Genome DNA sequencing around the EF-1 alpha multigene locus of Arabidopsis thaliana indicates a high gene density and a shuffling of noncoding regions

Reme1, a Copia retrotransposon in melon, is transcriptionally induced by UV light

For the first time, numerous sequences of Copia and Gypsy retrotransposons from the Cucumis melo genome have been obtained and analyzed. Phylogenetic analyses of sequences of both types of long terminal repeat (LTR) retrotransposons were carried out. The melon genome contains approximately 20,000 Gypsy and 6,800 Copia elements, comprising about 26% of its total size. Starting from a retrotransposon fragment, we have cloned and characterized an entire melon retrotransposon, named Reme1, which is 5,149 bp long. Reme1 belongs to the Superfamily Copia retrotransposons by its protein domain order and sequence similarity to other Copia elements of dicotyledons. The haploid genome of melon (var. "Piel de Sapo") contains about 120 copies of Reme1. Several copies of Reme1 are transcriptionally active, although at low levels, in melon leaves as analyzed by reverse-transcription PCR (RT-PCR) and sequencing. However, the transcript pool is considerably increased when melon leaves are treated with UV light, as has been seen for various retroelements in many organisms. The cDNAs of Reme1 transcripts showed less diversity than do Reme1 genomic sequences, suggesting that a subfamily of these elements is differentially responsive to UV.

Large-scale analysis of the barley transcriptome based on expressed sequence tags

To provide resources for barley genomics, 110,981 expressed sequence tags (ESTs) were generated from 22 cDNA libraries representing tissues at various developmental stages. This EST collection corresponds to approximately one-third of the 380,000 publicly available barley ESTs. Clustering and assembly resulted in 14,151 tentative consensi (TCs) and 11 073 singletons, altogether representing 25 224 putatively unique sequences. Of these, 17.5% showed no significant similarity to other barley ESTs present in dbEST. More than 41% of all barley genes are supposed to belong to multigene families and approximately 4% of the barley genes undergo alternative splicing. Based on the functional annotation of the set of unique sequences, the functional category 'Energy' was further analysed to reveal tissue- and stage-specific differences in gene expression. Hierarchical clustering of 362 differentially expressed TCs resulted in the identification of seven major clusters. The clusters reflect biochemical pathways predominantly activated in specific tissues and at various developmental stages. During seed germination glycolysis could be identified as the most predominant biochemical pathway. Germination-specific glycolysis is characterized by the coordinated expression of phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxykinase, whose antagonistic actions possibly regulate the flux of amino acids into protein biosynthesis and gluconeogenesis respectively. The expression of defence-related and antioxidant genes during germination might be controlled by the ethylene-signalling pathway as concluded from the coordinated expression of those genes and the transcription factors (TF) EIN3 and EREBPG. Moreover, because of their predominant expression in germinating seeds, TF of the AP2 and MYB type are presumably major regulators of germination.

Isolation and analysis of cDNA within a 300 kb Arabidopsis thaliana genomic region located around the 100 map unit of chromosome 1

In order to analyze the organization of genes located at the 100 map unit of chromosome 1, we screened cDNAs hybridized with approximately 300kb contiguous DNA using four P1 clones and one YAC clone. A total of 40 kinds of cDNA were isolated, and their entire sequences were determined. A comparison with the GenBank/EMBL database indicated that three of the cDNAs have been found in Arabidopsis, and that similar sequences to 18 of the cDNAs had been detected in Arabidopsis or other organisms. cDNAs were aligned on a physical map of the contiguous DNA, and the transcriptional direction of each cDNA was determined. This contiguous DNA contains a large direct repeat, which contains five genes. In addition, identical or very similar sequences to two cDNAs are located in a narrow region. Thus, a total of 50 genes were identified, and the gene density was revealed to be approximately one gene every 6kb. In addition, cDNA sequencing revealed the existence of unusual transcripts. A sequence of seven cDNAs seemed to have no significant open reading frames. Furthermore, the existence of antisense RNA and the possibility of alternative splicing were also revealed.

Classification of Arabidopsis thaliana gene sequences: clustering of coding sequences into two groups according to codon usage improves gene prediction

While genomic sequences are accumulating, finding the location of the genes remains a major issue that can be solved only for about a half of them by homology searches. Prediction methods are thus required, but unfortunately are not fully satisfying. Most prediction methods implicitly assume a unique model for genes. This is an oversimplification as demonstrated by the possibility to group coding sequences into several classes in Escherichia coli and other genomes. As no classification existed for Arabidopsis thaliana, we classified genes according to the statistical features of their coding sequences. A clustering algorithm using a codon usage model was developed and applied to coding sequences from A. thaliana, E. coli, and a mixture of both. By using it, Arabidopsis sequences were clustered into two classes. The CU1 and CU2 classes differed essentially by the choice of pyrimidine bases at the codon silent sites: CU2 genes often use C whereas CU1 genes prefer T. This classification discriminated the Arabidopsis genes according to their expressiveness, highly expressed genes being clustered in CU2 and genes expected to have a lower expression, such as the regulatory genes, in CU1. The algorithm separated the sequences of the Escherichia-Arabidopsis mixed data set into five classes according to the species, except for one class. This mixed class contained 89 % Arabidopsis genes from CU1 and 11 % E. coli genes, mostly horizontally transferred. Interestingly, most genes encoding organelle-targeted proteins, except the photosynthetic and photoassimilatory ones, were clustered in CU1. By tailoring the GeneMark CDS prediction algorithm to the observed coding sequence classes, its quality of prediction was greatly improved. Similar improvement can be expected with other prediction systems.

