Two Plastid Genome Configurations and Unprecedented Intraspecies Length Variation in the ACCD Coding Region in Medicago truncatula

Evolutionary studies have revealed localized hypermutation and associated gene losses in the plastid genome of legume species. To gain insights into mechanisms operating at the species level, we fully sequenced four, and partially sequenced six additional plastid genomes of the model legume Medicago truncatula. Three accessions, Jemalong 2HA, Borung and Paraggio belong to ssp.  truncatula, and R108 to ssp. tricycla. We report here that the R108 ptDNA has a ~45-kb inversion compared to ssp. truncatula.  The inversion was apparently mediated by a short, imperfect repeat. DNA gel blot analyses of seven additional ssp. tricycla accessions detected only one of the two alternative genome arrangements, represented by three and four accessions each. We also found that a salient feature of plastid genomes is a variable number of repeats in the accD and ycf1 coding regions. We report here that the accD repeats are recombinationally active, yielding variable length insertions and deletions in the central part of the coding region, while maintaining the conserved N- and C-termini of ACCD.  The length of ACCD was distinct in each of the ten sequenced ecotypes, ranging between 650 and 796 amino acids. The repeats in the ycf1 coding region were also recombinationally active, yielding short indels within the coding region. Thus, the plastid genome variability we report here could be linked to repeat-mediated genome rearrangements. However, the rate of recombination was sufficiently low, so that no heterogeneity of ptDNA could be observed in populations maintained by single-seed descent