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As a result, more than 71 % of genes now have a predicted function.

The Enzyme classification (EC) numbers were changed for 160 genes and were newly assigned to 431 genes.

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It was previously suggested that short genes may be overpredicted in GC-rich genomes because stop triplets are less frequent (Skovgaard et al., 2001; Fukuchi and Nichikawa, 2004).

This updated annotation is more conservative with respect to short ORFs.

The original annotation defined 6204 protein-encoding genes: 3341 on the chromosome (Capela et al., 2001), 1293 on p Sym A (Barnett et al., 2001), and 1570 on p Sym B (Finan et al., 2001).

There was no experimentally proven function for a vast majority of the predicted genes and 40 % could not be placed in a functional category.

Most rhizobia (order Rhizobiales) belong to families within the α-proteobacteria subdivision (Garrity et al., 2002), although symbiotic nitrogen-fixing β-proteobacteria (β-rhizobia) have also been reported (Chen et al., 2003; Rasolomampianina et al., 2005).