Mutational bias affects protein evolution in flowering plants

Amino acid sequences from several thousand homologous gene pairs were compared for two plant genomes, Oryza sativa and Arabidopsis thaliana. The Arabidopsis genes all have similar G+C (guanine plus cytosine) contents, whereas their homologs in rice span a wide range of G+C levels. The results show that those rice genes that display increased divergence in their nucleotide composition (specifically, increased G+C content) showed a corresponding, predictable change in the amino acid compositions of the encoded proteins relative to their Arabidopsis homologs. This trend was not seen in a "control" set of rice genes that had nucleotide contents closer to their Arabidopsis homologs. In addition to showing an overall difference in the amino acid composition of the homologous proteins, we were also able to investigate the biased patterns of amino acid substitution since the divergence of these two species. We found that the amino acid exchange matrix was highly asymmetric when comparing the High G+C rice genes with their Arabidopsis homologs. Finally, we investigated the possible causes of this biased pattern of sequence evolution. Our results indicate that the biased pattern of protein evolution is the consequence, rather than the cause, of the corresponding changes in nucleotide content. In fact, there is an even more marked asymmetry in the patterns of substitution at synonymous nucleotide sites. Surprisingly, there is a very strong negative correlation between the level of nucleotide bias and the length of the coding sequences within the rice genome. This difference in gene length may provide important clues about the underlying mechanisms.     

The origin of multiple B mating specificities in Coprinus cinereus

Mushrooms, such as Coprinus cinereus, possess large families of pheromones and G-protein-coupled receptors that are sequestered at the B mating-type locus and whose function is to confer vast numbers of different mating types. This ability results from complex patterns of cognate and noncognate pheromone/receptor pairings, which potentially offer a unique insight into the molecular interaction between receptor and ligand. In this study we have identified many more members of these families by molecular analysis of strains collected worldwide. There are three groups of genes at each B locus. We have identified two alleles of group 1, five alleles of group 2, and seven alleles of group 3, encoding in total 14 different receptors and 29 different pheromones. The specificity of many newly identified alleles was determined by transformation analysis. One striking finding was that receptors fall into groups based on sequence homology but these do not correspond to the groups defined by position, indicating that complex evolutionary processes gave rise to the B loci. While additional allelic versions may occur in nature, the number of B specificities possible by combination of the alleles that we describe is 70, close to previous estimates based on population analysis.     

The mating game: pollination and fertilization in flowering plants

Recent work has revealed signaling molecules that control pollination, including small peptides that mediate pollen recognition and glycoproteins that support pollen tube growth. The polarized growth of pollen tubes requires a calcium-mediated signal cascade, and cues derived from the haploid and diploid ovule cells guide pollen tubes to the eggs.     

The origin and function of self-incompatibility in flowering plants

Summary The evolutionary significance of self-incompatibility (SI) traditionally has been linked to reduced inbreeding through enforced outcrossing. This view is founded on the premise that outcrossing reduces inbreeding. It is important, when considering the evolutionary significance of any genetic system, to try to distinguish those factors related to the evolution of, from those related to the maintenance of, the system in question. Three factors are considered important for the maintenance of SI: (1) phylogenetic constraint in species descended from SI ancestors, (2) reduced inbreeding in populations, and (3) fitness benefits to individuals resulting from the avoidance of selfing. I suggest that the first two factors should be rejected when considering the origin of SI (whether one or more origins are hypothesized) and that the increase in individual fitness resulting from the avoidance of self-fertilization among individuals that are heterozygous for deleterious alleles may be sufficient to account for the origin of SI. Self-fertilization in plants (except in species that predominantly self-fertilize) generally results in a reduction in fitness of some individuals due to the increased expression of deleterious or lethal recessive alleles, regardless of the degree of inbreeding in the population or the frequency of the allele in question. Inbreeding is a consequence of population structure in many outcrossing plant species. Complex (multi-locus and multi-allelic) systems of SI exist that reduce inbreeding. However, it is argued that these are derived either from simpler systems of SI that may have very little or no effect on inbreeding, in which case any effect on level of inbreeding is secondary, or are not true self-incompatibility systems and are part of a regulatory system that serves to balance the level of inbreeding and outbreeding. Multi-locus and multi-allelic systems of SI and heteromorphic systems of SI are discussed in terms of derived versus ancestral characteristics. A reassessment of the role of breeding systems in the development of a population structure promoting inbreeding is suggested, which may have been of crucial importance in the success and diversification of angiosperms.     

