Matyas Buzgo

Floral gene resources from basal angiosperms for comparative genomics research

BackgroundThe Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and under intensive comparative genomic investigation, are separated by at least 125 million years of evolutionary time, and cannot in isolation provide a comprehensive perspective on structural and functional aspects of flowering plant genome dynamics. Here we discuss new genomic resources available to the scientific community, comprising cDNA libraries and Expressed Sequence Tag (EST) sequences for a suite of phylogenetically basal angiosperms specifically selected to bridge the evolutionary gaps between model plants and provide insights into gene content and genome structure in the earliest flowering plants.ResultsRandom sequencing of cDNAs from representatives of phylogenetically important eudicot, non-grass monocot, and gymnosperm lineages has so far (as of 12/1/04) generated 70,514 ESTs and 48,170 assembled unigenes. Efficient sorting of EST sequences into putative gene families based on whole Arabidopsis/rice proteome comparison has permitted ready identification of cDNA clones for finished sequencing. Preliminarily, (i) proportions of functional categories among sequenced floral genes seem representative of the entire Arabidopsis transcriptome, (ii) many known floral gene homologues have been captured, and (iii) phylogenetic analyses of ESTs are providing new insights into the process of gene family evolution in relation to the origin and diversification of the angiosperms.ConclusionInitial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage-specific gene duplication and functional divergence, and analyses of adaptive molecular evolution. Since not all genes in the floral transcriptome will be associated with flowering, these EST resources will also be of interest to plant scientists working on other functions, such as photosynthesis, signal transduction, and metabolic pathways.

Floral Developmental Morphology of Amborella trichopoda (Amborellaceae)

We investigated the early floral development of the monotypic genus Amborella, the sister to all other extant angiosperms. Examination of vegetative shoot development revealed that Amborella possesses both decussate and alternate phyllotaxy; one may simply be a special case of the other as a reaction to meristem size and shape. The transition from bracts to tepals is gradual, making it difficult to determine exactly where a flower begins in this species. Although flowers of Amborella are described as having spiral phyllotaxy, the periphery of the flower could be considered unidirectionally whorled. This new observation, together with observations of both spiral and whorled phyllotaxy in other basal angiosperms (e.g., Nuphar, Drimys, Ceratophyllum), further demonstrates the flexibility of floral development in basal angiosperms; i.e., some basal angiosperms are not fully committed to either spiral or whorled phyllotaxy. The developmental transitions between bracts and perianth, and between stamens and carpels, are continuous. However, the transition between perianth and sporophylls is more distinct, although tepals, stamens, and carpels appear to be structurally homologous. Both stamens and carpels share characteristics of the other sexual organ. We hypothesize that genes correlated with stamen identity (e.g., B‐class MADS‐box genes) may show a gradual change in expression pattern throughout the floral parts of Amborella and perhaps other basal angiosperms, corresponding to the observed gradual morphological transitions. This “fading borders” model of floral gene expression should be evaluated in Amborella and other basal angiosperms.

FLORAL STRUCTURE AND DEVELOPMENT OF ACORACEAE AND ITS SYSTEMATIC RELATIONSHIPS WITH BASAL ANGIOSPERMS

Flower development and anatomy of Acorus calamus and flower anatomy of A. gramineus were studied. Findings were compared with published reports on paleoherbs. Important developmental features include an abaxially median tepal that is initiated first and is similar to a flower‐subtending bract and unidirectional flower development with an inversion of organ initiation sequence in the second tepal whorl. The mature gynoecium is largely synascidiate, but early development of carpels is plicate, and the apocarpous portion persists up to anthesis. The carpels form dorsal bulges on the style, enclosing longitudinal intercarpellary slits. The dominance of the synascidiate portion and the apical position of the placenta result from a late and distinct basal elongation of the gynoecium. Stigma, pollen transmitting tract, and ovary are filled with secretion. Secretory papillae are present from the stigma to the placenta; papillae also occur on the rims of the integuments of the ovules. In the uppermost part of the inflorescence, the adaxial floral sectors are reduced in number and structure, and at the apex of the inflorescence, a peloria‐like structure is formed. Developmental and morphological similarities seem to be closer between Acorus and Piperales than between Acorus and other magnoliids.

Sequence and Expression Studies of A‐, B‐, and E‐Class MADS‐Box Homologues in Eupomatia (Eupomatiaceae): Support for the Bracteate Origin of the Calyptra

Eupomatia (Magnoliales, Eupomatiaceae) has flowers that bear a calyptra, an unusual organ that encloses the floral bud. The structural homology and evolutionary derivation of the calyptra are unknown, although some have proposed that it is a bract, while others favor a derivation from the perianth. To address the evolutionary origin of the calyptra, we isolated, sequenced, and characterized the expression of A‐, B‐, and E‐class MADS‐box homologues from Eupomatia bennettii and a close relative, Magnolia grandiflora (Magnoliaceae). The expression patterns of organ identity genes in floral organs of Eupomatia and Magnolia were very similar. However, the expression patterns of these MADS‐box genes indicated that the ABC model is not strictly applicable to either Eupomatia or Magnolia. For example, A‐class homologues were expressed in carpels and leaves of both Eupomatia and Magnolia. In the calyptra, expression levels of B‐ and E‐class homologues were low and almost identical to those observed in leaf tissue. In contrast, high levels of expression for B‐ and E‐class homologues were observed in the stamens, staminodes, and carpels. These gene expression data agree with recent developmental data and the interpretation of the calyptra as a bract. We also report the presence of various forms of alternatively spliced mRNAs in the cDNA pool from floral organs, and the implications of these mRNAs are discussed.

