Genomics / Proteomics
Duvall, Melvin R. , Leseberg, C. H. , Grennan, Colin P. .
Comparison of whole chloroplast genomes in grasses (Poaceae); Evolutionary insights related to Coix lacrymajobi, Microcalamus convallarioides, Puelia olyriformis and Joinvillea plicata.
Broad phylogenetic studies of plants are advancing due to the analysis of whole chloroplast genomes (plastomes). Investigations of plastomes within individual taxonomic families may also prove worthwhile. Here we present whole plastome analyses of three grasses, Coix lacrymajobi, Microcalamus convallarioides and Puelia olyriformis together with the outgroup Joinvillea plicata. More than 200 pairs of primers were designed in conserved regions of published grass plastomes. Primer pairs were positioned to flank overlapping 1200-base pair plastome fragments to facilitate assembly of complete sequences.
Concurrent with the relatively high sequence-conservation of the plastome is considerable cumulative variation that is useful for molecular evolutionary and phylogenetic studies within Poaceae. Readily interpreted mutational patterns were observed such as small inversions, a strong transition substitution bias and indels found within repeated regions that were suggestive of slipped-strand mispairings. Events altering gene expression, the size of the inverted repeats, and the overall sizes of plastomes were also observed.
Phylogenetic analyses were conducted on these and eight previously published plastomes. Maximum or near-maximum support was observed at all nodes in likelihood and branch and bound parsimony trees. Coix clustered with two species of Andropogoneae bearing bisexual florets and not with another monoecious andropogonid, confirming earlier work. The bambusoid/ehrhartoid/pooid (BEP) clade has not been consistently retrieved or strongly supported in any published analysis. Here, strong support was observed for the BEP clade that was not an artifact of the taxon-limited sampling. Issues left unresolved by the considerable efforts of the Grass Phylogeny Working Group, such as the positions of Streptogyna and Arundinaria, may be addressed with whole plastome data.
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Plastome data base
1 - Northern Illinois University, Department of Biological Sciences, Montgomery Hall, DeKalb, Illinois, 60115-2861, USA
2 - Northern Illinois Univesity, Department of Biological Sciences, Montgomery Hall, DeKalb, IL, 60115-2861, United States
complete plastome sequence
Grass Phylogeny Working Group.
Presentation Type: Oral Paper:Papers for Topics
Location: Boulevard A/Hilton
Date: Wednesday, July 11th, 2007
Time: 3:30 PM