Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project.
BLASTX alignment between 189.5 Mb of rice genomic sequence and translated Arabidopsis thaliana annotated coding sequences (CDS) identified 60 syntenic regions involving 4-22 rice orthologs covering < or =3.2 cM (centiMorgan). Most regions are <3 cM in length. A detailed and updated version of a table representing these regions is available on our web site. Thirty-five rice loci match two distinct A.thaliana loci, as expected from the duplicated nature of the A.thaliana genome. One A.thaliana locus matches two distinct rice regions, suggesting that rice chromosomal sequence duplications exist. A high level of rearrangement characterizing the 60 syntenic regions illustrates the ancient nature of the speciation between A.thaliana and rice. The apparent reduced level of microcollinearity implies the dispersion to new genomic locations, via transposon activity, of single or small clusters of genes in the rice genome, which represents a significant additional effector of plant genome evolution.
Salse
Jérôme
J
Laboratoire Génome et Développement des Plantes, Université de Perpignan (Centre National de la Recherche Scientifique, UMR 5096), 52 Avenue de Villeneuve, F-66860 Perpignan Cedex, France.
Piégu
Benoit
B
Cooke
Richard
R
Delseny
Michel
M
D017360:Arabidopsis / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D020440:Gene Duplication; D023061:Gene Order / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D009010:Monte Carlo Method; D012275:Oryza / Q000235:genetics*; D020161:Physical Chromosome Mapping; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D012984:Software; D013045:Species Specificity; D026801:Synteny / Q000235:genetics*
D004251:DNA Transposable Elements