Balancing selection and low recombination affect diversity near the self-incompatibility loci of the plant Arabidopsis lyrata

The self-incompatibility (S-) locus region of plants in the Brassica family is a small genome region. In Arabidopsis lyrata, the S-genes, SRK and SCR, encode the functional female and pollen recognition proteins, which must be coadapted to maintain correct associations between the two component genes, and thus self-incompatibility (SI). Recombinants would be self-compatible and thus probably disadvantageous in self-incompatible species. Therefore, tight linkage between the two genes in incompatibility systems is predicted to evolve to avoid producing such recombinant haplotypes. The evolution of low recombination in S-locus regions has not been rigorously tested. To test whether these regions' per-nucleotide recombination rates differ from those elsewhere in the genome, and to investigate whether the A. lyrata S-loci have the predicted effect on diversity in their immediate genome region, we studied diversity in genes that are linked to the S-loci but are not involved in incompatibility and are not under balancing selection. Compared with other A. lyrata loci, genes linked to the S-loci have extraordinarily high polymorphism. Our estimated recombination in this region, from fitting a model of the effects of S-allele polymorphism on linked neutral sites, supports the hypothesis of locally suppressed recombination around the S-locus.     

Molecular characterization of vegetative incompatibility genes that restrict hypovirus transmission in the chestnut blight fungus Cryphonectria parasitica

Genetic nonself recognition systems such as vegetative incompatibility operate in many filamentous fungi to regulate hyphal fusion between genetically dissimilar individuals and to restrict the spread of virulence-attenuating mycoviruses that have potential for biological control of pathogenic fungi. We report here the use of a comparative genomics approach to identify seven candidate polymorphic genes associated with four vegetative incompatibility (vic) loci of the chestnut blight fungus Cryphonectria parasitica. Disruption of candidate alleles in one of two strains that were heteroallelic at vic2, vic6, or vic7 resulted in enhanced virus transmission, but did not prevent barrage formation associated with mycelial incompatibility. Detailed characterization of the vic6 locus revealed the involvement of nonallelic interactions between two tightly linked genes in barrage formation, heterokaryon formation, and asymmetric, gene-specific influences on virus transmission. The combined results establish molecular identities of genes associated with four C. parasitica vic loci and provide insights into how these recognition factors interact to trigger incompatibility and restrict virus transmission.     

Physical and functional map of an Agrobacterium tumefaciens tumor-inducing plasmid that confers a narrow host range.

Agrobacterium tumefaciens Ag162 induces crown gall disease on an unusually narrow range of host plants. The 231-kilobase Ti plasmid which has been shown to determine host range, was subcloned into the vector pVCK102. By comparing overlaps of cloned insets, maps were constructed for the restriction endonucleases SalI, XhoI, EcoRI, and KpnI. Plasmid incompatibility, octopine catabolism, and at least six virulence genes were localized. Plasmid incompatibility between pTiAg162 and the wide host range plasmid pTiA6 consists of two components: mutual incompatibility and the apparent ability of pTiA6 to block RK2 replication if the pTiAg162 incompatibility locus is linked to the vector pVK102. The octopine catabolism locus maps within the 30 kilobases of DNA separating the two T-DNA regions of pTiAg162. Complementation of avirulent vir mutants of pTiA6 with clones of pTiAg162 DNA did not confer the host range of pTiAg162 but rather restored the wide host range of pTiA6. One potentially important difference between pTiA6 and pTiAg162 is that pTiAg162 T-DNA regions are widely separated.     

Multiple mechanisms for expression of incompatibility by broad-host-range plasmid RK2

By cloning fragments of plasmid DNA, we have shown that RK2 expresses incompatibility by more than one mechanism. One previously identified (R. J. Meyer, Mol. Gen, Genet. 177:155--161, 1979; Thomas et al., Mol. Gen. Genet. 181:1--7, 1981) determinant for incompatibility is linked to the origin of plasmid DNA replication. When cloned into a plasmid vector, this determinant prevents the stable inheritance of a coresident RK2. However, susceptibility to this mechanism of incompatibility requires an active RK2 replicon and is abolished if another replicator is provided. We have also cloned a second incompatibility determinant, encoded within the 54.1- to 56.4-kilobase region of RK2 DNA, which we call IncP-1(II). An RK2 derivative remains sensitive to IncP-1(II), even when it is not replicating by means of the RK2 replicon. The 54.1- to 56.4-kilobase DNA does not confer susceptibility to the IncP-1(II) mechanism, nor does it encode a detectable system for efficient plasmid partitioning. The incompatibility may be related to the expression of genes mapping in the 54.1- to 56.4-kilobase region, which are required for plasmid maintenance and suppression of plasmid-encoded killing functions.     

