The chloroplast genome of the gymnosperm Pinus contorta: a physical map and a complete collection of overlapping clones

Abstract

Summary Overlapping restriction fragments of chloroplast DNA from the conifer Pinus contorta were cloned. Out of a total of 49 clones, 33 comprise the minimum set required to represent the entire genome. Using the purified inserts of these clones as probes in filter hybridizations, all sites for the three restriction enzymes KpnI, HapI and SacI in the P. contorta chloroplast genome were mapped. Heterologous filter hybridizations and sequence analysis of some of the P. contorta clones were used to determine the position of 15 genes on the restriction map. The size of the genome, which lacks an inverted repeat organization, was found to be approximately 121 kilobase pairs (kbp). Unusual features of this genome are a duplication of the psbA gene and the presence of two genes, gidA and frxC, which are not found in angiosperms. The genome appeared essentially colinear with that of Pinus radiata, for which a map has previously been published. Two different restriction fragment length polymorphisms were found to be produced by variable numbers of copies of 124 bp-and 150 bp-long, tandemly repeated elements.