code ubiquitous proteins.     

植物逆境胁迫耐受性功能基因组研究进展

为了更加高效地利用基因工程技术提高植物对逆境胁迫的耐受性,需要在全基因组水平上对植物逆境胁迫耐受性的复杂机制进行整合性研究.植物逆境胁迫耐受性功能基因组的研究可概括为：利用胁迫特异性的表达序列标签(EST)及cDNA微阵列（或基因芯片）技术筛选与胁迫相关的候选基因,然后利用反向遗传学等技术对候选基因的功能进行研究,利用酵母双杂交、正向遗传学等技术对基因及基因产物间的相互关系进行研究.通过这些研究可以全面地了解植物对胁迫（渗透、干旱、极端温度）响应的复杂机制和相互作用以及相应的信号转导途径,从而为更加高效地利用基因工程技术提高植物对逆境胁迫的耐受性奠定基础.     

Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat

Nearly 900 SSRs (simple sequence repeats) were identified among 15,000 ESTs (expressed sequence tags) belonging to bread wheat ( Triticum aestivum L.). The SSRs were defined by their minimum length, which ranged from 14 to 21 bp. The maximum length ranged from 24 to 87 bp depending upon the length of the repeat unit itself (1–7 bp). The average density of SSRs was one SSR per 9.2 kb of EST sequence screened. The trinucleotide repeats were the most abundant SSRs detected. As a representative sample, 78 primer pairs were designed, which were also used to screen the dbEST entries for Hordeum vulgare and Triticum tauschii (donor of the D-genome of cultivated wheat) using a cut-off E (expectation) value of 0.01. On the basis of in silico analysis, up to 55.12% of the primer pairs exhibited transferability from Triticum to Hordeum, indicating that the sequences flanking the SSRs are not only conserved within a single genus but also between related genera in Poaceae. Primer pairs for the 78 SSRs were synthesized and used successfully for the study of (1) their transferability to 18 related wild species and five cereal species (barley, oat, rye, rice and maize); and (2) polymorphism between the parents of four mapping populations available with us. A subset of 20 EST-SSR primers was also used to assess genetic diversity in a collection of 52 elite exotic wheat genotypes. This was done with a view to compare their utility relative to other molecular markers (gSSRs, AFLPs, and SAMPL) previously used by us for the same purpose with the same set of 52 bread wheat genotypes. Although only a low level of polymorphism was detected, relative to that observed with genomic SSRs, the study suggested that EST-SSRs can be successfully used for a variety of purposes, and may actually prove superior to SSR markers extracted from genomic libraries for diversity estimation and transferability.Communicated by R. Hagemann     

Analysis of gene associated tandem repeat markers in Atlantic salmon (<Emphasis Type="Italic">Salmo salar L.</Emphasis>) populations: implications for restoration and conservation in the Baltic Sea

Patterns of genetic diversity and differentiation among five wild and four hatchery populations of Atlantic salmon in the Baltic Sea were assessed based on eight assumedly neutral microsatellite loci and six gene-associated markers, including four expressed sequence tag (EST) linked and two major histocompatibility complex (MHC) linked tandem repeat markers (micro- and mini-satellites). The coalescent simulations based on the method of Beaumont and Nichols (1996, Proc. R. Soc. Lond. Ser. B – Biol. Sci., 263, 1619–1626) indicated that two loci (MHCIIα and Ssa171, with the lowest and highest overall F_ST estimates, respectively) exhibited significant departures (P<0.05) from the neutral expectations. Another coalescent-based test for selective neutrality (Vitalis et al. 2001, Genetics, 158, 1811–1823) further supported the outlier status of the Ssa171 microsatellite locus but not of the MHCIIα linked minisatellite. In addition, actin related protein linked microsatellite locus was identified with this test as an outlier in six pairwise population comparisons. All genetic diversity estimates revealed more genetic variation in hatchery stocks than in the small wild salmon populations from the Gulf of Finland. However, the wild populations possessed alleles at gene-associated markers (e.g. MHCI and IGF) not found in the hatchery stocks, which together with moderate genetic differentiation and distinctive environmental conditions justifies the special conservation measures for the last remaining native salmon populations in the Gulf of Finland.     

DNA序列高维空间数字编码的运算法则

DNA序列的高维空间二进制数字编码,除可以对DNA序列的碱基结构、功能基团、碱基互补、氢键强弱等性质进行编码之外,还可以方便地进行 数学运算和逻辑运算。DNA序列高维空间数字编码的运算法则是：（1）根据DNA序列数码的奇偶性质,可以推导出其与末位碱基的对应关系。当DNA序列S的数值X（S）＝4n,4n 1,4n 2,4n 3时,其末位碱基依次为C,T,A,G（n=0,1,2,…）。（2）提出DNA序列高维空间的表观维数Nv,数值维数Nx及差异维数Nd的概念。当Nd=0时,首位碱基为A或G,当Nd=2n或2n 1(n=1,2,…）时,首痊碱基为（C）^n或（C）^nT。（3）推导出DNA序列点突变（单核苷酸多态性SNP）的运算法则。（4）推导出DNA重复序列（Tandem repeat)的运算法则。（5）提出DNA子序列（subsequence)的概念并定义DNA子序列的定值部Xi(digital value)和定位部Qi(location value)及其计算公式。（6）推导出DNA序列的延长运算、删除运算、缺失运算、插入运算、转位运算、换位运算和置换运算等的运算法则。（7）通过按位加运算求得DNA序列的汉明距离dh,碱基距离dh‘,基团距离dh″和共轭距离dG以及这些距离的意义与联系。（8）分析结果表明DNA序列的数字编码比常规的字符编码在数学运算上具有明显的优越性。     

Identification of expressed sequence tags (ESTs) of the highly transcribed genes in Aspergillus niger

Determined sequences of 285 randomly selected clones in a 3-directed cDNA library of Aspergillus niger could identify expressed seqeunce tags (ESTs) of genes highly expressed. One EST appeared seven times, one six times, one five times, four three times and 12 twice. Out of these 19 ESTs, ten were identified in GenBank, but none was of A. niger, suggesting that there are a lot of unidentified genes highly expressed in A. niger.