Abstract
The chloroplast DNA (cpDNA) inversion in the Asteraceae has been cited as a classic example of using genomic rearrangements for defining major lineages of plants. We further characterize cpDNA 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 end point of the smaller inversion is upstream of the trnE-UUC gene, and the other end point 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 end points are identified using comparative sequence alignments in the inversion regions. The phylogenetic distribution of two inversions is identical among the members of Asteraceae, suggesting that 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).
| Original language | English |
|---|---|
| Pages (from-to) | 1783-1792 |
| Number of pages | 10 |
| Journal | Molecular Biology and Evolution |
| Volume | 22 |
| Issue number | 9 |
| DOIs | |
| Publication status | Published - 2005 Sep 1 |
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Keywords
- Asteraceae
- Chloroplast DNA inversion
- Molecular clock
- Nonparametric rate smoothing
ASJC Scopus subject areas
- Genetics
- Biochemistry
- Genetics(clinical)
- Biochemistry, Genetics and Molecular Biology(all)
- Ecology, Evolution, Behavior and Systematics
- Agricultural and Biological Sciences (miscellaneous)
- Molecular Biology
Cite this
Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae). / Kim, Ki-Joong; Choi, Keung Sun; Jansen, Robert K.
In: Molecular Biology and Evolution, Vol. 22, No. 9, 01.09.2005, p. 1783-1792.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae)
AU - Kim, Ki-Joong
AU - Choi, Keung Sun
AU - Jansen, Robert K.
PY - 2005/9/1
Y1 - 2005/9/1
N2 - The chloroplast DNA (cpDNA) inversion in the Asteraceae has been cited as a classic example of using genomic rearrangements for defining major lineages of plants. We further characterize cpDNA 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 end point of the smaller inversion is upstream of the trnE-UUC gene, and the other end point 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 end points are identified using comparative sequence alignments in the inversion regions. The phylogenetic distribution of two inversions is identical among the members of Asteraceae, suggesting that 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).
AB - The chloroplast DNA (cpDNA) inversion in the Asteraceae has been cited as a classic example of using genomic rearrangements for defining major lineages of plants. We further characterize cpDNA 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 end point of the smaller inversion is upstream of the trnE-UUC gene, and the other end point 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 end points are identified using comparative sequence alignments in the inversion regions. The phylogenetic distribution of two inversions is identical among the members of Asteraceae, suggesting that 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).
KW - Asteraceae
KW - Chloroplast DNA inversion
KW - Molecular clock
KW - Nonparametric rate smoothing
UR - http://www.scopus.com/inward/record.url?scp=23944506347&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=23944506347&partnerID=8YFLogxK
U2 - 10.1093/molbev/msi174
DO - 10.1093/molbev/msi174
M3 - Article
C2 - 15917497
AN - SCOPUS:23944506347
VL - 22
SP - 1783
EP - 1792
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
SN - 0737-4038
IS - 9
ER -