Evolution of chloroplast genomes in gymnosperms and
insights into the phylogeny of seed plants
Shu-Miaw Chaw1 趙淑妙 (smchaw@sinica.edu.tw)
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.