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Unigene Set (unigene + set)
Selected AbstractsTranscriptomic study of apricot fruit (Prunus armeniaca) ripening among 13 006 expressed sequence tagsPHYSIOLOGIA PLANTARUM, Issue 3 2005Jérôme Grimplet To improve the knowledge of fruit ripening and to provide genomic resources for molecular breeding of apricot (Prunus armeniaca L), 13 006 expressed sequence tags (ESTs) were generated from three ,zap cDNA libraries of the pericarp tissues at different stages of development (Physiol Plant 105: 294,303), yielding 5219 (40%) Unigenes. At this stage, the very low interlibrary redundancy indicated that EST sampling of the transcriptome of apricot pericarp is still far from being saturated. Seventy-six percent of Unigenes displayed homologies with public sequences and were clustered into functional categories. The largest expressed categories were related to primary metabolism, stress response, and protein synthesis. Electronic Northern analysis revealed that stress-related proteins and cell wall modification-related enzymes strongly increased during ripening. Among 448 isoproteins (amino acid-level isogenes) detected in the Unigene set, 186 (42%) displayed significant homologies in their coding regions (nucleic acid-level isogenes). [source] ANALYSIS OF EXPRESSED SEQUENCE TAGS FROM THE GREEN ALGA ULVA LINZA (CHLOROPHYTA),JOURNAL OF PHYCOLOGY, Issue 6 2005Michele S. Stanley There is a general lack of genomic information available for chlorophyte seaweed genera such as Ulva, and in particular there is no information concerning the genes that contribute to adhesion and cell wall biosynthesis for this organism. Partial sequencing of cDNA libraries to generate expressed sequence tags (ESTs) is an effective means of gene discovery and characterization of expression patterns. In this study, a cDNA library was created from sporulating tissue of Ulva linza L. Initially, 650 ESTs were randomly selected from a cDNA library and sequenced from their 5, ends to obtain an indication of the level of redundancy of the library (21%). The library was normalized to enrich for rarer sequences, and a further 1920 ESTs were sequenced. These sequences were subjected to contig assembly that resulted in a unigene set of approximately 1104 ESTs. Forty-eight percent of these sequences exhibited significant similarity to sequences in the databases. Phylogenetic comparisons are made between selected sequences with similarity in the databases to proteins involved in aspects of extracellular matrix/cell wall assembly and adhesion. [source] New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genomeTHE PLANT JOURNAL, Issue 3 2004Jérôme Salse Summary A unigene set of 1411 contigs was constructed from 2629 redundant maize expressed sequence tags (ESTs) mapped on the maizeDB genetic map. Rice orthologous sequences were identified by blast alignment against the rice genomic sequence. A total of 1046 (74%) maize contigs were associated with their corresponding homologues in the rice genome and 656 (47%) defined as potential orthologous relationships. One hundred and seventeen (8%) maize EST contigs mapped to two distinct loci on the maize genetic map, reflecting the tetraploid nature of the maize genome. Among 492 mono-locus contigs, 344 (484 redundant ESTs) identify collinear blocks between maize chromosomes 2 and 4 and a single rice chromosome, defining six new collinear regions. Fine-scale analysis of collinearity between rice chromosomes 1 and 5 with maize chromosomes 3, 6 and 8 shows the presence of internal rearrangements within collinear regions. Mapping of maize contigs to two distinct loci on the rice sequence identifies five new duplication events in rice. Detailed analysis of a duplication between rice chromosomes 1 and 5 shows that 11% of the annotated genes from the chromosome 1 locus are found duplicated on the chromosome 5 paralogous counterpart, indicating a high degree of re-organisations. The implications of these findings for map-based cloning in collinear regions are discussed. [source] Establishment of T cell-specific and natural killer cell-specific unigene sets: towards high-throughput genomics of leukaemiaINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 6 2004J. Illiger Summary We report the establishment of highly non-redundant unigene sets consisting of cDNA clones derived from T lymphocytes and natural killer cells. Each set consists of 10 506 and 13 409 clones, respectively, arrayed on nylon membranes in duplicate. The sets provide an excellent tool for genome-wide gene expression analysis studies in immunology research. [source] Construction of a ,unigene' cDNA clone set by oligonucleotide fingerprinting allows access to 25 000 potential sugar beet genesTHE PLANT JOURNAL, Issue 5 2002Ralf Herwig Summary Access to the complete gene inventory of an organism is crucial to understanding physiological processes like development, differentiation, pathogenesis, or adaptation to the environment. Transcripts from many active genes are present at low copy numbers. Therefore, procedures that rely on random EST sequencing or on normalisation and subtraction methods have to produce massively redundant data to get access to low-abundance genes. Here, we present an improved oligonucleotide fingerprinting (ofp) approach to the genome of sugar beet (Beta vulgaris), a plant for which practically no molecular information has been available. To identify distinct genes and to provide a representative ,unigene' cDNA set for sugar beet, 159 936 cDNA clones were processed utilizing large-scale, high-throughput data generation and analysis methods. Data analysis yielded 30 444 ofp clusters reflecting the number of different genes in the original cDNA sample. A sample of 10 961 cDNA clones, each representing a different cluster, were selected for sequencing. Standard sequence analysis confirmed that 89% of these EST sequences did represent different genes. These results indicate that the full set of 30 444 ofp clusters represent up to 25 000 genes. We conclude that the ofp analysis pipeline is an accurate and effective way to construct large representative ,unigene' sets for any plant of interest with no requirement for prior molecular sequence data. [source] | ||||||||||