Identification and characterization of 43 novel polymorphic EST-SSR markers for arum lily,Zantedeschia aethiopica (Araceae)

• Premise of the study: A new set of microsatellite or simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) was developed for arum lily (Zantedeschia aethiopica), which is one of the most iconic and widely recognized ornamental plants in the world. • Methods and Results: Using 2175 unigenes derived from 4283 random ESTs in arum lily, 166 primer pairs were designed and tested for amplification in 24 accessions from Asia, Europe, and Africa. A total of 43 loci were polymorphic, with the number of alleles per locus ranging from two to 10. The observed heterozygosity, expected heterozygosity, and polymorphism information content ranged from 0.2313 to 0.8480, 0.3034 to 0.8648, and 0.1015 to 0.7364, respectively. • Conclusions: These novel polymorphic EST-SSR markers will facilitate future studies of genetic variation and molecular-assisted breeding systems in arum lily.     

Expressed sequence tags and mRNA expression levels of tagged cDNAs from watermelon anthers and developing seeds

To understand the molecular events that occur during reproductive organ development and to provide genetic resources for molecular breeding, we generated 328 expressed sequence tags (ESTs) from randomly selected clones of four watermelon cDNA libraries. These libraries were prepared from young and mature anthers, as well as the seed coat and inner seed tissues. EST clones found in the young anthers and inner seed tissues showed similarity with genes related to development and signal transduction. We could deduce that, especially in the developing inner seed tissues, important morphological processes were associated exclusively with seed and embryo development In addition, seed metabolism was tailored toward the accumulation of economically valuable storage compounds such as lipids. In the seed coat, EST clones showed similarity with genes that influence the transport or conversion of nutrients such as porin, sucrose synthase, L-asparaginase, and arginine decarboxylase. We also selected two cDNA clones from each of the four classes of ESTs for studying expression levels and patterns in the various organs. Among those eight clones, three (An88, Is124, and Sc68) were expressed preferentially in their particular organ.     

疫霉侵染下辣椒幼苗消减文库的构建与初步分析

为了分离和鉴定辣椒中疫霉诱导基因,以高抗疫霉病辣椒品种L11为材料,以接种辣椒疫霉菌的幼嫩叶片为处理（tester）,以未接种自然生长的幼嫩叶片为对照(driver),利用抑制性消减杂交技术(suppression subtractive hybridization,SSH)构建了疫霉侵染下辣椒幼苗的消减文库。从消减文库中随机挑取30个阳性克隆,提取质粒进行PCR鉴定,显示插入片段大小大部分集中在200～1 000 bp之间,文库质量良好。随机挑取40个克隆进行测序,共获得35个有效EST序列。经Blastx分析表明：有30个EST与GenBank中其他序列有同源性,5个EST为未知功能序列。已知功能的EST序列分别编码NAC转录因子、丝氨酸/苏氨酸蛋白激酶、P450单加氧酶、叶绿素a/b结合蛋白、谷胱甘肽转移酶、几丁质酶等,这些蛋白涉及抗病信号传递、抗氧化作用、转录调控及光合作用等多种生理过程。本研究为抗病基因克隆和系统研究疫霉侵染下辣椒基因的表达奠定了重要的理论基础。     

鸡下丘脑cDNA文库的构建及部分克隆ESTs序列初步分析

以鸡下丘脑为实验材料,以λgt10为载体,构建了鸡下丘脑cDNA文库。结果表明,文库的滴度为3.8×10     

Twenty-three novel microsatellite markers developed from Atlantic cod Gadus morhua L. expressed sequence tags

Twenty-three novel polymorphic microsatellite markers were developed from c. 2000 expressed sequence tags of Atlantic cod Gadus morhua L. Gene identity was determined at 12 loci, confirming the associated microsatellites as type I markers. These microsatellite markers provide useful tools for studies of population genetics and reproductive ecology and for constructing linkage maps of G. morhua .     

一种种系发生分析的新方法

利用所测定的猪脂肪组织表达序列标签以及来源于GenBank中非冗余核酸数据库和表达序列标签数据库中的人、牛及小鼠cDNA序列 ,在随机抽样方法建立的基础上 ,分别采集 70个已知功能基因的cDNA序列 ,分析了 4个物种 70× 15 0bp序列连接体的突变规律 ,建立了不同物种之间的综合种系发生分析方法。结果表明 ,在 4个物种 70个已知功能基因所构成的cDNA序列连接体同源性分析中 ,共发现 391个单碱基突变 ,不同物种之间的突变数量大大超过了同一物种基因组水平预测的 1/ 10 0 0。其中以C/T(T/C)转换和A/G(G/A)转换为主要的单碱基突变类型。种系发生分析结果表明 ,作为偶蹄目的猪和牛的遗传关系最近 ,其次是人类 ,小鼠与家猪和牛的遗传关系最远。 4种动物从共同祖先分化的顺序分别为小鼠最早 ,人类次之 ,然后为猪和牛     