The mating consequences of sexual segregation within inflorescences of flowering plants

Many co-sexual plants segregate female and male function among flowers on an inflorescence through dichogamy or the production of unisexual flowers. Sexual segregation may reduce self-pollination among flowers within inflorescences (geitonogamy), thereby increasing the pollen available for export to other plants. To assess these complementary roles we manipulated the simultaneously hermaphroditic (adichogamous) flowers of Eichhornia paniculata to produce ten-flowered inflorescences with either female above male flowers (female/male inflorescences) or male/female inflorescences, which competed for mating opportunities with five-flowered adichogamous inflorescences. Because of the upward movement of bumble-bees, selfing increased upward in adichogamous inflorescences (overall female selfing rate s+/-s.e.=0.320+/-0.026). Female flowers of male/female inflorescences selfed less than flowers in corresponding positions in adichogamous inflorescences so s fell to 0.135+/-0.027. In contrast, all-female flowers of female/male inflorescences selfed similarly to upper flowers on adichogamous inflorescences, elevating s (0.437+/-0.043). During 1997, male/female inflorescences sired more outcrossed seeds than female/male or adichogamous inflorescences, whereas during 1994 flowers on male/female inflorescences received fewer visits than those of adichogamous inflorescences, reducing their outcross siring success. Hence, sexual segregation limits geitonogamy and enhances outcross siring success when it does not affect pollinator behaviour, illustrating the importance of both female and male function in inflorescence design.     

Impact of mating systems on patterns of sequence polymorphism in flowering plants

A fundamental challenge in population genetics and molecular evolution is to understand the forces shaping the patterns of genetic diversity within and among species. Among them, mating systems are thought to have important influences on molecular diversity and genome evolution. Selfing is expected to reduce effective population size, Ne, and effective recombination rates, directly leading to reduced polymorphism and increased linkage disequilibrium compared with outcrossing. Increased isolation between populations also results directly from selfing or indirectly from evolutionary changes, such as small flowers and low pollen output, leading to greater differentiation of molecular markers than under outcrossing. The lower effective recombination rate increases the likelihood of hitch-hiking, further reducing within-deme diversity of selfers and thus increasing their genetic differentiation. There are also indirect effects on molecular evolutionary processes. Low Ne reduces the efficacy of selection; in selfers, selection should thus be less efficient in removing deleterious mutations. The rarity of heterozygous sites in selfers leads to infrequent action of biased conversion towards GC, which tends to increase sequences' GC content in the most highly recombining genome regions of outcrossers. To test these predictions in plants, we used a newly developed sequence polymorphism database to investigate the effects of mating system differences on sequence polymorphism and genome evolution in a wide set of plant species. We also took into account other life-history traits, including life form (whether annual or perennial herbs, and woody perennial) and the modes of pollination and seed dispersal, which are known to affect enzyme and DNA marker polymorphism. We show that among various life-history traits, mating systems have the greatest influence on patterns of polymorphism.     

Male and female synchrony and the regulation of mating in flowering plants

Successful mating clearly requires synchronous development of the male and female sexual organs. Evidence is accumulating that this synchrony of development also persists after pollination, with both pollen and pistil following complex, but highly integrated developmental pathways. The timing of the male-female interaction is crucial for the pistil, which, far from being a mature passive structure, is engaged in a continuing programme of development: only being receptive to the advances of the pollen for a relatively short window of time. This developmental programme is most conspicuous in the ovary, and this review focuses on the interaction between the male and female tissues in this structure. The review first considers pollen tube development in the ovary, concentrating of the mechanisms by which its growth is modulated at various control points associated with structures within the ovary. Second, alterations to this 'normal' developmental programme are reviewed and considered in the context of a breakdown of developmental synchrony. Finally, the consequences of male-female developmental synchrony and asynchrony are explored. Clearly, a synchronous male-female relationship leads to a successful fertilization. However, lack of synchrony also occurs, and could emerge as a powerful tool to investigate the regulation of mating.     

