Defective chlorophyll a/b-binding protein genes in the genome of a homosporous fern

Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes

Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum. Remarkably, despite that the two species diverged ~350 Mya, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications, and the resulting intragenomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species.

Patterns and Processes of Diploidization in Land Plants

Most land plants are now known to be ancient polyploids that have rediploidized. Diploidization involves many changes in genome organization that ultimately restore bivalent chromosome pairing and disomic inheritance, and resolve dosage and other issues caused by genome duplication. In this review, we discuss the nature of polyploidy and its impact on chromosome pairing behavior. We also provide an overview of two major and largely independent processes of diploidization: cytological diploidization and genic diploidization/fractionation. Finally, we compare variation in gene fractionation across land plants and highlight the differences in diploidization between plants and animals. Altogether, we demonstrate recent advancements in our understanding of variation in the patterns and processes of diploidization in land plants and provide a road map for future research to unlock the mysteries of diploidization and eukaryotic genome evolution.

The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly

Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.

Fluctuations in cell cycle, morphology and metabolism of Anemia phyllitidis gametophytes are the most important hallmarks of GA3-induced antheridiogenesis

The research object concerns partially explained mechanisms of plant hormone participation in male sex determination in plants, among them in A. phyllitidis gametophytes during GA₃-induced antheridiogenesis. To provide an explanation of the mechanisms of fluorescence and white-light microscopy, cytophotometric, autoradiographic and spectrophotometic methods were used to study cell cycle, the number of nucleoli, the amount of DiOC₆-stained IMN/ER, in which endoplasmic reticulum (ER) constitutes the main part, and its distribution as well as the amounts of proteins and chlorophylls and activities of acidic (Ac) and basic (Ba) phosphatases (Phases). It was revealed that antheridiogenesis was accompanied by cell cycle arrest at S-phase, changes of the number of nucleoli with simultaneous changes of the amount of IMN/ER and its distribution as well as fluctuations of protein amounts and of activities of acidic (Ac) and basic (Ba) phosphatases (Phases). The results indicated that initiation of antheridiogenesis in A. phyllitidis gametophytes by GA₃ was related to the elevation of GAs/ANs in the culture media, during its induction phase, and the elevation of IMN/ER and GAs/ANs amounts, during expression phase of this process.

An Exploration into Fern Genome Space

Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.

When Double is not Twice as Much

Gene and genome duplications provide a playground for various selective pressures and contribute significantly to genome complexity. It is assumed that the genomes of all major eukaryotic lineages possess duplicated regions that result from gene and genome duplication. There is evidence that the model plant Arabidopsis has been subjected to at least three whole-genome duplication events over the last 150-200 million years. As a result, many cellular processes are governed by redundantly acting gene families. Plants pass through two distinct life phases with a haploid gametophytic alternating with a diploid sporophytic generation. This ontogenetic difference in gene copy number has important implications for the outcome of deleterious mutations, which are masked by the second gene copy in diploid systems but expressed in a dominant fashion in haploid organisms. As a consequence, maintaining the activity of duplicated genes might be particularly advantageous during the haploid gametophytic generation. Here, we describe the distinctive features associated with the alteration of generations and discuss how activity profiles of duplicated genes might get modulated in a life phase dependent fashion.

Endoreplication in Anemia phyllitidis coincides with the development of gametophytes and male sex

Analyses of DNA content using fluorescence microcytophotometry showed that development of Anemia phyllitidis gametophytes coincided with endoreduplication process. The level of this process shown by the number of endopolyploid cells studied at the I-V arbitrarily established cellular gametophyte stages, was 3%, while at the VI-VII and VII* (male stages) were 10.5 and 4%, respectively. This process coincided with decreased mitotic activity of cells and concerned the cells with their profile area between 1100 and 13,000 microm(2). However, the correlation between cell size and its polyploidisation level was detected only for 12% of these cells. Endoreduplication during development of A. phyllitidis gametophytes seems to be connected with the end of cell cycle followed by the exit of cells from the cell cycle and with subsequent switch of proliferation to the postmitotic differentiation and/or to the endocycle. Endoreplication of A. phyllitidis gametophytes is a function of age, size and number of cells as well as type of gametophyte morphogenesis, which probably maintains the functional copies of genes whose number is restricted by elimination of cells from gametophytes by their death.

Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids

Polyploidy, or whole-genome duplication (WGD), is an important genomic feature for all eukaryotes, especially many plants and some animals. The common occurrence of polyploidy suggests an evolutionary advantage of having multiple sets of genetic material for adaptive evolution. However, increased gene and genome dosages in autopolyploids (duplications of a single genome) and allopolyploids (combinations of two or more divergent genomes) often cause genome instabilities, chromosome imbalances, regulatory incompatibilities, and reproductive failures. Therefore, new allopolyploids must establish a compatible relationship between alien cytoplasm and nuclei and between two divergent genomes, leading to rapid changes in genome structure, gene expression, and developmental traits such as fertility, inbreeding, apomixis, flowering time, and hybrid vigor. Although the underlying mechanisms for these changes are poorly understood, some themes are emerging. There is compelling evidence that changes in DNA sequence, cis- and trans-acting effects, chromatin modifications, RNA-mediated pathways, and regulatory networks modulate differential expression of homoeologous genes and phenotypic variation that may facilitate adaptive evolution in polyploid plants and domestication in crops.

Genetic map-based analysis of genome structure in the homosporous fern Ceratopteris richardii

Homosporous ferns have extremely high chromosome numbers relative to flowering plants, but the species with the lowest chromosome numbers show gene expression patterns typical of diploid organisms, suggesting that they may be diploidized ancient polyploids. To investigate the role of polyploidy in fern genome evolution, and to provide permanent genetic resources for this neglected group, we constructed a high-resolution genetic linkage map of the homosporous fern model species, Ceratopteris richardii (n = 39). Linkage map construction employed 488 doubled haploid lines (DHLs) that were genotyped for 368 RFLP, 358 AFLP, and 3 isozyme markers. Forty-one linkage groups were recovered, with average spacing between markers of 3.18 cM. Most loci (approximately 76%) are duplicated and most duplicates occur on different linkage groups, indicating that as in other eukaryotic genomes, gene duplication plays a prominent role in shaping the architecture of fern genomes. Although past polyploidization is a potential mechanism for the observed abundance of gene duplicates, a wide range in the number of gene duplicates as well as the absence of large syntenic regions consisting of duplicated gene copies implies that small-scale duplications may be the primary mode of gene duplication in C. richardii. Alternatively, evidence of past polyploidization(s) may be masked by extensive chromosomal rearrangements as well as smaller-scale duplications and deletions following polyploidization(s).

Differential methylation of genes and repeats in land plants

The hypomethylated fraction of plant genomes is usually enriched in genes and can be selectively cloned using methylation filtration (MF). Therefore, MF has been used as a gene enrichment technology in sorghum and maize, where gene enrichment was proportional to genome size. Here we apply MF to a broad variety of plant species spanning a wide range of genome sizes. Differential methylation of genic and non-genic sequences was observed in all species tested, from non-vascular to vascular plants, but in some cases, such as wheat and pine, a lower than expected level of enrichment was observed. Remarkably, hexaploid wheat and pine show a dramatically large number of gene-like sequences relative to other plants. In hexaploid wheat, this apparent excess of genes may reflect an abundance of methylated pseudogenes, which may thus be more prevalent in recent polyploids.

Consistency of Nicotiana attenuata's herbivore- and jasmonate-induced transcriptional responses in the allotetraploid species Nicotiana quadrivalvis and Nicotiana clevelandii

