Selected cDNA clones of Arabidopsis thaliana, isolated previously by suppression subtractive hybridisation, were used to differentiate between abiotic stress factors. Changes in expression patterns of 79 genes were examined by array analysis in Arabidopsis thaliana after fumigation with ozone and after short- or long-term mercuric-ion exposure. Substantial changes in the abundance of 42 transcripts were recorded in response to the treatments, and 6 transcript clusters were observed. The abundance of 37 mRNAs was increased more then 1.5-fold, whereas that of 5 mRNAs was reduced. The abundances of 5, 6 and 9 mRNAs were specifically increased by short-term mercury application, ozone fumigation, and long-term mercuric-ion exposure, respectively. The transcription of the other 5 transcripts was induced by both ozone and short-term mercuric-ion treatment. The abundance of 10 different mRNAs was increased by the different mercuric-ion applications. Two transcripts were induced by ozone fumigation, as well as long-term, mercury treatment. Finally, 5 transcripts were repressed by ozone exposure, and 3 out of them by short-term mercuric-ion treatment. These results show that the array technique can be used to analyse the expression pattern in Arabidopsis thaliana under ozone and mercuric-ion stress. Searches against the Arabidopsis database furthermore provide a classification of most genes. In addition possible cis-acting regulatory elements were identified by an in silico approach using the MIPS Arabidopsis thaliana database

The establishment of the plant life cycle in vitro, alteration of generations in vitro and/or cross breeding in vitro will stimulate the development of a breeding-oriented plant factory. Reports on plant life cycles in vitro are limited. In the present research, the complete life cycle of Arabidopsis thaliana was examined by culturing seeds under different conditions that included solidifying agent, temperature, vessel and air permeable membrane. When Arabidopsis seeds were cultured in 225 ml culture bottles with an air permeable membrane containing the Murashige and Skoog's medium, 30g/l sucrose and 8g/l agar at 22 deg C under a 16 h photoperiod with 35 micro moles of photosynthetic available photons/square m/sec, 100% of the cultures formed flowers and 67 % of the cultures produced seeds indicating that the life cycle of Arabidopsis was completed in vitro. One hundred % of the in vitro produced seeds were germinated in potted soil indicating that the in vitro produced seeds were viable. Young plants from the seeds were grown in potted soil and were morphologically normal. The in vitro produced seeds germinated and plants produced flowers in vitro, and the in vitro 3rd generation seeds were produced under the same conditions as the 2nd generation seeds were born in vitro. The present system may stimulate research on the plant life cycle in vitro, and be used as a general leading model.

Phytochelatins play an important role in heavy metal detoxification in plants as well as in other organisms. The Arabidopsis thaliana mutant cad1-3 does not produce detectable levels of phytochelatins in response to cadmium stress. The hypersensitivity of cad1-3 to cadmium stress is attributed to a mutation in the phytochelatin synthase 1 (AtPCS1) gene. However, A. thaliana also contains a functional phytochelatin synthase 2 (AtPCS2). In this study, we investigated why the cad1-3 mutant is hypersensitive to cadmium stress despite the presence of AtPCS2. Northern and Western blot analyses showed that expression of AtPCS2 is weak compared to AtPCS1 in both roots and shoots of transgenic Arabidopsis. The lower level of AtPCS2 expression was confirmed by RT-PCR analysis of wild type Arabidopsis.

We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.

Telomerase is the reverse transcriptase responsible for the maintenance of telomeric repeat sequences in most species that have been studied. Inactivation of telomerase causes telomere shortening and results in the loss of the telomere's protective function, which in mammals leads to cell-cycle arrest and apoptosis. Experiments performed on Arabidopsis thaliana mutants lacking telomerase activity revealed their unusually high tolerance for genome instability. Here we present molecular and cytogenetic analysis of two cell lines (A and B) derived from seeds of late-generation telomerase-deficient A. thaliana. These cultures have survived for about 3 years and are still viable. However, neither culture has adapted mechanisms to maintain terminal telomeric repeats. One culture (B) suffers from severe growth irregularities and a high degree of mortality. Karyological analysis revealed dramatic genomic rearrangements, a large variation in ploidy, and an extremely high percentage of anaphase bridges. The second cell line (A) survived an apparent crisis and phenotypically appears wild-type with respect to growth and morphology. Despite these indications of genome stabilization, a high percentage of anaphase bridges was observed in the A line. We conclude that the restructured chromosome termini provide the A line with partial protection from end-joining repair activities, thus allowing normal growth.

Expressed sequence tags (ESTs) represent a huge resource for the discovery of previously unknown genetic information and functional genome assignment. In this study we screened a collection of 178 292 ESTs from Arabidopsis thaliana by testing them against previously annotated genes of the Arabidopsis genome. We identified several hundreds of new transcripts that match the Arabidopsis genome at so far unassigned loci. The transcriptional activity of these loci was independently confirmed by comparison with the Salk Whole Genome Array Data. To a large extent, the newly identified transcriptionally active genomic regions do not encode 'classic' proteins, but instead generate non-coding RNAs and/or small peptide-coding RNAs of presently unknown biological function. More than 560 transcripts identified in this study are not represented by the Affymetrix GeneChip arrays currently widely used for expression profiling in A. thaliana. Our data strongly support the hypothesis that numerous previously unknown genes exist in the Arabidopsis genome.

We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.

Anthocyanins are major color pigments in plants. Their biosynthetic pathways are well established, and the majority of these biosynthetic enzymes have been identified in model plants such as Arabidopsis, maize, and petunia. One exception in Arabidopsis is UDP-glucose:flavonoid 3-O-glucosyltransferase (UF3GT). This enzyme is known as Bronze­1(Bz1) in maize, where it converts anthocyanidins to anthocyanins. Phylogenetic sequence analysis of the Arabidopsis thaliana UDP-glycosyltransferase (UGT) family previously indicated that UGT78D1, UGT78D2, and UGT78D3 cluster together with UF3GTs from other species.

The increased amount of data produced by large genome sequencing projects allows scientists to carry out important syntenic studies to a great extent. Detailed genetic maps and entirely or partially sequenced genomes are compared, and macro- and microsyntenic relations can be determined for different species. In our study, the syntenic relationships between key legume plants and two model plants, Arabidopsis thaliana and Populus trichocarpa were investigated. The comparison of the map position of 172 gene-based Medicago sativa markers to the organization of homologous A. thaliana genes could not identify any sign of macrosynteny between the two genomes. A 276 kb long section of chromosome 5 of the model legume Medicago truncatula was used to investigate potential microsynteny with the other legume Lotus japonicus, as well as with Arabidopsis and Populus. Besides the overall correlation found between the legume plants, the comparison revealed several microsyntenic regions in the two more distant plants with significant resemblance. Despite the large phylogenetic distance, clear microsyntenic regions between Medicago and Arabidopsis or Populus were detected unraveling new intragenomic evolutionary relations in Arabidopsis.