Diploid Generations Research Articles

PMRD: a curated database for genes and mutants involved in plant male reproduction

BackgroundMale reproduction is an essential biological event in the plant life cycle separating the diploid sporophyte and haploid gametophyte generations, which involves expression of approximately 20,000 genes. The control of male reproduction is also of economic importance for plant breeding and hybrid seed production. With the advent of forward and reverse genetics and genomic technologies, a large number of male reproduction-related genes have been identified. Thus it is extremely challenging for individual researchers to systematically collect, and continually update, all the available information on genes and mutants related to plant male reproduction. The aim of this study is to manually curate such gene and mutant information and provide a web-accessible resource to facilitate the effective study of plant male reproduction.DescriptionPlant Male Reproduction Database (PMRD) is a comprehensive resource for browsing and retrieving knowledge on genes and mutants related to plant male reproduction. It is based upon literature and biological databases and includes 506 male sterile genes and 484 mutants with defects of male reproduction from a variety of plant species. Based on Gene Ontology (GO) annotations and literature, information relating to a further 3697 male reproduction related genes were systematically collected and included, and using in text curation, gene expression and phenotypic information were captured from the literature. PMRD provides a web interface which allows users to easily access the curated annotations and genomic information, including full names, symbols, locations, sequences, expression patterns, functions of genes, mutant phenotypes, male sterile categories, and corresponding publications. PMRD also provides mini tools to search and browse expression patterns of genes in microarray datasets, run BLAST searches, convert gene ID and generate gene networks. In addition, a Mediawiki engine and a forum have been integrated within the database, allowing users to share their knowledge, make comments and discuss topics.ConclusionPMRD provides an integrated link between genetic studies and the rapidly growing genomic information. As such this database provides a global view of plant male reproduction and thus aids advances in this important area.

Evolution of the life cycle in land plants

Abstract All sexually reproducing eukaryotes have a life cycle consisting of a haploid and a diploid phase, marked by meiosis and syngamy (fertilization). Each phase is adapted to certain environmental conditions. In land plants, the recently reconstructed phylogeny indicates that the life cycle has evolved from a condition with a dominant free‐living haploid gametophyte to one with a dominant free‐living diploid sporophyte. The latter condition allows plants to produce more genotypic diversity by harnessing the diversity‐generating power of meiosis and fertilization, and is selectively favored as more solar energy is fixed and fed into the biosystem on earth and the environment becomes more heterogeneous entropically. Liverworts occupy an important position for understanding the origin of the diploid generation in the life cycle of land plants. Hornworts and lycophytes represent critical extant transitional groups in the change from the gametophyte to the sporophyte as the independent free‐living generation. Seed plants, with the most elaborate sporophyte and the most reduced gametophyte (except the megagametophyte in many gymnosperms), have the best developed sexual reproduction system that can be matched only by mammals among eukaryotes: an ancient and stable sex determination mechanism (heterospory) that enhances outcrossing, a highly bimodal and skewed distribution of sperm and egg numbers, a male‐driven mutation system, female specialization in mutation selection and nourishment of the offspring, and well developed internal fertilization. The study of evolution of the land plant life cycle requires a multidisciplinary approach that considers morphology, development, genetics, phylogeny, ecology, and evolution in an integrated fashion, and will deepen our understanding of plant evolution.

171 Merge of EvoDevo and paleobotany to infer the common ancestor of land plants and evolutionary mechanisms of extended diploid generation and branching in land plants

171 Merge of EvoDevo and paleobotany to infer the common ancestor of land plants and evolutionary mechanisms of extended diploid generation and branching in land plants

Plants

Plants

The evolution of the land plant life cycle

The extant land plants are unique among the monophyletic clade of photosynthetic eukaryotes, which consists of the green algae (chlorophytes), the charophycean algae (charophytes), numerous groups of unicellular algae (prasinophytes) and the embryophytes, by possessing, firstly, a sexual life cycle characterized by an alternation between a haploid, gametophytic and a diploid, sporophytic multicellular generation; secondly, the formation of egg cells within multicellular structures called archegonia; and, thirdly, the retention of the zygote and diploid sporophyte embryo within the archegonium. We review the developmental, paleobotanical and molecular evidence indicating that: the embryophytes descended from a charophyte-like ancestor; this common ancestor had a life cycle with only a haploid multicellular generation; and the most ancient (c. 410 Myr old) land plants (e.g. Cooksonia, Rhynia and Zosterophyllum) had a dimorphic life cycle (i.e. their haploid and diploid generations were morphologically different). On the basis of these findings, we suggest that the multicellular reproductive structures of extant charophytes and embryophytes are developmentally homologous, and that those of the embryophytes evolved by virtue of the co-option and re-deployment of ancient algal homeodomain gene networks.

