The "typical" plant about which we biology professors often pontificate does not exist: It is a fictional entity we have created in our feeble attempts to bring order and simplicity to the amazing complexity and diversity presented by the plant world. Nevertheless, in this post-genomic era, rice (Oryza sativa) and Arabidopsis are often presented as examples of a "typical" monocot and a "typical" dicot, respectively. While the genomic analyses of model systems such as Arabidopsis and rice have provided profound insights into the molecular functions of these two species, and by extrapolation, of plant species in general, it is important to realize that the intensive study of these model systems also has its limitations. Consider Arabidopsis: This "typical" dicot has its share of peculiar adaptations. For example, unlike most angiosperms, Arabidopsis does not form mycorrhizal associations. Or consider Arabidopsis's chemical defense strategy: Glucosinolates are the chief weapon in its chemical arsenalnot flavonoids, as are used by most other angiosperms. Although the absence of these two typical plant adaptations might be viewed as peculiarities of an otherwise typical dicot, there are, in fact, many important physiological processes in the plant kingdom that Arabidopsis, with its limited repertoire of adaptations, cannot be used to address. For example, what can the study of Arabidopsis teach us about the physiology of tuberization, or the resumption of cambial activity in spring, or the beating of flagella, or C4 photosynthesis, or the biochemistry of nodule function? The answer is, "Not much."

Arabidopsis is, and will continue to be, an immensely important model system in plant biology, and as such, Plant Physiology will continue in the foreseeable future to devote many of its pages to cutting-edge research that uses Arabidopsis as a model system. But Plant Physiology is not and never will be the Journal of Arabidopsis Research. Clearly, Arabidopsis is an inferior, or even an impossible, system for studying many important plant processes. In such instances, plant scientists should not hesitate to seek alternative model organisms even though the molecular biology of these alternative species is less completely known or absent. Our Journal will continue to publish the widest scope of plant-related articles executed at the highest level regardless of the model system employed. As might be expected, in the excitement of the first year of the post-genomic era, many important research advances not employing the "genome-completed" species have not received as much attention as they rightfully deserve. This Special Issue, a Celebration of Plant Diversity, is an attempt to remedy this imbalance.

Several of the updates included in this Special Issue are devoted to the specific interactions that certain plant species have with other living organisms that cannot be studied in Arabidopsis. Gadkar et al. (pp. 1493-1499) discuss the subtle shades of host specificity and host recognition that mediate the development of arbuscular-mycorrhizal symbioses and the value of mutants in understanding how these phosphate-acquiring associations arise. Hirsch et al. (pp. 1484-1492) address the question of what is so special about the Rhizobia-legume symbiosis that the development of N₂-fixing nodules is almost exclusively restricted to these two organisms. Keyes et al. (pp. 1508-1512) summarize the advances that have been made in understanding how parasitic plants sense and invade their host plants.

Other contributions are devoted to the molecular biology of plant diseases that are also best studied in a diversity of plant model systems. Scholthof (pp. 1476-1483) focuses on the interactions of pathogenic fungi, bacteria, and viruses with their respective natural plant hosts. Fluhr (pp. 1367-1374) summarizes our knowledge of plant resistance (R) genes that code for the cellular factors participating in recognition of the invading pathogens. The rapid evolution of R-genes makes species-specific studies mandatory.

Many plants have evolved marvelous adaptations to counter various abiotic stresses they encounter in extremis in their specific environments. Bressan et al. (pp. 1354-1360) suggest using salt cress (Thellungiella halophila) as a model plant to study extreme salt stress tolerance. Bartels and Salamini (pp. 1346-1353) provide many reasons why Craterostigma plantagineum is a promising experimental system for understanding the molecular and biochemical events that are involved in extreme desiccation tolerance. The adaptations that plants have evolved to biotic stresses can also be quite species specific. Building upon recent exciting work on the native annual Nicotiana attenuata, Baldwin (pp. 1449-1458) analyzes the defense responses induced by wounding in this species and argues the need for placing our new molecular understanding of the complex signaling cascades engaged in responses to herbivore attack into an ecological context. Sometimes the simultaneous study of many different species can also expedite our elucidation of biochemical processes, as Winkel-Shirley (pp. 1399-1404) illustrates in her discussion of how a variety of systems have helped to unravel flavonoid biosynthesis in plants.

