Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

Matthew Parks; Richard Cronn; Aaron Liston

doi:10.1186/1741-7007-7-84

Treesearch

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

Formally Refereed

Authors:

Matthew Parks, Richard Cronn, Aaron Liston

Year:

2009

Type:

Scientific Journal

Station:

Pacific Northwest Research Station

DOI:

https://doi.org/10.1186/1741-7007-7-84

Source:

BMC Biology. 7(84). 17 p

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Abstract

We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome) generated using multiplexed massively parallel sequencing. We found that 30/33 ingroup nodes resolved wlth > 95-percent bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high-quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve Pinus, particularly in rapidly radiating clades. Metaanalysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera.

Keywords

Pinus, chloroplast genome, massively parallel sequencing, multiplex DNA sequencing, phylogenomics

Citation

Parks, M.; Cronn, R.; Liston, A. 2009. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biology. 7(84). 17 p.