A polycomb repressive complex 2 gene regulates apogamy and gives evolutionary insights into early land plant evolution

Land plants have distinct developmental programs in haploid (gametophyte) and diploid (sporophyte) generations. Although usually the two programs strictly alternate at fertilization and meiosis, one program can be induced during the other program. In a process called apogamy, cells of the gametophyte other than the egg cell initiate sporophyte development. Here, we report for the moss Physcomitrella patens that apogamy resulted from deletion of the gene orthologous to the Arabidopsis thaliana CURLY LEAF (PpCLF), which encodes a component of polycomb repressive complex 2 (PRC2). In the deletion lines, a gametophytic vegetative cell frequently gave rise to a sporophyte-like body. This body grew indeterminately from an apical cell with the character of a sporophytic pluripotent stem cell but did not form a sporangium. Furthermore, with continued culture, the sporophyte-like body branched. Sporophyte branching is almost unknown among extant bryophytes. When PpCLF was expressed in the deletion lines once the sporophyte-like bodies had formed, pluripotent stem cell activity was arrested and a sporangium-like organ formed. Supported by the observed pattern of PpCLF expression, these results demonstrate that, in the gametophyte, PpCLF represses initiation of a sporophytic pluripotent stem cell and, in the sporophyte, represses that stem cell activity and induces reproductive organ development. In land plants, branching, along with indeterminate apical growth and delayed initiation of spore-bearing reproductive organs, were conspicuous innovations for the evolution of a dominant sporophyte plant body. Our study provides insights into the role of PRC2 gene regulation for sustaining evolutionary innovation in land plants.

Convergences and divergences in polar auxin transport and shoot development in land plant evolution

A shoot is a reiterated structure consisting of stems and leaves and is the prevailing body plan in most land plant lineages. Vascular plants form shoots in the diploid generation, whereas mosses do so in the haploid generation.1 However, whether these plants use similar molecular mechanisms in shoot development and how the genetic networks for shoot development evolved is not clear. In our recent paper,2 we examined polar auxin transport in several mosses, which is essential for shoot development in angiosperms. Surprisingly, we did not detect polar auxin transport in the gametophytic shoots of mosses, but did detect it in the sporophytes, which have no shoot structure, indicating that shoots in vascular plants and mosses are most likely regulated differently. Here we discuss the convergent evolution of shoots and diverged auxin regulation in land plants.

First observations of heterococcolithophore–holococcolithophore life cycle combinations in the family Pontosphaeraceae (Calcihaptophycideae, Haptophyta)

Coccolithophores (Calcihaptophycideae, Haptophyta) are characterised by a heteromorphic life cycle with alternating haploid and diploid generations. Typically, diploid cells produce heterococcoliths, whereas haploid cells produce holococcoliths. An important source of evidence for coccolithophore life cycles comes from observations of combination coccospheres, which are cells bearing both types of coccoliths and thus interpreted as capturing the transition from haploid to diploid phase or vice-versa. Such observations are rare and many heterococcolith and holococcolith-bearing taxa remain non-associated to a life cycle phase counter-part. Information on life cycles is even completely missing for entire lineages. Here we report the first observations of heterococcolithophore–holococcolithophore combinations in the family Pontosphaeraceae, consisting of the associations of the morpho-species Scyphosphaera apsteinii with Syracolithus schilleri and of Pontosphaera japonica with an undescribed Syracolithus-like holococcolithophore. These new observations provide clear evidence that the Pontosphaeraceae have dimorphic haplo-diploid life cycles, further supporting the hypothesis that this life cycle pattern is ubiquitous among calcihaptophytes. Moreover, our results highlight a high degree of morphological convergence between holococcolithophores belonging to different lineages, since Syracolithus-like holococcolithophores are also present in the life cycle of species within the Helicosphaeraceae and Calcidiscaceae, the latter family being phylogenetically distant from the Pontosphaeraceae. These morphological resemblances may provide evidence for: (1) morpho-structural constraints on holococcolith construction, and/or (2) ecological convergence of the haploid phases of different coccolithophores.