Plants have a diversity of carbon fixation pathways that cannot be adequately addressed using C3 model systems such as rice or Arabidopsis. Cushman (pp. 1439-1448) compares different potential model systems for Crassulacean acid metabolism research. Ueno (pp. 1524-1532) describes the effect of transitions between waterlogged and non-waterlogged conditions on the differentiation of photosynthetic characteristics in the amphibious sedge Eleocharis vivipara. The switch between C3 and C4 photosynthetic modes involves complex structural and biochemical transitions, and E. vivipara provides an attractive model to study the underlying molecular mechanisms and signaling networks.

The species-isolating mechanisms of plant reproduction have also provided enormous diversity within the plant kingdom. Dieocy is widespread among angiosperms and offers a system to study the evolution of sex chromosomes. Chromosomal sex determination systems in plants have evolved independently many times and include both heteromorphic XY and X:A (X chromosome:autosome ratio) systems. In his contribution, Negrutiu (pp. 1418-1424) concentrates on Silene latifolia, where cytogenetic and molecular studies suggest a recent origin of the XY system, offering the opportunity to study early steps in the evolution of heteromorphic sex determination systems. The genetic control mechanisms for the photoperiodic flowering response has been extensively studied in the long-day plant Arabidopsis. The recent progress in genome analysis of rice has opened new possibilities to study the control of flowering time in a short-day plant, where many insights have come from the study of natural variation and quantitative trait loci analyses. Interestingly, as discussed by Yano et al. (pp. 1425-1429), many of the genes involved in the control of flowering time involved in these distinct photoperiodic responses are remarkably similar at the molecular level. Vainstein et al. (pp. 1383-1389) examine how the unique and complex signatures of floral scent necessitate the integration of modern techniques with non-conventional model systems, such as flowers of Clarkia breweri, snapdragon (Antirrhinum majus), and rose (Rosa hybrida), which are useful not for their ease of molecular study, but for their fragrance characteristics and amenability to chemical and biochemical analyses. Yu and Goh (pp. 1390-1393) make the case in favor of using orchids to study plant reproduction.

The morphological adaptations of certain plant species are often so unique or exaggerated, or are just not present in Arabidopsis, that they may only be adequately studied in the species that possess them. Fernie and Willmitzer (pp. 1459-1465) discuss tuber development in potato (Solanum tuberosum) as an example of a developmental process that cannot be studied in the currently sequenced model plant systems. Similarly, Kim and Triplett (pp. 1361-1366) summarize our knowledge of the molecular biology of cotton fiber synthesis and argue that cotton fibers provide an excellent system for studying cell wall biosynthesis in general. Bharathan and Sinha (pp. 1533-1538) discuss the role of KNOX1, LORICAULA/LEAFY, and PHANTASTICA in leaf development and discuss their role in compound leaf evolution.

Many of the attributes of the perennial growth habit, such as wood formation and dormancy, also cannot be studied in rice and Arabidopsis. Plomion et al. (pp. 1513-1523) argue that trees remain the best system for testing models of xylogenesis and cambial activity, and the molecular biology underlying seasonal cycles of dormancy, wood maturation, and heartwood production. Shimizu-Sato and Mori (pp. 1405-1413) summarize the regulation and possible mechanisms of axillary bud formation and dormancy in a variety of plant species.

