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Ebb and flow of the chloroplast inverted repeat
S E Goulding1, R G Olmstead, C W Morden
1Department of Genetics, University of Dublin, Trinity College, Ireland.
Molecular & General Genetics : MGG
|August 27, 1996
Summary
Chloroplast DNA inverted repeats (IR) endpoints vary in flowering plants. This study quantifies IR movement in Nicotiana species, revealing gene conversion for small expansions and a large rearrangement in Nicotiana acuminata.
Area of Science:
- Molecular Biology
- Plant Genetics
- Evolutionary Biology
Background:
- The large inverted repeat (IR) regions of chloroplast DNA exhibit variations in their endpoints among flowering plant species.
- Understanding these variations is crucial for elucidating the mechanisms of IR expansion and contraction.
Purpose of the Study:
- To quantify the extent of IR endpoint variation in Nicotiana species and other dicots.
- To investigate the mechanisms driving IR expansion and contraction.
- To analyze the IR-large single-copy (IR-LSC) junction rearrangements.
Main Methods:
- Comparative DNA sequencing of IR-LSC junctions across 13 Nicotiana species and other dicots.
- Phylogenetic analysis using restriction site data.
- Identification and characterization of gene structures, including truncated genes like rps19'.
Main Results:
- Most Nicotiana species show IR termination within or upstream of the rps19 gene, with variable rps19' lengths.
- Phylogenetic analysis indicates both IR expansion and contraction within the Nicotiana genus.
- A significant 12 kb IR expansion was identified in Nicotiana acuminata, involving a rearrangement within the clpP gene.
Conclusions:
- Gene conversion is proposed as a mechanism for small, seemingly random IR expansions in Nicotiana.
- A large-scale IR expansion in Nicotiana acuminata occurred via double-strand DNA break and recombination.
- Nicotiana acuminata preserves evidence of a previous IR-LSC junction, acting as a molecular fossil.