Class 1 KNOX genes are not involved in shoot development in the moss Physcomitrella patens but do function in sporophyte development

Although the number and form of metazoan organs are determined in the embryo, plants continuously form organs via pluripotent stem cells contained within the meristem. Flowering plants have an indeterminate meristem in their diploid generation, whereas the common ancestor of land plants is inferred to have formed an indeterminate meristem in its haploid generation, as observed in the extant basal land plants, bryophytes, including mosses. It is hypothesized that the underlying gene networks for the diploid meristem were initially present in the haploid generation of the basal land plants and were eventually co-opted for expression in the diploid generation. In flowering plants, the class 1 KNOTTED1-LIKE HOMEOBOX (KNOX) transcription factors are essential for the function of the indeterminate apical meristem. Here, we show that the class 1 KNOX orthologs function in the diploid organ, with determinate growth in the moss Physcomitrella patens, but do not function in the haploid indeterminate meristem. We propose that the genetic networks governing the indeterminate meristem in land plants are variable, and the networks governing the diploid indeterminate meristem with the class 1 KNOX genes likely evolved de novo in the flowering plant lineage.

Homologous Versus Antithetic Alternation of Generations and the Origin of Sporophytes

The late-nineteenth/early-twentieth century debate over homologous versus antithetic alternation of generations is reviewed. Supporters of both theories, at first, used Coleochaete as a model for the origin of land-plant life cycles. The early debate focused on the morphological interpretation of the sporophyte and on whether vascular cryptogams had bryophyte-like ancestors. The terms of the debate shifted after the discovery that the alternation of morphological generations was accompanied by an alternation of chromosome number. Supporters of homologous alternation now promoted a model in which land plants had been derived from an algal ancestor with an isomorphic alternation of haploid and diploid generations whereas supporters of antithetic alternation favored a model in which land plants were derived from a haploid algal ancestor with zygotic meiosis. Modern evidence that embryophytes are derived from charophycean green algae is more compatible with an updated version of the antithetic theory.

Convergent evolution of shoots in land plants: lack of auxin polar transport in moss shoots

The shoot is a repeated structure made up of stems and leaves and is the basic body plan in land plants. Vascular plants form a shoot in the diploid generation, whereas nonvascular plants such as mosses form a shoot in the haploid generation. It is not clear whether all land plants use similar molecular mechanisms in shoot development or how the genetic networks for shoot development evolved. The control of auxin distribution, especially by polar auxin transport, is essential for shoot development in flowering plants. We did not detect polar auxin transport in the gametophytic shoots of several mosses, but did detect it in the sporophytes of mosses without shoot structure. Treatment with auxin transport inhibitors resulted in abnormal embryo development, as in flowering plants, but did not cause any morphological changes in the haploid shoots. We fused the soybean auxin-inducible promoter GH3 with a GUS reporter gene and used it to indirectly detect auxin distribution in the moss Physcomitrella patens. An auxin transport inhibitor NPA did not cause any changes in the putative distribution of auxin in the haploid shoot. These results indicate that polar auxin transport is not involved in haploid shoot development in mosses and that shoots in vascular plants and mosses are most likely regulated differently during development.

Chapter Four: Life Cycles in Major Lineages of Photosynthetic Eukaryotes, with a Special Reference to the Origin of Land Plants

Meiosis and fertilization represent two fundamental events in the origin, development, and evolution of the eukaryotic life cycle. A life cycle with alternation of generations evolved independently in multiple diverse eukaryote lineages, and variations of this type of life cycle can be found in the photosynthetic red, brown, and green algae and embryophyte land plants. The adaptive advantages of maintaining two multicellular stages necessary for sexual reproduction have been explored on both ecological and genetic levels. However, no hypothesis has been found to be applicable across the diverse lineages. This review summarizes the types of life cycles found in photosynthetic eukaryotes, focusing on those lineages that exhibit an alternation of generations and the adaptive advantages such life cycles may confer. The evolution of the embryophyte lineage and its transition from an aquatic to terrestrial habitat are discussed, as is how the first-diverging embryophyte lineage, the liverworts, display intermediate life cycle characteristics between those of their green algal ancestors and later-evolving embryophytes. In addition, the adaptive advantages of maintaining two multicellular stages are reviewed, particularly the evolution of a multicellular sporophyte through delayed zygotic meiosis and its resulting genetic complexity. The hypothesis developed by Svedelius in 1927 is favored that a lengthened diploid generation with simultaneous increase of the body size allows production of a large number of genetically different gametes via meiosis, which further leads to production of diverse offspring after fertilization.

