Construction of 12 EST libraries and characterization of a 12,226 EST dataset for chicory (Cichorium intybus) root, leaves and nodules in the context of carbohydrate metabolism investigation

<p>Abstract</p> <p>Background</p> <p>The industrial chicory, <it>Cichorium intybus</it>, is a member of the <it>Asteraceae </it>family that accumulates fructan of the inulin type in its root. Inulin is a low calories sweetener, a texture agent and a health promoting ingredient due to its prebiotic properties. Average inulin chain length is a critical parameter that is genotype and temperature dependent. In the context of the study of carbohydrate metabolism and to get insight into the transcriptome of chicory root and to visualize temporal changes of gene expression during the growing season, we obtained and characterized 10 cDNA libraries from chicory roots regularly sampled in field during a growing season. A leaf and a nodule libraries were also obtained for comparison.</p> <p>Results</p> <p>Approximately 1,000 Expressed Sequence Tags (EST) were obtained from each of twelve cDNA libraries resulting in a 12,226 EST dataset. Clustering of these ESTs returned 1,922 contigs and 4,869 singlets for a total of 6,791 putative unigenes. All ESTs were compared to public sequence databases and functionally classified. Data were specifically searched for sequences related to carbohydrate metabolism. Season wide evolution of functional classes was evaluated by comparing libraries at the level of functional categories and unigenes distribution.</p> <p>Conclusion</p> <p>This chicory EST dataset provides a season wide outlook of the genes expressed in the root and to a minor extent in leaves and nodules. The dataset contains more than 200 sequences related to carbohydrate metabolism and 3,500 new ESTs when compared to other recently released chicory EST datasets, probably because of the season wide coverage of the root samples. We believe that these sequences will contribute to accelerate research and breeding of the industrial chicory as well as of closely related species.</p

Nucleotide sequence analysis of a 40 kb segment on the right arm of yeast chromosome XV reveals 18 open reading frames including a new pyruvate kinase and three homologues to chromosome I genes.

We have determined the nucleotide sequence of a 40 kb fragment from the right arm of chromosome XV of Saccharomyces cerevisiae. Subsequent analysis revealed 18 non-overlapping open reading frames (ORFs) numbered from 06257 to 06357, an ARS, two tRNA genes and a Ty2 with its flanking elements. Ten ORFs have been sequenced previously: TEA1, RPA43, RPA190, SGC1 (also called TYE7) REV1, PUT4, CIN1, MNE and MRE4 (also called MEK1). Among the others, two seem to code for a new pyruvate kinase and for a new ubiquitin-conjugating enzyme; three have interesting homology with genes located on the left arm of chromosome I. This similarity with chromosome I extends to the left of the sequence presented here (Parle et al., submitted to Yeast). The homologous genes on the two chromosomes are placed in the same relative order

The sequence of 55 kb on the left arm of yeast chromosome XVI identifies a small nuclear RNA, a new putative protein kinase and two new putative regulators.

We have sequenced and analysed a 55786 bp fragment located on the left arm of chromosome XVI of Saccharomyces cerevisiae. The sequence contains 29 non-overlapping open reading frames (ORFs) longer than 300 bp, among which 12 genes have previously been sequenced: OYE3, REV3, SVS1, BEM4, CDC60, KIP2, PEP4, SPK1, PAL1, KES1, SNR17B and RPL37A. Three new ORFs, P2591, P2594 and P2597 are highly homologous to the human phosphotyrosyl phosphatase activator PTPA, to the pleiotropic regulator PRL1 of PP1 and PP2a protein phosphatases in plants and to the protein kinase PAR-1 in Caenorhabditis elegans, respectively. Three other ORFs, P2545, P2567 and P2578 have significant homology with ORFs of unknown function located on yeast chromosomes VIII, XVI and IV respectively

The product of the YCR105 gene located on the chromosome III from Saccharomyces cerevisiae presents homologies to ATP-dependent permeases.

During the systematic sequencing of chromosome III from Saccharomyces cerevisiae, carried out by a network of laboratories sponsored by the Commission of the European Community, we have identified the open reading frame YCR105 located on fragment J11D from the circular derivative of chromosome III in strain XJ24-24a (Palzkill et al., 1986). YCR105 is immediately centromere proximal to the PGK gene (opposite strand) on the right arm of chromosome III about 20 kb from the centromere

The Sequence of An 8.8-kb Segment On the Left Arm of Chromosome-ii From Saccharomyces-cerevisiae Reveals 4 New Open Reading Frames Including Homologs of Animal Dna-polymerase Alpha-primases and Bacterial Gtp Cyclohydrolase-ii

The DNA sequence of two contiguous 7648 bp and 1194 bp BamHI fragments from the cosmid alpha 1201 located about 60 kb from the centromere on the left arm of chromosome II from Saccharomyces cerevisiae has been determined. Sequence analysis reveals four new open reading frames longer than 300 bp: YBL0415 (309 bp), YBL0416(4539 bp), YBL0417 (1035 bp) and YBL0414 (2115 bp), which extends into the neighbouring 5.2 kb BamHI fragment. The YBL0414 shows homologies to the mouse 68 kDa and Drosophila melanogaster 76 kDa subunits of the DNA polymerase alpha-primase complex. The YBL0417 is homologous to bacterial GTP cyclohydrolase II (EC 3.5.4.25). The sequence has been deposited in the EMBC data library under Accession Number X74738