人肾上腺基因表达谱的建立及其功能的新认识

为深入理解人类肾上腺（AD）的功能,构建了正常人肾上腺cDNA文库,并利用大规模表达序列标签（ESTs）测序和生物信息学技术,研究显示参与基因/蛋白表达的基因类型表达最多,其次为能量代谢类.肾上腺中表达丰度最高的3个基因均为参与类固醇合成的酶类和蛋白.一些重要的基因首次显示在肾上腺表达,包括神经激素和神经肽,如促肾上腺皮质激素释放激素（CRH）,黑色素浓激素（MCH）,urocortin,可卡因和安非他明调节肽（CART）和垂体腺苷酸环化酶激活肽（PACAP）;许多重要介质的受体,如细胞因子、神经肽及神经递质受体;参与胆固醇代谢的基因,如LDL受体、HDL结合蛋白和胆固醇合成酶.研究结果表明在肾上腺表达丰度最高的基因与该器官的功能特异性有关,除类固醇激素外,许多神经肽、细胞因子在肾上腺产生,肾上腺与体内其他重要的系统间存在广泛的应答,而且在人肾上腺局部可能存在一个CRH-ACTH-皮质醇调节网络.     

Development and characterization of expressed sequence tags for the turkey (Meleagris gallopavo) genome and comparative sequence analysis with other birds

Twenty-one randomly selected clones from a turkey (Meleagris gallopavo) pituitary complementary DNA (cDNA) library were sequenced to develop expressed sequence tags (ESTs) for this economically important avian species whose genome is among the least understood. Primers specific for the ESTs were used to produce amplicons from the genomic DNA of turkey, chicken (Gallus gallus), guinea fowl (Numidia meleagris), pigeon (Columba domestica), and quail (Corturnix japonica). The amplicons were sequenced and analyzed for sequence variation within- and similarity among-species and with GenBank database sequences. The proportion of shared bases between the turkey sequence and the consensus sequence from each of the other species ranged from 72% to 93% between turkey and pigeon and quail and between turkey and chicken, respectively. The total number of single nucleotide polymorphisms (SNPs) observed ranged from 3 in quail to 18 in chicken out of 4898 and 5265 bases analyzed, respectively. The most frequent nucleotide variation observed was a C-->T transition. Linkage analysis of one such SNP in the backcross progeny of the East Lansing reference DNA panel, localized TUS0005, the chicken sequence derived from primers specific for turkey TUT2E EST, to chromosome 4. The ESTs reported, as well as the SNPs may provide a useful resource for ongoing efforts to develop high utility genome maps for the turkey and chicken. The primers described can also be used as a tool in future investigations directed at further understanding the biology of the guinea fowl, pigeon and quail and their relatedness to the turkey.     

家蚕第12连锁群EST-SSR标记的筛选和分析

为了探究家蚕Bombyx mori EST-SSR标记的多态性, 对检索获得的家蚕第12连锁群的4 465条EST序列进行了分析, 整理和拼接后得到581条非冗余EST序列, 总长度约为480 kb。其中, 有122条序列中共检测到154个EST-SSR, 占所研究的EST序列的2.73%, 平均每3.12 kb 含有一个EST-SSR。在所检测的EST-SSR中, 三核苷酸和四核苷酸重复是主导类型, 分别占总数的36.36%和28.57%,大部分表现为Perfect形式; 核苷酸重复平均长度约为16.2 bp, 最长为30 bp。进一步进行同源性分析, 发现有26条序列可以在NCBI中检索到同源序列, 在这些序列中一共含有40个SSR, 其中14个(35.0%)位于5′-UTR, 11个(27.5%)位于3′-UTR, 15个(37.5%)位于CDS区。根据筛选到的微卫星序列设计11对引物, 其中8对引物有扩增产物, 且条带清晰; 应用引物ES1204对8个家蚕品种进行PCR扩增都呈现多态性。结果说明通过家蚕EST数据库发掘SSR标记是一条可行的途径。     

GENOMIC INSIGHTS INTO EVOLUTIONARY RELATIONSHIPS AMONG HETEROKONT LINEAGES EMPHASIZING THE PHAEOPHYCEAE1

Heterokonts comprise a large and diverse group of organisms unified by the heterokont biflagellate condition. Monophyly of many of these lineages is well established, but evolutionary relationships among the various lineages remain elusive. Among these lineages, the brown algae (Phaeophyceae) are a monophyletic, taxonomically diverse, and ecologically critical group common to marine environments. Despite their biological and scientific importance, consensus regarding brown algal phylogeny and taxonomic relationships is missing. Our long‐term research goal is to produce a well‐resolved taxon‐rich phylogeny of the class to assess evolutionary patterns and taxonomic relationships among brown algal lineages and their relationship to other closely related heterokont groups. To accomplish this goal and augment existing loci for phaeophycean‐wide systematic studies, we generated expressed sequence tags (ESTs) from several major brown algal lineages and from the heterokont lineage representing the closest sister group to brown algae. To date, we have successfully constructed cDNA libraries for two lineages (Choristocarpus tenellus Zanardini and Schizocladia ischiensis E. C. Henry, Okuda et H. Kawai) and in the library test phase obtained up to 1,600 ESTs per organism. Annotation results showed a gene discovery rate of 45%–50% for each library revealing 500–700 unique genes from each organism. We have identified several potential genes for phylogenetic inference and used these loci for preliminary molecular clock analyses. Our molecular clock analysis suggests that the basal divergence in brown algae occurred around the time of the pennate‐centric diatom divergence. Here we report this analysis and other uses of ESTs in brown algal phylogenomics and the utility of these data for resolving the phylogeny of this group.