Sequence analysis of a 40-kb Arabidopsis thaliana genomic region located at the top of chromosome 1

As a contribution to the European Scientists Sequencing Arabidopsis (BIOTECH ESSA) project, a contig of almost 40kb has been sequenced at the extreme top of chromosome 1, around the Arabidopsis thaliana gene coding for a member of the 1-aminocyclopropane-1-carboxylate synthesis gene family. The region contains, besides the ACS1 gene itself, 10 putative genes, all new for Arabidopsis. Among these are three genes encoding kinases, a late embryogenesis-abundant protein, a MADS box-containing protein, a dehydrogenase, and a Myb-related transcription factor. In addition, six cDNAs have been sequenced that correspond to this region.

Members of the Arabidopsis actin gene family are widely dispersed in the genome

Plant genomes are subjected to a variety of DNA turnover mechanisms that are thought to result in rapid expansion and presumable contraction of gene copy number. The evolutionary history of the 10 actin genes in Arabidopsis thaliana is well characterized and can be traced to the origin of vascular plant genomes. Knowledge about the genomic position of each actin gene may be the key to tracing landmark genomic duplication events that define plant families or genera and facilitate further mutant isolation. All 10 actin genes were mapped by following the segregation of cleaved amplified polymorphisms between two ecotypes and identifying actin gene locations among yeast artificial chromosomes. The Arabidopsis actin genes are widely dispersed on four different chromosomes (1, 2, 3, and 5). Even the members of three closely related and recently duplicated pairs of actin genes are unlinked. Several other cytoskeletal genes (profilins, tubulins) that might have evolved in concert with actins were also mapped, but showed few patterns consistent with that evolutionary history. Thus, the events that gave rise to the actin gene family have been obscured either by the duplication of very small genic fragments or by extensive rearrangement of the genome.

Large-scale sequencing of plant genomes

The large number of ESTs generated for Arabidopsis and rice in recent years now act as an important complement to whole genome sequencing projects. The Arabidopsis Genome Initiative has begun a coordinated effort to sequence the entire genome and, as a result, increasing numbers of large sequence entries can be found in the public databases. In addition, the mitochondrial genome of Arabidopsis has been completely sequenced. Genome sequencing studies and the public sequence databases have begun to influence the direction of diverse areas of research from physiology to evolution.

Analysis of a 14-kb fragment containing a putative cell wall gene and a candidate for the ARA1, arabinose kinase, gene from chromosome IV of Arabidopsis thaliana

An Arabidopsis thaliana genomic DNA fragment of 14kb has been characterized in the framework of the E.S.S.A. programme. Computational and molecular approaches identified three novel gene sequences coding, respectively, for a protein of unknown function, a putative membrane-anchored cell wall protein and an arabinose kinase gene corresponding to the locus ARA1. The latter two genes named AtSEB1 and AtISA1 have been characterized in detail. They are very different in their organization, codon usage and level of expression. Homologues of AtSEB1 and AtISA1 have been identified. Sequence comparisons showed that the former genes contained a long 5' extension coding for an N-terminal domain probably specifying subcellular localization. Cloning and sequencing of the cognate cDNA for the AtISA1 homologue in A. thaliana, named GAL1, indicate that it encodes for a galactokinase-like protein. Our results highlight the integrative outcome of a systematic sequencing project in which links between biochemically and genetically characterized mutants, ESTs and genomic sequence data are generated.

A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome

The contiguous DNA sequence of a 60 kb genomic interval of barley chromosome 4HL has been assembled. The region harbours a single and novel gypsy -like retrotransposon, designated BAGY-1. Only three genes appear to reside in the genomic stretch. One predicts a plant homologue of ribophorin I, a subunit of the oligosaccharyltransferase-protein complex located in the rough endoplasmatic reticulum. The second is similar to the Drosophila g1 gene encoding a ring finger protein involved in developmental processes. The observed gene density is approximately 5-fold lower than in the best characterized dicot genome of Arabidopsis but 6- to 10-fold higher than expected from an equidistant gene distribution in the complex barley genome. Our data suggest that the 60 kb genomic interval represents part of a gene island, a seemingly distinctive feature of grass genomes.

Sequence analysis of a 24-kb contiguous genomic region at the Arabidopsis thaliana PFL locus on chromosome 1

As part of the European Union program of European Scientist Sequencing Arabidopsis (ESSA), the DNA sequence of a 24.053-bp insert of cosmid clone CC17J13 was determined. The cosmid is located on chromosome 1 at the PFL locus (position 30 cM). Analysis of the sequence and comparison to public databases predicts seven genes in this area, thus approximately one gene every 3.3 kb. Three cDNAs corresponding to genes in this region were also sequenced. The homologies and/or possible functions of the (putative) genes are discussed. Proteins encoded by genes in this region include a polyadenylate-binding protein (PAB-3) and a GTP-binding protein (Rab7) as well as a novel protein, possibly involved in double-stranded RNA unwinding and apoptosis. Intriguingly, the gene encoding the PAB-3 protein, which is very specifically expressed, is flanked by putative matrix attachment regions.