Using Genomics to Study Evolutionary Origins of See ds

Today’s gymnosperms are relicts from groups of plants whose history extends to nearly 300 million years ago when seeds first evolved. Consequently gymnosperms have been studied in relation to the fossil record to uncover important clues to understand the appearance and evolution of seeds and pollen. Extant gymnosperms are restricted to four surviving orders: the Gnetales, Coniferales, Ginkgoales and Cycadales, providing a marvelous biological source of data which has only recently been examined at the molecular level. Efforts to understand the molecular evolution of the gymnosperms has examined the expression of gymnosperms genes with similarity to genes in angiosperms involved in the development of leaves and reproductive structures via a degenerate based primer approach. Lately, genomic approaches have been engaged to understand what genes are involved in the evolution and development of gymnosperm structures. Below is a description of genomic and molecular studies currently to understand evolution in the gymnosperms. 1. THE RISE OF THE SEED PLANTS The emergence of the seed plants is among one of the most significant developments to occur in the evolution of terrestrial plants (FOSTER and GIFFORD 1974)). Through dramatic changes in reproductive strategies, the seed plants (spermatophytes), which include the angiosperms and gymnosperms, were able to overcome one of the key barriers to reproductive efficiency. In non-seed plants, such as ferns, the gametophyte is photosynthetic, free living (exosporic) and not vascularized. Consequently fertilization can only occur in wet environments where flagellated gametes can swim from their source, the antheridia, to the archegonia to fertilize the egg. Because of their dependence on water mediated fertilization, hybridization in non-seed plants can occur only between close neighboring individuals as swimming sperm can only travel short distances. In contrast to non-seed plants, the seed plant megametophyte is retained within the spore wall (endosporic) and also within the maternal tissue. That is the megagametophyte is contained within the diploid integuments to form the ovule (Figure 1). Gamete transfer does not require water as a medium but rather it is the male gametophyte that is transferred. The male microgametophyte in seed plants is transported as a desiccation-resistant pollen grain directly to the ovule (or ovule enclosing carpel), often many miles away. Upon reaching the female reproductive structure, a tube grows from the pollen, subsequently bringing the male gamete to the female gametophyte and ultimately to the egg. Similar to the pollen grain, the female gametophyte is also dessication C. G. Williams (ed.), Landscapes, Genomics and Transgenic Conifers, 85-106. resistant via protection by diploid tissue, the nucellus and integuments. The megagametophyte is no longer free-living, or photosynthetic and must receive nutrients from the vascularized, sporophytic parent during its development. The megagametophyte remains dependent on the maternal parent during pollination and later while the pollen tube is growing prior to fertilization. In most cases fertilization occurs while the megagametophyte is attached to the sporophyte, while in the oldest surviving seed plants fertilization occurs after the ovule has been shed, such as in cycads and gingko. Upon fertilization the ovule becomes a seed. Within the seed, the megagametophyte function has been modified to serve primarily as nutrient storage tissue to sustain the developing embryo (In the angiosperms nutritive tissue typically comes from other tissue types including endosperm and cotyledons, while in gymnosperms nutrition primarily comes from the gametophyte). Upon maturity the seed becomes dehiscent and subsequently transported (by biotic or non-biotic sources) to a new locale with the possibility of finding favorable growing conditions. Consequently the mature seed consists of three generations: the maternal sporophyte, the gametophyte and the new embryonic sporophyte. Thus the ovule/seed is a major developmental innovation that enables long distance fertilization as well as dispersal of a diaspore containing both the embryo and storages tissue for its establishment in a process unique in land plants. In addition to their important role enabling long distance fertilization, seeds are fundamentally important for humans. Seeds provide food, fiber and industrial goods. Considering their importance to society, a better understanding of the origins of seeds requires innovative studies to explain seed evolution. The oldest surviving seed plants are the gymnosperms, which exhibit a number of plesiomorphic (ancient) conditions reminiscent of the early fossil seed plants. Gymnosperms are hypothesized to have descended from the progymnosperms (ROTHWELL 1988), which date back in the fossil record to approximately 285-350 MYA (ROTHWELL and SCHECKLER 1988) to 359-385 MYA (TAYLOR and TAYLOR 1993). One theory contends that the original gymnosperms were the seed ferns (FOSTER and GIFFORD 1974). The last common ancestor of extant seed plants and extant ferns is estimated by molecular clocks to have existed approximately 275-290 MYA (SAVARD et al., 1994). When molecular clock estimates include fossil calibration points, gymnosperms age ranges from 345 to 360 MYA depending on whether lycophyte or gymnosperm fossils, respectively, are used as calibration points estimations exists spanning nearly 100 million years. The discovery of new fossils from extinct gymnosperms and expanded molecular clock studies with deeper sequencing initiatives should help narrow this estimation gap. 1.1. Today’s gymnosperms: remnants of early seed plants Conflicting results between morphological and molecular data sets have made it difficult to define the precise phylogenetic hierarchy of the four extant gymnosperm clades: the Gnetales, Coniferales, Ginkgoales and Cycadales (DOYLE 1998; MAGOLLON and SANDERSON 2002; RYDIN et al., 2002). Among the gymnosperms, (SOLTIS et al., 2002b). Thus, considerable variation in gymnosperm age 86 E.D. BRENNER AND D. STEVENSON