Ovarian self‐incompatibility in Narcissus papyraceus (Amaryllidaceae) is the result of a pre‐zygotic response

Ovarian self‐incompatibility, including pre‐ and post‐zygotic reactions, is a complex mechanism for which we still lack many details relating to its function and significance. The joint presence of ovarian self‐incompatibility with style polymorphism is a rare combination that is found in the genus Narcissus. Usually, style polymorphic species have heteromorphic (diallelic and linked to style length locus) incompatibility, which prevents fertilization between individuals of the same morph, thereby helping to maintain equal proportions of floral morphs in populations. However, when present, self‐incompatibility in Narcissus is not linked to style polymorphism and cross‐fertilization within each morph is possible. Hence, self‐incompatibility in Narcissus is of particular interest when attempting to unravel the nature of the rejection reaction and aiming to assess possible cryptic differences in the fertilization process in intra‐ and inter‐morph crosses, which might ultimately explain the wide variation of morph‐ratio in the field. We examined the breeding system of Narcissus papyraceus, a style‐dimorphic species that has biased morph ratios in most of its populations. We studied pollen‐tube growth in the pistil and ovule fate after experimentally controlled hand pollinations. The growth of pollen tubes in self‐ and intra‐ and inter‐morph crosses was similar up to the point of micropyle penetration in both morphs but, subsequently, a pre‐zygotic failure appeared to affect male and female gametophytes in selfed pistils. A high proportion of ovules from self‐pollinated flowers showed signs of collapse and self‐pollen tubes were blocked or behaved abnormally before entering the embryo sac. Self‐incompatibility was stronger in the long‐styled morph than in the short‐styled morph. We did not find any conclusive sign of differential functioning between intra‐ and inter‐morph cross‐pollinations in any morph. These results enable us to rule out the possible effects of pollen–pistil interactions in N. papyraceus as a cause of morph‐ratio biases and confirm the exceptional nature of the self‐incompatibility mechanism in this polymorphic species. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 629–643.     

UNIDIRECTIONAL INCOMPATIBILITY BETWEEN POPULATIONS OF DROSOPHILA SIMULANS

Drosophila simulans females from a strain collected at Watsonville, CA produce very few offspring when mated with males from a strain collected at Riverside 510 km away. This incompatibility does not exist in the reciprocal cross. In the incompatible cross, mating and oviposition are normal, but eggs fail to hatch. A survey of other California populations indicates that unidirectional incompatibility is widespread. The incompatibility is maternally inherited over one generation. Using older Riverside males or rearing the strains at 28°C suppresses incompatibility. Culturing the strains on medium with tetracycline restores compatibility, suggesting the involvement of a microorganism.     

IncD, a genetic locus in F responsible for incompatibility with several plasmids of the IncFI group

Summary Cloning of mini-F DNA segments has led to the identification and mapping of a locus, incD, involved in incompatibility reactions with many IncFI plasmids. The cloned incD locus expressed incompatibility with F, R386, and six other IncFI plasmids but not with ColV3-K30 or pHH507 which lack sequence homology with the incD region. A sequence of 360 bp (48.66–49.02 FKB) was found to be sufficient for expression of incD incompatibility. Multicopy vectors containing incD are compatible with each other, but can be displaced by mini-F plasmids deleted for incD. These results indicate that incD-mediated incompatibility reactions require the presence of replication genes to which incD is normally linked. The degree of incompatibility exercised by incD is moderate compared with that of other inc loci in F, suggesting that incD is involved in an aspect of plasmid maintennce, such as partition, different from the functions of the other inc loci.     