We examined the consistency of the native diploid Nicotiana attenuata (Na)'s herbivore-induced transcriptional changes in the two allotetraploid natives, Nicotiana clevelandii (Nc) and Nicotiana quadrivalvis (Nq), which are thought to be derived from hybridizations with an ancestral Na. An analysis of nuclear-encoded chloroplast-expressed Gln synthetase gene (ncpGS) sequences found strong similarity between Nc and Na and between N. trigonophylla and the two allopolyploids. All species were elicited with methyl jasmonate (MeJA), or were wounded and treated with either water, Manduca sexta oral secretions and regurgitant (R), or the two most abundant fatty acid amino acid conjugates (F) in R to simulate herbivory. The induced transcriptional responses in all three species were compared with a cDNA microarray enriched in Na genes. Na had the fastest transcriptional responses followed by Nc and then Nq. Na's R- and F-elicited responses were more similar to those from Nq, while the MeJA- or wound-elicited responses were more consistent in Nc. Treatment of wounds with the full cocktail of elicitors found in R elicits more complex responses than does treatment with F. The species differ in their elicited JA responses, and these differences are mirrored in the expression of oxylipin genes (LOX, HPL, AOS, and alpha-DOX) and downstream JA-elicited genes (TD). Elicitation decreases the expression of growth-related genes in all three species. We propose that this is a valuable system to examine the modification of complex, polygenic, adaptive responses during allopolyploid speciation.

Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing

Most eukaryotes have genomes that exhibit high levels of gene redundancy, much of which seems to have arisen from one or more cycles of genome doubling. Polyploidy has been particularly prominent during flowering plant evolution, yielding duplicated genes (homoeologs) whose expression may be retained or lost either as an immediate consequence of polyploidization or on an evolutionary timescale. Expression of 40 homoeologous gene pairs was assayed by cDNA-single-stranded conformation polymorphism in natural (1- to 2-million-yr-old) and synthetic tetraploid cotton (Gossypium) to determine whether homoeologous gene pairs are expressed at equal levels after polyploid formation. Silencing or unequal expression of one homoeolog was documented for 10 of 40 genes examined in ovules of Gossypium hirsutum. Assays of homoeolog expression in 10 organs revealed variable expression levels and silencing, depending on the gene and organ examined. Remarkably, silencing and biased expression of some gene pairs are reciprocal and developmentally regulated, with one homoeolog showing silencing in some organs and the other being silenced in other organs, suggesting rapid subfunctionalization. Duplicate gene expression was examined in additional natural polyploids to characterize the pace at which expression alteration evolves. Analysis of a synthetic tetraploid revealed homoeolog expression and silencing patterns that sometimes mirrored those of the natural tetraploid. Both long-term and immediate responses to polyploidization were implicated. Data suggest that some silencing events are epigenetically induced during the allopolyploidization process.

Protein-coding genes are epigenetically regulated in Arabidopsis polyploids

The fate of redundant genes resulting from genome duplication is poorly understood. Previous studies indicated that ribosomal RNA genes from one parental origin are epigenetically silenced during interspecific hybridization or polyploidization. Regulatory mechanisms for protein-coding genes in polyploid genomes are unknown, partly because of difficulty in studying expression patterns of homologous genes. Here we apply amplified fragment length polymorphism (AFLP)-cDNA display to perform a genome-wide screen for orthologous genes silenced in Arabidopsis suecica, an allotetraploid derived from Arabidopsis thaliana and Cardaminopsis arenosa. We identified ten genes that are silenced from either A. thaliana or C. arenosa origin in A. suecica and located in four of the five A. thaliana chromosomes. These genes represent a variety of RNA and predicted proteins including four transcription factors such as TCP3. The silenced genes in the vicinity of TCP3 are hypermethylated and reactivated by blocking DNA methylation, suggesting epigenetic regulation is involved in the expression of orthologous genes in polyploid genomes. Compared with classic genetic mutations, epigenetic regulation may be advantageous for selection and adaptation of polyploid species during evolution and development.

