Arabidopsis enters the post-sequencing era

Abstract

Four Nature papers 1.xSee all References, 2.xSequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Theologis, A et al. Nature. 2000; 408: 816–820Crossref | PubMed | Scopus (141)See all References, 3.xSequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Salanoubat, M et al. Nature. 2000; 408: 820–822Crossref | PubMed | Scopus (106)See all References, 4.xSequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Tabata, S et al. Nature. 2000; 408: 823–826Crossref | PubMed | Scopus (98)See all References report the nearly completed sequencing of the Arabidopsis thaliana (accession Columbia) genome, providing the first glimpse of an entire plant genome. Since the project began in 1996, 115.4 Mb of the estimated 125 Mb five-chromosome genome has been sequenced. The remaining gaps include two rDNA repeat regions and certain centromeric sequences. The completed sequence provides scientists with a better understanding of plant genome evolution, gene function, and the level of homology between animals and plants. With this information in hand, the plant research community is poised to enter the post-sequencing era.Using gene prediction programs, 25 498 genes, with an average size of ∼2 Kb, are predicted in the Arabidopsis genome. This is more genes than in any other sequenced organism. Interestingly, some of these expressed genes are located in centromeres. This apparent gene amplification in the plant lineage does not coincide with an overall increase in protein families because 10 000–15 000 families are seen in the three sequenced multicellular species – Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana – suggesting that this is the basic number of protein types required for multicellularity. Comparisons with other plant species and examination of the overall genome structure suggest that at least one whole genome duplication event probably occurred ∼12 million years ago, yielding a tetraploid. Subsequent genome reorganization and deletion have led to the diploid system now seen in Arabidopsis.This putative genome duplication, in addition to various tandem gene duplications, has led to a significant increase in gene family size. In Arabidopsis, 37.4% of the gene families have more than five members, compared with 12.1% for D. melanogaster and 24.0% for C. elegans. Gene duplications have probably established functional redundancy in many cases, explaining why many plant mutants do not have an obvious phenotype. Horizontal transfer of genes from the plastid and mitochondrial genomes to the nuclear genome has also been prevalent. The seemingly greater genome malleability in Arabidopsis might be necessary to allow for new functions in an evolving environment – alternative promoters and alternative splicing are less common in plants. Based on homology, putative gene functions have been assigned to 69% of the genes. Only 9% of the Arabidopsis genes had been identified through traditional experimentation.Comparing the Arabidopsis gene set with those of the other sequenced multicellular organisms suggests that basic intracellular processes, such as translation, are conserved, whereas intercellular processes, such as development, often use different proteins. This makes sense because the common ancestor of plants and animals was a single-celled eukaryote with multicellularity arising independently in the two lineages. Although plants and animals started with the same general nuclear gene cohort, different gene families have been differentially expanded and consolidated to fulfill various functions. For example, plants use MADS box transcription factors for regulating spatial patterning, whereas homeobox genes fill this role in animals. Differences in intracellular processes generally seem to be because of the presence of the plant cell wall.With the completion of the Arabidopsis genome project, the research emphasis is shifting from the identification of genes to the delineation of gene functions. Of particular interest will be discovering functions for genes with unclassified functions, and those genes belonging to the ∼150 plant-specific protein families. In addition, although putative functions have been assigned to many genes based on homology, it is possible that they actually have different roles. Functional redundancy within the genome will need to be considered when conducting these studies. Increasing our understanding of Arabidopsis gene function will inevitably expand our ability to improve crop plants.