Genetic Footprints of Stamen Ancestors Guide Perianth Evolution in Persea (Lauraceae)

The perianth of Persea americana (Lauraceae) consists of two whorls of morphologically similar laminar organs, termed tepals. Closely related Persea borbonia, however, produces a dimorphic perianth with smaller outer tepals. To assess whether homologues of floral organ identity genes in Persea may play a role in shaping this dimorphic perianth, we compared their expression patterns in the two species. A homologue of AP1 (A‐function) is expressed at low levels in both perianth types but was not tepal specific. Homologues of AGL6, however, show the tepal‐specific expression pattern expected of A‐function genes. Homologues of AP3 and PI (B‐function) are expressed in tepals of both perianth types, indicating that perianth dimorphism in Persea is not regulated by these genes. Differential expression across the dimorphic perianth as absence late in outer tepal development was evident for homologues of AG (C‐function) and SEP3 (E‐function). Genetic studies in model systems indicate a conserved role for AG homologues in specifying stamen and carpel identity, but the expression pattern in Persea indicates a novel role in perianth development. On the basis of gene expression and the occasional presence of tepaloid organs in stamen whorls, we hypothesize that the tepals of Persea and perhaps other Lauraceae are derived from stamens.

Expression of Floral Regulators in Basal Angiosperms and the Origin and Evolution of ABC‐Function

Abstract The ABC‐model of floral organ identity explains the regular, sequential development of sepals, petals, stamens, and carpels in eudicot flowers. This general model, based on studies of the derived eudicots Arabidopsis and Antirrhinum, may apply to nearly all eudicots, most of which are characterized by discrete whorls of floral organs. However, floral morphology of basal angiosperms is typically characterized by variable numbers of floral parts and gradual transitions among floral organs, and it is unclear that the ABC‐model applies to such flowers. Here we explore the origin and evolution of ABC‐function through consideration of expression data for homologs of ABC‐genes for basal angiosperms and conclude that the ABC‐model represents an evolutionarily derived regulatory network that arose through spatial restriction of regulatory gene expression.

An EST database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron

Liriodendron tulipifera L. was selected by the Floral Genome Project for identification of new genes related to floral diversity in basal angiosperms. A large, non-normalized cDNA library was constructed from premeiotic and meiotic floral buds and sequenced to generate a database of 9,531 high-quality expressed sequence tags. These sequences clustered into 6,520 unigenes, of which 5,251 were singletons, and 1,269 were in contigs. Homologs of genes regulating many aspects of flower development were identified, including those for organ identity and development, cell and tissue differentiation, and cell-cycle control. Almost 5% of the transcriptome consisted of homologs to known floral gene families. Homologs of most of the genes involved in cell-wall construction were also recovered. This provides a new opportunity for comparative studies in lignin biosynthesis, a trait of key importance in the evolution of land plants and in the utilization of fiber from economically important tree species, such as Liriodendron. Also of note is that 1,089 unigenes did not match any sequence in the public databases, including the complete genomes of Arabidopsis, rice, and Populus. Some of these novel genes might be unique in basal angiosperm species and, when better characterized, may be informative for understanding the origins of diverged gene families. Thus, the Liriodendron expressed sequence tag database and library will help bridge our understanding of the mechanisms of flower initiation and development that are shared among basal angiosperms, eudicots, and monocots, and provide new opportunities for comparative analysis of gene families across angiosperm species.

FLORAL DEVELOPMENTAL MORPHOLOGY OF PERSEA AMERICANA (AVOCADO, LAURACEAE): THE ODDITIES OF MALE ORGAN IDENTITY

A floral developmental series was determined for Persea americana (Lauraceae, avocado), and the floral morphology of this species was compared with available data for other members of Persea. We compared the structure of the inflorescence and flower with that of vegetative shoots with respect to phyllotaxy and leaf shape. The inflorescence is a determinate thyrse (panicle) with variable numbers of lateral branches. Staminal glands in Persea may represent abaxial‐marginal emergences rather than stamens. However, these glands are occasionally involved in transitions to pollen sacs and ovary margins. Stigmas, pollen sacs, staminal appendages, glands of staminodes, and margins of tepals share features that are subjectively associated with “androecia.” In the innermost androecial whorl, staminodial glands appear united because of the reduction of the middle portion to a staminodial apex. The apex of staminodes is homologous to the filament and anther, as well as to the stigma of the carpel, and corresponds to the connective tip in other basal angiosperms. In Persea, the connective and the staminode apex also correspond to the body of the tepal (i.e., all but the margin). Above a constriction (stipe), the carpel forms a cross zone bearing the single ovule; this cross zone also corresponds to the thecae in stamens, similar to observations for other basal angiosperms.