Sexual conflict and the alternation of haploid and diploid generations.

Land plants possess a multicellular diploid stage (sporophyte) that begins development while attached to a multicellular haploid progenitor (gametophyte). Although the closest algal relatives of land plants lack a multicellular sporophyte, they do produce a zygote that grows while attached to the maternal gametophyte. The diploid offspring shares one haploid set of genes with the haploid mother that supplies it with resources and a paternal haploid complement that is not shared with the mother. Sexual conflict can arise within the diploid offspring because the offspring's maternal genome will be transmitted in its entirety to all other sexual and asexual offspring that the mother may produce, but the offspring's paternally derived genes may be absent from these other offspring. Thus, the selective forces favouring the evolution of genomic imprinting may have been present from the origin of modern land plants. In bryophytes, where gametophytes are long-lived and capable of multiple bouts of asexual and sexual reproduction, we predict strong sexual conflict over allocation to sporophytes. Female gametophytes of pteridophytes produce a single sporophyte and often lack means of asexual reproduction. Therefore, sexual conflict is predicted to be attenuated. Finally, we explore similarities among models of mate choice, offspring choice and segregation distortion.

Characterization of MADS-box genes in charophycean green algae and its implication for the evolution of MADS-box genes

The MADS-box genes of land plants are extensively diverged to form a superfamily and are important in various aspects of development including the specification of floral organs as homeotic selector genes. The closest relatives of land plants are the freshwater green algae charophyceans. To study the origin and evolution of land plant MADS-box genes, we characterized these genes in three charophycean green algae: the stonewort Chara globularis, the coleochaete Coleochaete scutata, and the desmid Closterium peracerosum-strigosum-littorale complex. Phylogenetic analyses suggested that MADS-box genes diverged extensively in the land plant lineage after the separation of charophyceans from land plants. The stonewort C. globularis mRNA was specifically detected in the oogonium and antheridium together with the egg and spermatozoid during their differentiation. The expression of the C. peracerosum-strigosum-littorale-complex gene increased when vegetative cells began to differentiate into gametangial cells and decreased after fertilization. These expression patterns suggest that the precursors of land plant MADS-box genes originally functioned in haploid reproductive cell differentiation and that the haploid MADS-box genes were recruited into a diploid generation during the evolution of land plants.

The Innate Immunity of a Marine Red Alga Involves Oxylipins from Both the Eicosanoid and Octadecanoid Pathways

The oxygenated derivatives of fatty acids, known as oxylipins, are pivotal signaling molecules in animals and terrestrial plants. In animal systems, eicosanoids regulate cell differentiation, immune responses, and homeostasis. In contrast, terrestrial plants use derivatives of C18 and C16 fatty acids as developmental or defense hormones. Marine algae have emerged early in the evolution of eukaryotes as several distinct phyla, independent from the animal and green-plant lineages. The occurrence of oxylipins of the eicosanoid family is well documented in marine red algae, but their biological roles remain an enigma. Here we address the hypothesis that they are involved with the defense mechanisms of the red alga Chondrus crispus. By investigating its association with a green algal endophyte Acrochaete operculata, which becomes invasive in the diploid generation of this red alga, we showed that (1) when challenged by pathogen extracts, the resistant haploid phase of C. crispus produced both C20 and C18 oxylipins, (2) elicitation with pathogen extracts or methyl jasmonate activated the metabolism of C20 and C18 polyunsaturated fatty acids to generate hydroperoxides and cyclopentenones such as prostaglandins and jasmonates, and (3) C20 and C18 hydroperoxides as well as methyl jasmonate did induce shikimate dehydrogenase and Phe ammonialyase activities in C. crispus and conferred an induced resistance to the diploid phase, while inhibitors of fatty acid oxidation reduced the natural resistance of the haploid generation. The dual nature of oxylipin metabolism in this alga suggests that early eukaryotes featured both animal- (eicosanoids) and plant-like (octadecanoids) oxylipins as essential components of innate immunity mechanisms.

Unique features of the plant life cycle and their consequences.

