| Structure and organization of land plant chloroplast (cp) DNA is considered highly conserved but few groups have been examined. Aspects of the basic structure and organization, primarily gene order and characteristics of the large inverted repeat, were determined in this study for the chloroplast genomes of representatives of each major extant lineage of vascular land plant: Lycopodium, Selaginella, Isoetes, Equisetum, Psilotum, Botrychium, Marattia, Osmunda, Lygodium, Ginkgo, many conifers, Cycas, Encephalartos, Gnetum, Ephedra, and Welwitschia. Comparisons to bryophyte and angiosperm chloroplast DNA (cpDNA) were made based on the published work of others. Osmunda, Adiantum, Ginkgo, and conifers in the family Pinaceae were the only non-angiosperm vascular plant cpDNAs previously characterized.; Strategies were developed to rapidly assess the distribution of structural variants. Physical maps were also generated for some regions of the genome. Data were collected to determine: (1) the distribution of the 30-kbp inversion that differentiates the cpDNA gene order of tobacco and liverwort, (2) the pattern of gene duplications during the extension of the inverted repeat, (3) the pattern of loss of one copy of the inverted repeat in conifer cpDNA, and (4) the distribution of inversions within conifers. The 30-kbp inversion data support the basal placement of the lycopsids within vascular plants and contradict the basal placement of the psilopsids. An unusual derived condition, the anomolous position of ORF2280, is found linking Ginkgo and cycads. The loss of the inverted repeat throughout conifers supports the monophyly of the group, including Taxaceae. Gene duplication data support monophyly of Gnetales and a Gnetales-angiosperm sister-group relationship. |
