Newly developed primers for complete ycf1 amplification in Pinus (Pinaceae) chloroplasts with possible family-wide utility

American Journal of Botany

Volumn 98, Issue 7, 2011, Pages

  Parks, Matthew ^a   Liston, Aaron ^a   Cronn, Rich ^b  

^a OREGON STATE UNIVERSITY   (United States)

^b PACIFIC NORTHWEST RESEARCH STATION   (United States)

Author keywords

Chloroplast; Pinaceae; Pinus; Ycfl

Indexed keywords

PRIMER DNA;

CHLOROPLAST; CONIFEROUS TREE; GENETIC ANALYSIS; GENETIC MARKER; GENETIC VARIATION; PHYLOGENETICS; POLYMERASE CHAIN REACTION; RANGE SIZE;

ARTICLE; CHLOROPLAST; DNA SEQUENCE; ECOTYPE; GENE LOCUS; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PINE; POLYMERASE CHAIN REACTION;

CHLOROPLASTS; DNA PRIMERS; ECOTYPE; GENETIC LOCI; MOLECULAR SEQUENCE DATA; PINUS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

PINACEAE;

EID: 80054989952     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.1100088     Document Type: Article

References (9)

1. Cronn, R., A. Liston, M. Parks, D. S. Gernandt, R. Shen, and T. Mockler. 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Research 36: e122.
2. Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Research 8: 186-194.
3. Gernandt, D. S., S. Hernández-León, E. Salgado-Hernández, and P. l. Rosa. 2009. Phylogenetic relationships of Pinus subsection Ponderosae inferred from rapidly evolving cpDNA regions. Systematic Botany 34: 481-491.
4. Gernandt, D. S., G. Lopez, S. O. Garcia, and A. Liston. 2005. Phylogeny and classification of Pinus. Taxon 54: 29-42.
5. Hall, T. A. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
6. Librado, P., and J. Rozas. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics (Oxford, England) 25: 1451-1452.
7. Parks, M., R. Cronn, and A. Liston. 2009. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biology 7: 84.
8. Richterich, P. 1998. Estimation of errors in " raw " DNA sequences: A validation study. Genome Research 8: 251-259.
9. Wakasugi, T., J. Tsudzuki, S. Ito, K. Nakashima, T. Tsudzuki, and M. Sugiura. 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proceedings of the National Academy of Sciences, USA 91: 9794-9798.