Evolution of incompatibility systems in plants: Complementarity and the mating locus in flowering plants and fungi

Summary The restriction of sexual pairing by a specificity gene is considered to be an ancient development in the plant kingdom. The diversity and general parallelism of incompatibility systems seen amongst the phyla at the present time can be rationalized in terms of the association of various derived forms of the ancestral specificity unit with differing spectra of accessory factors controlling sexual physiology in the different phyla. Sexual morphogenesis has become divided into distinct phases under the control of complementary genes. These phases are initiated by a regulatory system of Co-ordinator genes which control the order in which groups of morphogenetic genes are expressed during development. The entire sexual cycle will be completed only if all the complementary groups are activated in the appropriate sequence. The present article discusses essential features of the evolution of the breeding locus in different phyla. These features are consistent in themselves with the present data and are not dependent on the proposed ancient origin of the specificity gene.The above hypothesis throws light on the (1) evolution of the complex mating loci in flowering plants and fungi; (2) evolution of complementary incompatibility and heteromorphic incompatibility in flowering plants; (3) anomalous cross-compatibility behaviour of mutants in the fungus Schizophyllum commune; (4) nature of homothallism in higher fungi; (5) mode of origin of new functional self-incompatibility alleles; and (6) homogenic and heterogenic incompatibility.     

Molecular evolution of Bowman-Birk type proteinase inhibitors in flowering plants

The Bowman-Birk family (BBI) of proteinase inhibitors is probably the most studied family of plant inhibitors. We describe the primary structure and the gene expression profile of 14 putative BBIs from the sugarcane expressed sequence tag database and show how we used these newly discovered sequences together with 87 previously described BBI sequences from the GenBank database to construct phylogenetic trees for the BBI family. Phylogenetic analysis revealed that BBI-type inhibitors from monocotyledonous and dicotyledonous plants could be clearly separated into different groups, while the overall topology of the BBI tree suggests a different pattern of evolution for BBI families in flowering plants. We also found that BBI proteinase inhibitors from dicotyledonous plants were well conserved, accumulating only slight differences during their evolution. In addition, we found that BBIs from monocotyledonous plants were highly variable, indicating an interesting process of evolution based on internal gene duplications and mutation events.     

Divergent mating systems and parental conflict as a barrier to hybridization in flowering plants

Parental conflicts can lead to antagonistic coevolution of the sexes and of parental genomes. Within a population, the resulting antagonistic effects should balance, but crosses between populations can reveal conflict. Parental conflict is less intense in self-pollinating plants than in outcrossers because outcrossing plants are pollinated by multiple pollen donors unrelated to the seed parent, while a self-pollinating plant is primarily pollinated by one individual (itself). Therefore, in crosses between plants with differing mating systems, outcrossing parents are expected to "overpower" selfing parents. We call this the weak inbreeder/strong outbreeder (WISO) hypothesis. Prezygotically, such overpowering can alter pollination success, and we argue that our hypothesis explains a common pattern of unilateral incompatibility, in which pollen from self-incompatible populations fertilizes ovules of self-compatible individuals but the reciprocal cross fails. A postzygotic manifestation of overpowering is aberrant seed development due to parent-of-origin effects such as genomic imprinting. We evaluate evidence for the WISO hypothesis by reviewing published accounts of crosses between plants of different mating systems. Many, but not all, of such reports support our hypothesis. Since parental conflicts can perturb fertilization and development, such conflicts may strengthen reproductive barriers between populations, contributing to speciation.     

