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 o f chromosome 1, we screened cDNAs hybridized with approximately 300 kb cont iguous DNA using four P1 clones and one YAC clone. A total of 40 kinds of c DNA 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 be en detected in Arabidopsis or other organisms. cDNAs were aligned on a phys ical map of the contiguous DNA, and the transcriptional direction of each c DNA was determined. This contiguous DNA contains a large direct repeat, whi ch 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 i dentified, and the gene density was revealed to be approximately one gene e very 6 kb. In addition, cDNA sequencing revealed the existence of unusual t ranscripts. A sequence of seven cDNAs seemed to have no significant open re ading frames. Furthermore, the existence of antisense RNA and the possibili ty of alternative splicing were also revealed. (C) 1999 Elsevier Science B. V. All rights reserved.