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MBE Advance Access published online on May 25, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi174
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org
Accepted May 12, 2005

Research Article

Two Chloroplast DNA Inversions Originated Simultaneously During the Early Evolution of the Sunflower Family (Asteraceae)

Ki-Joong Kim 1*, Keung-Sun Choi 1, and Robert K. Jansen 2

1 School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
2 Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712

* To whom correspondence should be addressed.
Ki-Joong Kim, E-mail: kimkj{at}korea.ac.kr


  Abstract

The chloroplast DNA inversion in the Asteraceae has been cited as a classic example of using genomic rearrangements for defining major lineages of plants. We further characterize chloroplast DNA inversions in the Asteraceae using extensive sequence comparisons among 56 species, including representatives of all major clades of the family and related families. We determine the boundaries of the 22 kb (now known as 22.8 kb) inversion that defines a major split within the Asteraceae, and in the process, we characterize the second and a new, smaller 3.3 kb inversion that occurs at one end of the larger inversion. One endpoint of the smaller inversion is upstream of the trnE-UUC gene and the other endpoint is located between the trnC-GCA and rpoB genes. Although a diverse sampling of Asteraceae experienced substantial length variation and base substitution during the long evolutionary history subsequent to the inversion events, the precise locations of the inversion endpoints are identified using comparative sequence alignments in the inversion regions. The phylogenetic distribution of two inversions is identical among the members of Asteraceae suggesting the inversion events likely occurred simultaneously or within a short time period shortly after the origin of the family. Estimates of divergence times based on ndhF and rbcL sequences suggest that two inversions originated during the late Eocene (38-42 mya). The divergence time estimates also suggest that the Asteraceae originated in the mid Eocene (42-47 mya).

Keywords: Chloroplast DNA inversion; nonparametric rate smoothing; molecular clock; Asteraceae.
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