The role of genetic and genomic attributes in the success of polyploids

In 1950, G. Ledyard Stebbins devoted two chapters of his book Variation and Evolution in Plants (Columbia Univ. Press, New York) to polyploidy, one on occurrence and nature and one on distribution and significance. Fifty years later, many of the questions Stebbins posed have not been answered, and many new questions have arisen. In this paper, we review some of the genetic attributes of polyploids that have been suggested to account for the tremendous success of polyploid plants. Based on a limited number of studies, we conclude: (i) Polyploids, both individuals and populations, generally maintain higher levels of heterozygosity than do their diploid progenitors. (ii) Polyploids exhibit less inbreeding depression than do their diploid parents and can therefore tolerate higher levels of selfing; polyploid ferns indeed have higher levels of selfing than do their diploid parents, but polyploid angiosperms do not differ in outcrossing rates from their diploid parents. (iii) Most polyploid species are polyphyletic, having formed recurrently from genetically different diploid parents. This mode of formation incorporates genetic diversity from multiple progenitor populations into the polyploid "species"; thus, genetic diversity in polyploid species is much higher than expected by models of polyploid formation involving a single origin. (iv) Genome rearrangement may be a common attribute of polyploids, based on evidence from genome in situ hybridization (GISH), restriction fragment length polymorphism (RFLP) analysis, and chromosome mapping. (v) Several groups of plants may be ancient polyploids, with large regions of homologous DNA. These duplicated genes and genomes can undergo divergent evolution and evolve new functions. These genetic and genomic attributes of polyploids may have both biochemical and ecological benefits that contribute to the success of polyploids in nature.

Genetic and epigenetic interactions in allopolyploid plants

Allopolyploid plants are hybrids that contain two copies of the genome from each parent. Whereas wild and cultivated allopolyploids are well adapted, man-made allopolyploids are typically unstable, displaying homeotic transformation and lethality as well as chromosomal rearrangements and changes in the number and distribution of repeated DNA sequences within heterochromatin. Large increases in the length of some chromosomes has been documented in allopolyploid hybrids and could be caused by the activation of dormant retrotransposons, as shown to be the case in marsupial hybrids. Synthetic (man-made) allotetraploids of Arabidopsis exhibit rapid changes in gene regulation, including gene silencing. These regulatory abnormalities could derive from ploidy changes and/or incompatible interactions between parental genomes, although comparison of auto- and allopolyploids suggests that intergenomic incompatibilities play the major role. Models to explain intergenomic incompatibilities incorporate both genetic and epigenetic mechanisms. In one model, the activation of heterochromatic transposons (McClintock's genomic shock) may lead to widespread perturbation of gene expression, perhaps by a silencing interaction between activated transposons and euchromatic genes. Qualitatively similar responses, of lesser intensity, may occur in intraspecific hybrids. Therefore, insight into genome function gained from the study of allopolyploidy may be applicable to hybrids of any type and may even elucidate positive interactions, such as those responsible for hybrid vigor.

Genome evolution in polyploids

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.

Genome evolution in polyploids

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.

A short history of MADS-box genes in plants

Evolutionary developmental genetics (evodevotics) is a novel scientific endeavor which assumes that changes in developmental control genes are a major aspect of evolutionary changes in morphology. Understanding the phylogeny of developmental control genes may thus help us to understand the evolution of plant and animal form. The principles of evodevotics are exemplified by outlining the role of MADS-box genes in the evolution of plant reproductive structures. In extant eudicotyledonous flowering plants, MADS-box genes act as homeotic selector genes determining floral organ identity and as floral meristem identity genes. By reviewing current knowledge about MADS-box genes in ferns, gymnosperms and different types of angiosperms, we demonstrate that the phylogeny of MADS-box genes was strongly correlated with the origin and evolution of plant reproductive structures such as ovules and flowers. It seems likely, therefore, that changes in MADS-box gene structure, expression and function have been a major cause for innovations in reproductive development during land plant evolution, such as seed, flower and fruit formation.

Multiple ribosomal RNA gene loci in the genome of the homosporous fern Ceratopteris richardii

The genomes of homosporous ferns are largely uncharacterized, but they appear to differ from gymnosperms and angiosperms in key aspects, such as high chromosome numbers at the diploid level, and thus provide a unique perspective on plant genome structure and evolution. Using the model homosporous fern Ceratopteris richardii, loci encoding ribosomal RNA sequences (rDNA genes) were detected using fluorescent in situ hybridization. At least two major rDNA loci were visible in all cases, and six or more weakly hybridizing signals were observed in most cytological preparations. These results are consistent with models of homosporous fern evolution via cycles of polyploidy followed by gene silencing. They are also consistent with other models of fern genome evolution. With the exception of the weakly hybridizing signals, these data are similar to analogous reports of one or two major rDNA loci in diploid angiosperms. These results suggest that the gross morphology of rDNA loci are similar between diploid homosporous ferns and angiosperms, but that important clues to rDNA gene and chromosome evolution in homosporous ferns may reside in the analysis of their minor rDNA sequences.Key words: rDNA, in situ hybridization, homosporous ferns, evolution, gene silencing, polyploidy.

