Newly developed primers for complete ycf1 amplification in Pinus (Pinaceae) chloroplasts with possible family-wide utility
Author(s)
Parks, M
Liston, A
Cronn, R
Griffith University Author(s)
Year published
2011
Metadata
Show full item recordAbstract
堐remise of the study: Primers were designed to amplify the highly variable locus ycf1 from all 11 subsections of Pinus to facilitate plastome assemblies based on short sequence reads as well as future phylogenetic and population genetic analyses. 堍ethods and Results: Primer design was based on alignment of 33 Pinus and four Pinaceae plastomes with mostly incomplete ycf1 sequences. Sanger sequencing of 12 Pinus accessions resulted in open reading frames ranging in size from 5.2 to 6.1 kbp. Highest sequence diversity was identified in two regions totaling 5.5 kbp aligned length, which can be targeted in all pine subsections ...
View more >堐remise of the study: Primers were designed to amplify the highly variable locus ycf1 from all 11 subsections of Pinus to facilitate plastome assemblies based on short sequence reads as well as future phylogenetic and population genetic analyses. 堍ethods and Results: Primer design was based on alignment of 33 Pinus and four Pinaceae plastomes with mostly incomplete ycf1 sequences. Sanger sequencing of 12 Pinus accessions resulted in open reading frames ranging in size from 5.2 to 6.1 kbp. Highest sequence diversity was identified in two regions totaling 5.5 kbp aligned length, which can be targeted in all pine subsections with three primer combinations. Preliminary results suggest the primers described also amplify homologous targets in the broader Pinaceae. 堃onclusions: The successful design and implementation of PCR primers spanning the large, variable locus ycf1 in Pinus represents the development of a valuable tool in pine genetic studies, and should facilitate studies throughout Pinaceae.
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View more >堐remise of the study: Primers were designed to amplify the highly variable locus ycf1 from all 11 subsections of Pinus to facilitate plastome assemblies based on short sequence reads as well as future phylogenetic and population genetic analyses. 堍ethods and Results: Primer design was based on alignment of 33 Pinus and four Pinaceae plastomes with mostly incomplete ycf1 sequences. Sanger sequencing of 12 Pinus accessions resulted in open reading frames ranging in size from 5.2 to 6.1 kbp. Highest sequence diversity was identified in two regions totaling 5.5 kbp aligned length, which can be targeted in all pine subsections with three primer combinations. Preliminary results suggest the primers described also amplify homologous targets in the broader Pinaceae. 堃onclusions: The successful design and implementation of PCR primers spanning the large, variable locus ycf1 in Pinus represents the development of a valuable tool in pine genetic studies, and should facilitate studies throughout Pinaceae.
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Journal Title
American Journal of Botany
Volume
98
Issue
7
Subject
Ecology
Evolutionary biology
Plant and fungus systematics and taxonomy
Plant biology