Self-incompatibility in flowering plants

Self-pollination in some groups of plants is prevented by a sophisticated biochemical signalling system. The molecule active in the female emerges as a highly charged glycoprotein, but the identity of the male determinant remains unknown. Studies of both the molecular biology and the physiology of the interaction suggest that the female polypeptide belongs to a family of glycoproteins which may play an additional, and more general, role in pollination. Pollen compatibility is controlled by one of two genetic systems and new information indicates a mechanism by which they may have arisen, together with the different stigma types with which they are correlated.     

How plants see themselves--self-incompatibility in flowering plants

Plants have been propagating themselves by cloning for millennia. It is, however, widely recognised that mixing genes with other individuals of the same species makes better evolutionary sense, as it provides the variation that is the raw material for natural selection. How, then, do some plants prevent self-fertilisation?     

Infraspecific categories in flowering plants

Infraspecific categories imply infraspecific classification, but there are few species whose internal diversity has been sufficiently studied to permit this in any detail. Important variation may be physiological, continuous and unassociated with convenient morphological markers. Conspicuous variation may be biologically trivial and the use of names for these variants gives a misleading view of the species-structure. If we are to classify we must know the relation between the internal and external characters. The suitability of a hierarchical system cannot be assumed. Informal classifications are likely to be of more use than those provided by the Code of Nomenclature. Nevertheless variation undesignated may easily become variation overlooked.     

Egg activation in flowering plants

Compared to animals and algae, egg activation in flowering plants is still poorly understood because of the inaccessibility and complexity of the fertilization process which is double and internal. However, the development of in vitro fertilization (IVF) systems in maize and a few other plants, despite some limitations, offers new possibilities for the study of early post- fusional events and signals leading to egg activation under defined conditions. This review reports recent data on calcium events induced by gamete fusion during maize IVF and presents perspectives on the role of calcium in egg activation and in early development. Received: 2 December 2000 / Accepted: 7 June 2001     

Infraspecific categories in flowering plants

Infraspecific categories imply infraspecific classification, but there are few species whose internal diversity has been sufficiently studied to permit this in any detail. Important variation may be physiological, continuous and unassociated with convenient morphological markers. Conspicuous variation may be biologically trivial and the use of names for these variants gives a misleading view of the species-structure. If we are to classify we must know the relation between the internal and external characters. The suitability of a hierarchical system cannot be assumed. Informal classifications are likely to be of more use than those provided by the Code of Nomenclature. Nevertheless variation undesignated may easily become variation overlooked.     

Cryptic dioecy in flowering plants

In some dioecious plant species, mates and/or females have large and presumably costly opposite-sex structures that are sterile. This is termed 'cryptic dioecy'. Several new cases of cryptic dioecy have recently been studied. They may give information about the minimal requirements for the evolution of separate sexes from hermaphroditism, because the most important differences contributing to the initial advantage of the breeding system have not been obscured by further developments. Reviewed in this light, cryptic dioecy can provide evidence on the role of reallocation of reproductive resources in the evolution of dioecy.     

Sex chromosomes in flowering plants

Sex chromosomes in dioecious and polygamous plants evolved as a mechanism for ensuring outcrossing to increase genetic variation in the offspring. Sex specificity has evolved in 75% of plant families by male sterile or female sterile mutations, but well-defined heteromorphic sex chromosomes are known in only four plant families. A pivotal event in sex chromosome evolution, suppression of recombination at the sex determination locus and its neighboring regions, might be lacking in most dioecious species. However, once recombination is suppressed around the sex determination region, an incipient Y chromosome starts to differentiate by accumulating deleterious mutations, transposable element insertions, chromosomal rearrangements, and selection for male-specific alleles. Some plant species have recently evolved homomorphic sex chromosomes near the inception of this evolutionary process, while a few other species have sufficiently diverged heteromorphic sex chromosomes. Comparative analysis of carefully selected plant species together with some fish species promises new insights into the origins of sex chromosomes and the selective forces driving their evolution.