title: Two distinct plastid genome configurations and unprecedented intraspecies length variation in the accD coding region in Medicago truncatula.
abstract: 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 with the ptDNA in ssp. truncatula, 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. Furthermore, we found a variable number of repeats in the essential accD and ycf1 coding regions. The repeats within accD are recombinationally active, yielding variable-length insertions and deletions in the central part of the coding region. The length of ACCD was distinct in each of the 10 sequenced ecotypes, ranging between 650 and 796 amino acids. The repeats in the ycf1 coding region are also recombinationally active, yielding short indels in 10 regions of the reading frames. 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.
authors.affiliation: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA.
authors.forename: Csanad
authors.initials: C
authors.lastname: Gurdon
authors.affiliation: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA maliga@waksman.rutgers.edu.
authors.forename: Pal
authors.initials: P
authors.lastname: Maliga
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D017343:Genes, Plant; D054627:Genome, Plastid; D054643:INDEL Mutation; D046913:Medicago truncatula / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D018515:Plant Leaves / Q000235:genetics; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity
keywords: Medicago truncatula; accD; plastid genome; ptDNA; ycf1