EVOLUTION OF LIGHT-REGULATED PLANT PROMOTERS

In this review, we address the phylogenetic and structural relationships between light-responsive promoter regions from a range of plant genes, that could explain both their common dependence on specific photoreceptor-associated transduction pathways and their functional versatility. The well-known multipartite light-responsive elements (LREs) of flowering plants share sequences very similar to motifs in the promoters of orthologous genes from conifers, ferns, and mosses, whose genes are expressed in absence of light. Therefore, composite LREs have apparently evolved from cis-regulatory units involved in other promoter functions, a notion with significant implications to our understanding of the structural and functional organization of angiosperm LREs.

Nucleotide distribution in gymnosperm nuclear sequences suggests a model for GC-content change in land-plant nuclear genomes

Nuclear protein coding sequences from gymnosperms are currently scarce. We have determined 4 kb of nuclear protein coding sequences from gynosperms and have collected and analyzed > 60 kb of nuclear sequences from gymnosperms and nonspermatophytes in order to better understand processes influencing genome evolution in plants. We show that conifers possess both biased and nonbiased genes with respect to GC content, as found in monocots, suggesting that the common ancestor of conifers and monocots may have possessed both biased and nonbiased genes. The lack of biased genes in dicots is suggested to be a derived character for this lineage. We present a simple but speculative model of land-plant genome evolution which considers changes in GC bias and CpG frequency, respectively, as independent processes and which can account for several puzzling aspects of observed nucleotide frequencies in plant genes.

Hypothesis for the evolution of three-helix Chl a/b and Chl a/c light-harvesting antenna proteins from two-helix and four-helix ancestors

The nuclear-encoded Chl a/b and Chl a/c antenna proteins of photosynthetic eukaryotes are part of an extended family of proteins that also includes the early light-induced proteins (ELIPs) and the 22 kDa intrinsic protein of PS II (encoded by psbS gene). All members of this family have three transmembrane helices except for the psbS protein, which has four. The amino acid sequences of these proteins are compared and related to the three-dimensional structure of pea LHC II Type I (Kühlbrandt and Wang, Nature 350: 130-134, 1991). The similarity of psbS to the three-helix members of the family suggests that the latter arose from a four-helix ancestor that lost its C-terminal helix by deletion. Strong internal similarity between the two halves of the psbS protein suggests that it in turn arose as the result of the duplication of a gene encoding a two-helix protein. Since psbS is reported to be present in at least one cyanobacterium, the ancestral four-helix protein may have been present prior to the endosymbiotic event or events that gave rise to the photosynthetic eukaryotes. The Chl a/b and Chl a/c antenna proteins, and the immunologically-related proteins in the rhodophytes may have had a common ancestor which was present in the early photosynthetic eukaryotes, and predated their division into rhodophyte, chromophyte and chlorophyte lineages. The LHC I-LHC II divergence probably occurred before the separation of higher plants from chlorophyte algae and euglenophytes, and the different Types of LHC I and LHC II proteins arose prior to the separation of angiosperms and gymnosperms.

Structure of the pine (Pinus thunbergii) chlorophyll a/b-binding protein gene expressed in the absence of light

A gene for chlorophyll a/b-binding protein (cab) of pine (Pinus thumbergii) was isolated and sequenced. The gene (cab-6) contains an intron at a position equivalent to the type II cab genes of angiosperms. Transcript mapping analyses show that the amount of the mRNA in the dark is about half of that in the light. The cab-6 gene is expressed in dark-grown seedlings at a very high level, differing from angiosperm cab genes which are induced by light. The cab-6 gene typifies the coniferous plant cab genes in light-independent gene expression.

