梅花鹿鹿茸尖端组织ESTs分析

文章通过对东北梅花鹿(Cervus nippon hortulorum)鹿茸尖端组织cDNA文库随机测序获得了906条高质量ESTs,906条ESTs拼接后代表了701个Unigenes,其中包括重叠群86个,单拷贝615个。Blast分析显示具已知和推测功能的基因580个(82.7%),通过Gene Ontology(GO)分类对获得的580个功能基因进行了包括分子功能、生物过程和细胞组分在内的3个层次的功能注释,并根据BLAST的注释结果及进一步的筛选与分析,共得到39条与鹿茸尖端组织生长发育相关的基因。cDNA文库的构建和ESTs分析填补了鹿科动物在NCBI公共数据库上基因组信息的空白,并为科学的开发和利用梅花鹿资源提供了重要的理论依据。     

Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat

The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to related large-genome species has revolutionized molecular genetics and breeding strategies for improving those crops. Comparative sequence analysis methods can be used to cross-reference genes between species maps, enhance the resolution of comparative maps, study patterns of gene evolution, identify conserved regions of the genomes, and facilitate interspecies gene cloning. In this study, 5,780 Triticeae ESTs that have been physically mapped using wheat (Triticum aestivum L.) deletion lines and segregating populations were compared using NCBI BLASTN to the first draft of the public rice (Oryza sativa L.) genome sequence data from 3,280 ordered BAC/PAC clones. A rice genome view of the homoeologous wheat genome locations based on sequence analysis shows general similarity to the previously published comparative maps based on Southern analysis of RFLP. For most rice chromosomes there is a preponderance of wheat genes from one or two wheat chromosomes. The physical locations of non-conserved regions were not consistent across rice chromosomes. Some wheat ESTs with multiple wheat genome locations are associated with the non-conserved regions of similarity between rice and wheat. The inverse view, showing the relationship between the wheat deletion map and rice genomic sequence, revealed the breakdown of gene content and order at the resolution conferred by the physical chromosome deletions in the wheat genome. An average of 35% of the putative single copy genes that were mapped to the most conserved bins matched rice chromosomes other than the one that was most similar. This suggests that there has been an abundance of rearrangements, insertions, deletions, and duplications eroding the wheat-rice genome relationship that may complicate the use of rice as a model for cross-species transfer of information in non-conserved regions.     

A Genomics Approach Using Expressed Sequence Tags and Microarrays in Ripening Apple Fruit (<Emphasis Type="Italic">Malus domestica</Emphasis> Borkh.)

Apple (Malus domestica Borkh.), an important horticultural crop, produces human health-promoting metabolites during fruit ripening. Because that process, which involves complex biochemical and physiological changes, is genetically programmed, molecular and genetic approaches have been taken to understand the associated cellular mechanisms. The release of 151,687 apple expressed sequence tags (ESTs) into a public database has made possible large-scale studies of expression. Analysis of apple ESTs allows for the identification and characterization of genes with potential roles in fruit development, particularly those related to aroma production and protein degradation during ripening. Apple cDNA and oligonucleotide microarrays have been generated for more comprehensive examinations. Such tools are powerful means for elucidating the molecular events involved in metabolite biosynthesis and physiological changes and will also enable researchers to understand how to control that ripening process.     

Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity

The Poales (which include the grasses) and Asparagales [which include onion (Allium cepa L.) and other Allium species] are the two most economically important monocot orders. Enormous genomic resources have been developed for the grasses; however, their applicability to other major monocot groups, such as the Asparagales, is unclear. Expressed sequence tags (ESTs) from onion that showed significant similarities (80% similarity over at least 70% of the sequence) to single positions in the rice genome were selected. One hundred new genetic markers developed from these ESTs were added to the intraspecific map derived from the BYG15-23×AC43 segregating family, producing 14 linkage groups encompassing 1,907 cM at LOD 4. Onion linkage groups were assigned to chromosomes using alien addition lines of Allium fistulosum L. carrying single onion chromosomes. Visual comparisons of genetic linkage in onion with physical linkage in rice revealed scant colinearity; however, short regions of colinearity could be identified. Our results demonstrate that the grasses may not be appropriate genomic models for other major monocot groups such as the Asparagales; this will make it necessary to develop genomic resources for these important plants. Electronic Supplementary Material Supplementary material is available for this article at     

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     

Generation and analysis of expressed sequence tags from the mangrove plant, Acanthus ebracteatus Vahl

Salinity is a major abiotic stress that greatly affects plant growth and crop production. Sodium ions in saline soil are toxic to plants because of their adverse effects on potassium nutrition, cytosolic enzyme activities, photosynthesis, and metabolism. It is important to identify genes involved in salinity tolerance from mangrove plants that survive under saline conditions. In this study, a total of 864 randomly selected cDNA clones were isolated and sequenced from the primary cDNA library of Acanthus ebracteatus. Among the 521 readable sequences, 138 of them were assembled into 43 contigs, whereas 383 were singletons. Sequence analyses demonstrated that 349 of these expressed sequence tags showed significant homology to functional proteins, of which 18% are particularly interesting as they correspond to genes involved in stress response. Some of these clones, including putative mannitol dehydrogenase, plastidic aldolase, secretory peroxidase, ascorbate peroxidase, and vacuolar H⁺-ATPase, may be related to osmotic homeostasis, ionic homeostasis, and detoxification.     

A linkage map of the pea (Pisum sativum L.) genome containing cloned sequences of known function and expressed sequence tags (ESTs)

 A linkage map of the pea (Pisum sativum L.) genome is presented which is based on F₂ plants produced by crossing the marrowfat cultivar ‘Primo’ and the blue-pea breeding line ‘OSU442-15’. This linkage map consists of 209 markers and covers 1330 cM (Kosambi units) and includes RFLP, RAPD and AFLP markers. By mapping a number of anchor loci, the ‘Primo’בOSU442-15’ map has been related to other pea linkage maps. A feature of the map is the incorporation of 29 loci representing genes of known function, obtained from other laboratories. The map also contains RFLP loci detected using sequence-characterized cDNA clones developed in our laboratory. The putative identities of 38 of these cDNA clones were assigned by examining public-sequence databases for protein or nucleotide-sequence similarities. The conversion of sequence-characterized pea cDNAs into PCR-amplifiable and polymorphic sequence-tagged sites (STSs) was investigated using 18 pairs of primers designed for single-copy sequences. Eleven polymorphic STSs were developed. Received: 18 June 1997 / Accepted: 11 August 1997     

Discovery of genes for ginsenoside biosynthesis by analysis of ginseng expressed sequence tags

Expressed sequence tags (ESTs) provide a valuable tool that can be used to identify genes in secondary metabolite biosynthesis. Ginseng (Panax ginseng C.A Meyer) is a medicinal plant that accumulates ginsenosides in roots. We sequenced 11,636 ESTs from five ginseng libraries in order to create a gene resource for biosynthesis of ginsenosides, which are thought to be the major active component in roots. Only 59% of the ginseng ESTs exhibited significant homology to previously known polypeptide sequences. Stress- and pathogen-response proteins were most abundant in 4-year-old ginseng roots. ESTs involved in ginsenoside biosynthesis were identified by a keyword search of BLASTX results and a domain search of ginseng ESTs. We identified 4 oxidosqualene cyclase candidates involved in the cyclization reaction of 2,3-oxidosqualene, 9 nine cytochrome P450 and 12 glycosyltransferse candidates, which may be involved in modification of the triterpene backbone.Abbreviations cDNA Complementary DNA - ESTs Expressed sequence tagsCommunicated by I.S. Chung