Skip to page content
USDA Forest Service

Research & Development Treesearch

Treesearch Home
About Treesearch
Contact Us
Research & Development
Forest Products Lab
International Institute of Tropical Forestry
Pacific Northwest
Pacific Southwest
Rocky Mountain
Southern Research Station
Help - We Participate  Government Made Easy

Global Forest Information Service

US Forest Service
P.O. Box 96090
Washington, D.C.

(202) 205-8333

You are here: Home / Search / Publication Information
Bookmark and Share

Publication Information

View PDF (783 KB)

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

Author: Parks, Matthew; Cronn, Richard; Liston, Aaron;

Date: 2009

Source: BMC Biology. 7(84). 17 p

Publication Series: Scientific Journal (JRNL)

Description: 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

Publication Notes:

  • We recommend that you also print this page and attach it to the printout of the article, to retain the full citation information.
  • This article was written and prepared by U.S. Government employees on official time, and is therefore in the public domain.



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.


 [ Get Acrobat ]  Get the latest version of the Adobe Acrobat reader or Acrobat Reader for Windows with Search and Accessibility

USDA logo which links to the department's national site. Forest Service logo which links to the agency's national site.