Evolution of Chloroplast Genomes in Gymnosperms and Insights Into the Phylogeny of Seed Plants

Evolution of chloroplast genomes in gymnosperms and insights into the phylogeny of seed plants

Shu-Miaw Chaw1 趙淑妙 ([email protected])

Research Center for Biodiversity, Academia Sinica, Taiwan

Chloroplasts where photosynthesis takes place have distinct functional genomes from those of mitochondria and nucleus. The chloroplast genomes (cpDNAs) were derived from cyanobacteria via endosymbiosis. Modern cpDNAs contain only about 5-10% as many genes as those of their free-living cousins, because majority of chloroplast genes have been lost or transferred to the nucleus during the course of evolution. Gymnosperms comprise ca. 1000 living species in four orders (Cycadales, Ginkgoales, Gnetales, and Pinales) and 24 families. They are inextricably linked to the origins and early divergence of seed plants. By far, nearly 35 cpDNAs of flowering plants have been completely sequenced, but only two of them were gymnosperms (both are the Pinus). We have determined and analyzed the surprising structures of two cpDNAs of gymnosperms, Cycas taitungensis (Taitung cycad; a rare species confined to mountain valleys of eastern Taiwan) and a representative of Gnetales, Gnetum parvifolium (a vine confined to southern China). In the cpDNA organization Cycas is more similar to ferns than to pines. An ancient signature of tufA gene is first reported in the cpDNAs of cycads, Ginkgo, and Anthoceros (a hornwort). On the other hand, both cpDNAs of pines and Gnetales resemble each other in the loss of all ndh genes and shift of IR/LSC junctions, which suggests a close relationship between Gnetales and Pinales. A new view of the lost of one IR in the Pinus is proposed. Our phylogenetic analyses of a larger cpDNA dataset (37 taxa) further strengthen the view that extant gymnosperms constitute a monophyletic clade and the seeds evolved only once. We demonstrate that comparative cpDNA organization is a very powerful tool for reconstructing ancient evolutionary relationships in seed plants. Our lab is currently expanding the survey of cpDNAs across the diversified gymnosperms for a better understanding of the evolution of organellar genes and gene orders, and for addressing questions in seed plant phylogeny.