Skip to page content
USDA Forest Service
  
Treesearch

Research & Development Treesearch

 
Treesearch Home
About Treesearch
Contact Us
Research & Development
Forest Products Lab
International Institute of Tropical Forestry
Northern
Pacific Northwest
Pacific Southwest
Rocky Mountain
Southern Research Station
Help
 

Science.gov - We Participate


USA.gov  Government Made Easy


Global Forest Information Service

US Forest Service
P.O. Box 96090
Washington, D.C.
20090-6090

(202) 205-8333

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

Publication Information

View PDF (317 KB)

Title: Multiplexed fragaria chloroplast genome sequencing

Author: Njuguna, W.; Liston, A.; Cronn, R.; Bassil, N.V.;

Date: 2010

Source: ISHS Acta Horticulturae 859: 315-321

Publication Series: Scientific Journal (JRNL)

Description: A method to sequence multiple chloroplast genomes using ultra high throughput sequencing technologies was recently described. Complete chloroplast genome sequences can resolve phylogenetic relationships at low taxonomic levels and identify informative point mutations and indels. The objective of this research was to sequence multiple Fragaria chloroplast genomes using the Illumina Genome Analyzer. Sixty-three PCR fragments from 22 species were sequenced in four multiplex sequencing runs. Plastome sequences were assembled using a combination of de novo and reference guided assembly with F. vesca ‘Hawaii 4’ providing the reference. De novo assembly resulted in plastome coverage of 43-74%, and reference guided assembly increased the plastome coverage to 76-82%. The alignment of sequenced chloroplast genomes was 96,438 bp and contained 319 parsimony-informative sites which will be useful in identifying chloroplast genome regions of high sequence variation for testing evolutionary relationships.

Keywords: high-throughput sequencing, polyploidy, reference genome, sequence alignments, microreads

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.

XML: View XML

Citation:


Njuguna, W.; Liston, A.; Cronn, R.; Bassil, N.V. 2010. Multiplexed fragaria chloroplast genome sequencing. In: Basil, N.V.; Martin, R., eds. International Symposium on Molecular Markers in Horticulture. ISHS Acta Horticulturae 859: 315-321.

 


 [ 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.