Figure 1.

Structure of the symbiotic plasmid p42d of R. etli CNF42. The structure of p42d is represented in five concentric circles. Outermost circle, relevant regions referred to in the text: NRa, b and c, regions containing nitrogenase structural genes; FIX1 and FIX2, clusters containing nitrogen-fixation genes; NOD, major cluster of nodulation genes; CPX, cluster for cytochrome P450; TRA, cluster for tra genes; REP, replicator region; TSSIII and IV, clusters for transport secretion system genes. The 125 kb region that contains most of the symbiotic genes, described in the text as a putative mobile element, is shown in green. Second circle, organization of predicted CDSs located according to the direction of transcription color-coded as below; those transcribed on the plus strand are shown in the outer half of the circle. For each class, the number of CDSs and the percentage of the total are: hypothetical (70) 19.5% (dark red); hypothetical conserved (62) 17.3% (red); integration recombination (55) 15.3% (purple); various enzymatic functions (45) 12.3% (khaki); transport secretion systems (37) 10.3% (gray); nitrogen fixation (35) 9.8% (yellow); nodulation (18) 5% (dark blue); transcriptional regulation (15) 4.2% (light blue); plasmid maintenance (10) 2.8% (orange); electron transfer (7) 2.1% (magenta); chemotaxis (3) 0.8% (pink); and polysaccharide synthesis (2) 0.6% (green). Third circle, elements related to insertion sequences (ERIS). Putative partial ISs (purple), and putative complete ISs (black). Fourth circle, reiterated DNA families. The major reiterated families (see text) are shown in different colors. Innermost circle, potential genomic rearrangements. Arrowheads indicate the sites for homologous recombination leading to genomic rearrangements. Black lines connect sites for amplification or deletion events; red lines connect sites for inversion.