title: Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts.
abstract: BACKGROUND
  Fabaceae (legumes) is one of the largest families of flowering plants, and some members are important crops. In contrast to what we know about their great diversity or economic importance, our knowledge at the genomic level of chloroplast genomes (cpDNAs or plastomes) for these crops is limited.
  
  
  RESULTS
  We sequenced the complete genome of the common bean (Phaseolus vulgaris cv. Negro Jamapa) chloroplast. The plastome of P. vulgaris is a 150,285 bp circular molecule. It has gene content similar to that of other legume plastomes, but contains two pseudogenes, rpl33 and rps16. A distinct inversion occurred at the junction points of trnH-GUG/rpl14 and rps19/rps8, as in adzuki bean 1. These two pseudogenes and the inversion were confirmed in 10 varieties representing the two domestication centers of the bean. Genomic comparative analysis indicated that inversions generally occur in legume plastomes and the magnitude and localization of insertions/deletions (indels) also vary. The analysis of repeat sequences demonstrated that patterns and sequences of tandem repeats had an important impact on sequence diversification between legume plastomes and tandem repeats did not belong to dispersed repeats. Interestingly, P. vulgaris plastome had higher evolutionary rates of change on both genomic and gene levels than G. max, which could be the consequence of pressure from both mutation and natural selection.
  
  
  CONCLUSIONS
  Legume chloroplast genomes are widely diversified in gene content, gene order, indel structure, abundance and localization of repetitive sequences, intracellular sequence exchange and evolutionary rates. The P. vulgaris plastome is a rapidly evolving genome.
authors.affiliation: Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, C.P 62210, Cuernavaca, Morelos, México. gxianwu@ccg.unam.mx
authors.forename: Xianwu
authors.initials: X
authors.lastname: Guo
authors.forename: Santiago
authors.initials: S
authors.lastname: Castillo-Ramírez
authors.forename: Víctor
authors.initials: V
authors.lastname: González
authors.forename: Patricia
authors.initials: P
authors.lastname: Bustos
authors.forename: José Luís
authors.initials: JL
authors.lastname: Fernández-Vázquez
authors.forename: Rosa Isela
authors.initials: RI
authors.lastname: Santamaría
authors.forename: Jesús
authors.initials: J
authors.lastname: Arellano
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Cevallos
authors.forename: Guillermo
authors.initials: G
authors.lastname: Dávila
mesh_terms: D002736:Chloroplasts / Q000235:genetics*; D004270:DNA, Circular / Q000032:analysis*; D019143:Evolution, Molecular; D018745:Genome, Plant / Q000235:genetics*; D027805:Phaseolus / Q000235:genetics*; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017384:Sequence Deletion; D020080:Tandem Repeat Sequences
chemical_list: D004270:DNA, Circular