Continuous development, the absence of a germline, flexible and reversible cellular differentiation, and the existence of haploid and diploid generations--both of which express genes--are characteristics that distinguish plants from animals. Because these differences alter the impact of mutations, animals and plants experience varied selection pressures. Despite different life-cycles, both flowering plants and multicellular animals have evolved complex sensing mechanisms that act after fertilization as 'quality checks' on reproduction, and that detect chromosome dosage and the parent of origin for specific genes. Although flowering plant embryos escape such surveillance in vitro, embryo success in the seed often depends on a healthy endosperm--a nutritive tissue that is produced by a second fertilization event in which maternal and paternal gene contributions can be monitored immediately after fertilization and throughout development.

The evolution of the life cycle of brown seaweeds

The brown seaweeds (Phaeophyta) are well-suited for testing theories of the evolution of the sexual alternation of haploid and diploid generations because of the great diversity of life cycles within the phylum. Three theories are investigated in this paper. (1) Diploid growth evolves because it has the effect of complementing deleterious recessive mutations. This is rejected because (a) ancestral haplonty is not a parsimonious inference from current phylogenies; (b) the exaggeration of diploid growth does not evolve in a comb-like fashion; (c) forms with predominantly haploid growth have evolved from smaller isomorphic ancestors; and (d) there is no correlation between haploid growth and monoecy. (2) Diploid growth evolves when gamete dimorphism leads to intense sexual selection, favouring the production of genetically diverse gametes through meiosis. This is rejected because there is no correlation between the dominance of the diploid generation and the degree of gamete dimorphism. It is possible to show that gamete dimorphism itself has evolved in the Phaeophyta through the increase in size of the macrogamete in forms that have evolved larger sporophytes. (3) Microthalli become specialized as gametophytes because fusion is promoted by releasing gametes into the boundary layer; macrothalli become specialized as sporophytes because dispersal is promoted by releasing zoospores into the water column. This is consistent with the sexual and reproductive biology of Phaeophyta. The classic sexual cycle can then be interpreted as evolving from an asexual alternation of microthallus and macrothallus, governed largely by environmental factors, through selection for the appropriate association of ploidy with vegetative size. The exceptions to this general rule are forms in which gametes are released from macrothalli, where a different suite of sexual characters has evolved.

The evolution of the life cycle of brown seaweeds

The brown seaweeds (Phaeophyta) are well-suited for testing theories of the evolution of the sexual alternation of haploid and diploid generations because of the great diversity of life cycles within the phylum. Three theories are investigated in this paper. (1) Diploid growth evolves because it has the effect of complementing deleterious recessive mutations. This is rejected because (a) ancestral haplonty is not a parsimonious inference from current phylogenies; (b) the exaggeration of diploid growth does not evolve in a comb-like fashion; (c) forms with predominantly haploid growth have evolved from smaller isomorphic ancestors; and (d) there is no correlation between haploid growth and monoecy. (2) Diploid growth evolves when gamete dimorphism leads to intense sexual selection, favouring the production of genetically diverse gametes through meiosis. This is rejected because diere is no correlation between the dominance of the diploid generation and the degree of gamete dimorphism. It is possible to show that gamete dimorphism itself has evolved in the Phaeophyta through the increase in size of the macrogamete in forms that have evolved larger sporophytes. (3) Microthalli become specialized as gametophytes because fusion is promoted by releasing gametes into the boundary layer; macrothalli become specialized as sporophytes because dispersal is promoted by releasing zoospores into the water column. This is consistent with the sexual and reproductive biology of Phaeophyta. The classic sexual cycle can then be interpreted as evolving from an asexual alternation of microthallus and macrothallus, governed largely by environmental factors, through selection for the appropriate association of ploidy with vegetative size. The exceptions to this general rule are forms in which gametes are released from macrothalli, where a different suite of sexual characters has evolved.

Genetic characterization of hadad, a mutant disrupting female gametogenesis in Arabidopsis thaliana.

The plant life cycle alternates between a diploid and a haploid generation, the spore-producing sporophyte and the gamete-producing gametophyte. Unlike in animals, where meiotic products differentiate directly into gametes, the haploid spores of plants divide mitotically to form a multicellular haploid organism. The differentiation of gametes occurs later in the development of the gametophyte.

Sources and consequences of phenotypic and genotypic plasticity in flowering plants

Plants possess a characteristic life cycle with an alternation of haploid and diploid generations, continual somatic organogenesis, and no germ line. There is a close interrelationship between phenotypic plasticity in response to a variable environment, mechanisms generating heritable changes, and cell fate determination during embryogenesis and somatic growth. Gain-of-function mutations may make a substantial contribution to diversity in angiosperm morphology and biochemistry.