Pacific Northwest Research Station

Title: Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines

Author: Whittall, J.B.; Syring, J.; Parks, M.; Buenrostro, J.; Dick, C.; Liston, A.; Cronn, R.

Date: 2010

Source: Molecular Biology. 19(Suppl. 1): 100-114

Description: Critical to conservation efforts and other investigations at low taxonomic levels, DNA sequence data offer important insights into the distinctiveness, biogeographic partitioning, and evolutionary histories of species. The resolving power of DNA sequences is often limited by insufficient variability at the intraspecific level. This is particularly true of studies involving plant organelles, as the conservative mutation rate of chloroplasts and mitochondria makes it difficult to detect polymorphisms necessary to track genealogical relationships among individuals, populations, and closely related taxa through space and time. Massively parallel sequencing (MPS) makes it possible to acquire entire organelle genome sequences to identify cryptic variation that would be difficult to detect otherwise. We are using MPS to evaluate intraspecific chloroplast-level divergence across biogeographic boundaries in narrowly endemic and widespread species of Pinus. We focus on one of the world's rarest pines--Torrey pine (Pinus torreyana)--owing to its conservation interest and because it provides a marked contrast to more widespread pine species. Detailed analysis of nearly 90 percent (~105 000 bp each) of these chloroplast genomes shows that mainland and island populations of Torrey pine differ at five sites in their plastome, with the differences fixed between populations. This is an exceptionally low level of divergence (1 polymorphism/~21 kb), yet it is comparable to intraspecific divergence present in widespread pine species and species complexes. Population-level organelle genome sequencing offers new vistas into the timing and magnitude of divergence within species, and is certain to provide greater insight into pollen dispersal, migration patterns and evolutionary dynamics in plants.

Keywords: chloroplast genome, multiplex sequencing-by-synthesis, next-generation sequencing, Pinus

View and Print this Publication (4.3 MB)

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.
• You may send email to pnw_pnwpubs@fs.fed.us to request a hard copy of this publication. (Please specify exactly which publication you are requesting and your mailing address.)

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

Citation

Whittall, J.B.; Syring, J.; Parks, M.; Buenrostro, J.; Dick, C.; Liston, A.; Cronn, R.  2010.  Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines.   Molecular Biology. 19(Suppl. 1): 100-114.