Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae).
OBJECTIVE
Complete chloroplast genome studies can help resolve relationships among large, complex plant lineages such as Asteraceae. We present the first whole plastome from the Madieae tribe and compare its sequence variation to other chloroplast genomes in Asteraceae.


METHODS
We used high throughput sequencing to obtain the Lasthenia burkei chloroplast genome. We compared sequence structure and rates of molecular evolution in the small single copy (SSC), large single copy (LSC), and inverted repeat (IR) regions to those for eight Asteraceae accessions and one Solanaceae accession.


RESULTS
The chloroplast sequence of L. burkei is 150 746 bp and contains 81 unique protein coding genes and 4 coding ribosomal RNA sequences. We identified three major inversions in the L. burkei chloroplast, all of which have been found in other Asteraceae lineages, and a previously unreported inversion in Lactuca sativa. Regions flanking inversions contained tRNA sequences, but did not have particularly high G + C content. Substitution rates varied among the SSC, LSC, and IR regions, and rates of evolution within each region varied among species. Some observed differences in rates of molecular evolution may be explained by the relative proportion of coding to noncoding sequence within regions.


CONCLUSIONS
Rates of molecular evolution vary substantially within and among chloroplast genomes, and major inversion events may be promoted by the presence of tRNAs. Collectively, these results provide insight into different mechanisms that may promote intramolecular recombination and the inversion of large genomic regions in the plastome.
Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907 USA.
Joseph F
JF
Walker
Michael J
MJ
Zanis
Nancy C
NC
Emery
D019659:Asteraceae / Q000235:genetics*; D007446:Chromosome Inversion; D019143:Evolution, Molecular; D014644:Genetic Variation; D054628:Genome, Chloroplast; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA
Asteraceae; Lasthenia burkei; Madieae; intramolecular recombination; inversion; phylogenetics; plastome; whole chloroplast genome