Rapid evolutionary change of common bean (<it>Phaseolus vulgaris </it>L) plastome, and the genomic diversification of legume chloroplasts

• Main Authors: Dávila Guillermo, Cevallos Miguel A, Arellano Jesús, Santamaría Rosa, Luís Fernández-Vázquez José, Bustos Patricia, González Víctor, Castillo-Ramírez Santiago, Guo Xianwu
• Format: Article
• Language: English
• Published: BMC 2007-07-01
• Series: BMC Genomics
• Online Access: http://www.biomedcentral.com/1471-2164/8/228

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>We sequenced the complete genome of the common bean (<it>Phaseolus vulgari</it>s cv. Negro Jamapa) chloroplast. The plastome of <it>P. vulgaris </it>is a 150,285 bp circular molecule. It has gene content similar to that of other legume plastomes, but contains two pseudogenes, <it>rpl</it>33 and <it>rps</it>16. A distinct inversion occurred at the junction points of <it>trn</it>H-GUG/<it>rpl</it>14 and <it>rps</it>19/<it>rps</it>8, as in adzuki bean <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. 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, <it>P. vulgaris </it>plastome had higher evolutionary rates of change on both genomic and gene levels than <it>G. max</it>, which could be the consequence of pressure from both mutation and natural selection.</p> <p>Conclusion</p> <p>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 <it>P. vulgaris </it>plastome is a rapidly evolving genome.</p>