Several articles discuss the advantages and disadvantages of "single-cell" or "isolated tissue" systems. Geelen and Inzé (pp. 1375-1379) remind the reader of the utility of tobacco (Nicotiana tabacum) BY suspension cultured cells, and Sheen (pp. 1466-1475) provides a very convincing case in favor of using maize (Zea mays) and Arabidopsis mesophyll protoplasts, in combination with transgenetic and genetic approaches, to study signal transduction. She offers many examples of how studies using protoplast systems can provide a framework for whole plant analysis of tissue- or cell-type-specific pathways in knockout mutants and transgenic plants. McCann et al. (pp. 1380-1382) discuss how studies of isolated tissue of non-woody plants, most notably Zinnia, are useful for understanding the molecular biology of xylem formation

Development regulation is another area of study in which some plant species may prove to be more amenable to study than rice or Arabidopsis. In contrast to angiosperms, pines and other gymnosperms form well-developed suspensors in somatic embryogenic cultures. This creates a useful system for studying suspensor development. In a study of gene expression during the early stages of conifer embryogenesis, Ciavatta et al. (pp. 1556-1567) identify a transcript that is abundant in immature Pinus taeda zygotic and somatic embryos, but which is undetectable in later-stage embryos, megagametophytes, and roots, stems, and needles from 1-year-old seedlings. This transcript encodes an aquaglyceroporin that is highly expressed in the suspensor of P. taeda. As a further example of how it is often not possible to extrapolate from a model species to other organisms, Li et al. (pp. 1414-1417) provide evidence that jasmonic acid (JA) plays an important role in female reproductive development in tomato (Lycopersicon esculentum). This is in contrast to the situation in Arabidopsis, where JA signaling regulates male (but not female) gametophyte development.

Lower plants also afford convenient or unique systems for the study of certain processes in plants. Zurzolo and Bowler (pp. 1339-1345) review many interesting features related to the formation of the diatom cell wall during the most unusual cytokinesis that normally occurs in these species. The advantages and disadvantages of Chlamydomonas as a model system are discussed by Rochaix (pp. 1394-1398), Hicks et al. (pp. 1334-1338), and Silflow and Lefebvre (pp. 1500-1507).

With the completion of the Arabidopsis genome, and emerging sequences of important crop plants in progress, some plant biologists are pondering which plant genomes should be decoded next. Daly et al. (pp. 1328-1333) argue that plant systematics should be used to identify which genomes in the plant kingdom should be searched, sampled, and studied, especially for comparative genomics and phylogenetics. Draper et al. (pp. 1539-1555) propose that Brachypodium distachyon be embraced as a new model grass system for functional genomic studies. Like Arabidopsis, it has a small genome (approximately 125 Mb), a relatively short life cycle, and a small size (approximately 20 cm at maturity), in addition to many other desirable features. Schaefer and Zrd (pp. 1430-1438) remind us that mosses are one of the oldest groups of land plants that colonize extremely diverse habitats. The dominant haploid gametophyte has a simple developmental pattern and similar responses to plant growth factors and environmental stimuli as observed in other land plants. Mutant phenotypes can be easily isolated, and the development of gene-targeting strategies has quickly made Physcomitrella patens a system of choice for functional genomics.

The creation and planning of this Special Issue has drawn on the expertise of many of our editors. In particular, we would like to thank Steve Ball, Carlos Ballare, Vitaly Citovsky, Gloria Coruzzi, Ueli Grossniklaus, Wilhelm Gruissem, Ann Hirsch, Martin Hulskapm, and Susan Wessler for their expeditious processing of the manuscripts and thoughtful comments and suggestions concerning this Special Issue and its particular contributions. Special Issues, of course, require an even greater effort than usual on the already hard-worked publication staff of Plant Physiology, most notably, Melissa Junior, Lauren Ransome, Leslie Malone, and Ash Csikos. We are also very grateful to Mrs. Tu Qin, who has helped with this and many other issues here at the Plant Research Laboratory, Michigan State University. We cannot thank all these people enough for their professionalism and commitment to our Journal.