Sequences flanking the hexameric G-box core CACGTG affect the specificity of protein binding

The CACGTG G-box motif is a highly conserved DNA sequence that has been identified in the 5' upstream region of plant genes exhibiting regulation by a variety of environmental signals and physiological cues. Gel mobility shift assays using a panel of G-box oligonucleotides differing in their flanking sequences identified two types of binding activity (A and B) in a cauliflower nuclear extract. Competition gel retardation assays demonstrated that the two types of binding activity were distinct. Type A binding activity interacted with oligonucleotides designated as class I elements, whereas type B binding activity interacted strongly with class II elements and weakly with class I elements. A third class of elements, null elements, did not exhibit any detectable binding under our assay conditions. Gel retardation analysis of nonpalindromic hybrid G-box oligonucleotides indicated that hybrid elements of the same class exhibited binding affinity commensurate with the affinity of the weaker element, hybrid class I/II elements exhibited only type B binding, and hybrid class I/null and class II/null elements did not show any detectable binding activity. These binding activities can be explained by the affinity of bZip G-box binding homo- or heterodimer subunits for G-box half sites. These experiments led to a set of classification rules that can predict the binding activity of all reported plant G-box motifs containing the consensus hexameric core. Tissue- and/or development-specific expression of genes containing G-box motifs may be regulated by the affinity of G-box proteins for the different classes of G-box elements.

Evolutionary conservation of the chlorophyll a/b-binding proteins: cDNAs encoding type I, II and III LHC I polypeptides from the gymnosperm Scots pine

cDNAs encoding three different LHC I polypeptides (Type I, Type II and Type III) from the gymnosperm Scots pine (Pinus sylvestris L.) were isolated and sequences. Comparisons of the deduced amino acid sequences with the corresponding tomato sequences showed that all three proteins were highly conserved although less so than the LHC II proteins. The similarities between mature Scots pine and tomato Types I, II and III LHC I proteins were 80%, 87% and 85%, respectively. Two of the five His residues that are found in AXXXH sequences, which have been identified as putative chlorophyll ligands in the Type I and Type II proteins, were not conserved. The same two regions of high homology between the different LHC proteins, which have been identified in tomato, were also found in the Scots pine proteins. Within the conserved regions, the Type I and Type II proteins had the highest similarity; however, the Type II and Type III proteins also showed a similarity in the central region. The results suggest that all flowering plants (gymnosperms and angiosperms) probably have the same set of LHC polypeptides. A new nomenclature for the genes encoding LHC polypeptides (formerly cab genes) is proposed. The names lha and lhb are suggested for genes encoding LHC I and LHC II proteins, respectively, analogous to the nomenclature for the genes encoding other photosynthetic proteins.

Characterization of a cDNA encoding a PSII-associated chlorophyll a/b-binding protein (CAB) from Chlamydomonas moewusii fitting into neither type I nor type II

A full-length 1010-bp cDNA clone from Chlamydomonas moewusii coding for the precursor of a chlorophyll a/b-binding protein (CAB) was characterized. Northern analysis shows hybridization to a single 1150-base light-stimulated mRNA. Complementary hybrid-selected mRNAs were translated in vitro; SDS-PAGE indicates the synthesis of three polypeptides of 25, 27 and 28 kDa. Comparison of the deduced polypeptide sequence with other published CABs reveals greater similarity with PSII-associated proteins but, as with other algal CABs, our sequence does not meet established criteria for inclusion into either type I or type II, so branching of CABs into two types seems to have occurred after the divergence between algae and land plants.

Gene silencing in a polyploid homosporous fern: paleopolyploidy revisited

Because of their high chromosome numbers, homosporous vascular plants were considered paleopolyploids until recent enzyme electrophoretic studies rejected this hypothesis by showing that they express only diploid numbers of isozymes. In polyploid sporophytes of the homosporous fern pelleae rufa, however, progressive diminution of phosphoglucoisomerase activities encoded by one ancestral genome culminates in tetraploid plants exhibiting a completely diploidized electrophoretic phenotype for this enzyme. The demonstration that such gene silencing can make a polyploid fern look isozymically like a diploid questions the validity of isozyme evidence for testing the paleopolyploid hypothesis and supports the proposed role of polyploidization followed by genetic diploidizaton in the evolutionary history of homosporous pteridohytes.