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The D4 set: primers that target highly variable intron loops in plant chloroplast genomes
Author(s) -
WATTS CHAD D.,
FISHER AMANDA E.,
SHRUM CELENA D.,
NEWBOLD WENDY L.,
HANSEN SHANNALEE,
LIU CHANG,
KELCHNER SCOT A.
Publication year - 2008
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/j.1755-0998.2008.02229.x
Subject(s) - biology , genome , chloroplast , intron , genetics , computational biology , set (abstract data type) , gene , computer science , programming language
Chloroplast group II introns offer high‐quality, rapidly evolving single‐copy loci for comparative sequence analysis. These introns feature diagnostic secondary structures with loops that are among the least evolutionarily constrained sequence in plastomes. We exploited these structures to develop universal primers that amplify and sequence the large Domain IV (D4) loop in several angiosperm introns. With a single sequence read, we recover 300–600 nucleotides of highly variable sequence across angiosperms, with rates of change that are equal to or higher than many of the best known intergenic spacers in plant chloroplast genomes.