Sea urchin bindin divergence predicts gamete compatibility

Studies on the evolution of reproductive proteins have shown that they tend to evolve more rapidly than other proteins, frequently under positive selection. Progress on understanding the implications of these patterns is possible for marine invertebrates, where molecular evolution can be linked to gamete compatibility. In this study, we surveyed data from the literature from five genera of sea urchins for which there was information on gamete compatibility, divergence of the sperm-egg recognition protein bindin, and mitochondrial divergence. We draw three conclusions: (1) bindin divergence at nonsynonymous sites predicts gamete compatibility, whereas (2) bindin divergence at synonymous sites and mitochondrial DNA divergence do not, and (3) as few as 10 amino acid changes in bindin can lead to complete gamete incompatibility between species. Using mitochondrial divergence as a proxy for time, we find that complete gamete incompatibility can evolve in approximately one and a half million years, whereas sister species can maintain complete gamete compatibility for as long as five million years.     

Unilateral incompatibility in Capsicum (Solanaceae): occurrence and taxonomic distribution

BACKGROUND AND AIMS: Unilateral incompatibility (UI) occurs when pollinations between species are successful in one direction but not in the other. Self-incompatible (SI) species frequently show UI with genetically related, self-compatible (SC) species, as pollen of SI species is compatible on the SC pistil, but not vice versa. Many examples of unilateral incompatibility, and all those which have been studied most intensively, are found in the Solanaceae, particularly Lycopersicon, Solanum, Nicotiana and Petunia. The genus Capsicum is evolutionarily somewhat distant from Lycopersicon and Solanum and even further removed from Nicotiana and Petunia. Unilateral incompatibility has also been reported in Capsicum; however, this is the first comprehensive study of crosses between all readily available species in the genus. METHODS: All readily available (wild and domesticated) species in the genus are used as plant material, including the three genera from the Capsicum pubescens complex plus eight other species. Pollinations were made on pot-grown plants in a glasshouse. The number of pistils pollinated per cross varied (from five to 40 pistils per plant), depending on the numbers of flowers available. Pistils were collected 24 h after pollination and fixed for 3-24 h. After staining, pistils were mounted in a drop of stain, squashed gently under a cover slip and examined microscopically under ultra-violet light for pollen tube growth. KEY RESULTS: Unilateral incompatibility is confirmed in the C. pubescens complex. Its direction conforms to that predominant in the Solanaceae and other families, i.e. pistils of self-incompatible species, or self-compatible taxa closely related to self-incompatible species, inhibit pollen tubes of self-compatible species. CONCLUSIONS: Unilateral incompatibility in Capsicum does not seem to have arisen to prevent introgression of self-compatibility into self-incompatible taxa, but as a by-product of divergence of the C. pubescens complex from the remainder of the genus.     

Characterization of a diagnostic Fab fragment binding trimeric Lewis X

Lewis X trisaccharides normally function as essential cell–cell interaction mediators. However, oligomers of Lewis X trisaccharides expressed by the parasite Schistosoma mansoni seem to be related to its evasion of the immune response of its human host. Here we show that monoclonal antibody 54‐5C10‐A, which is used to diagnose schistosomiasis in humans, interacts with oligomers of at least three Lewis X trisaccharides, but not with monomeric Lewis X. We describe the sequence and the 2.5 Å crystal structure of its Fab fragment and infer a possible mode of binding of the polymeric Lewis X from docking studies. Our studies indicate a radically different mode of binding compared to Fab 291‐2G3‐A, which is specific for monomeric Lewis X, thus providing a structural explanation of the diagnostic success of 54‐5C10‐A. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Vegetative Incompatibility and the Mating-Type Locus in the Cellular Slime Mold DICTYOSTELIUM DISCOIDEUM

The genetic basis of vegetative incompatibility in the cellular slime mold, Dictyostelium discoideum, is elucidated. Vegetatively compatible haploid strains from parasexual diploids at a frequency of between 10^-6 and 10^-5, whereas "escaped" diploids are formed between vegetatively incompatible strains at a frequency of ~10^-8. There is probably only a single vegetative incompatibility site, which appears to be located at, or closely linked to, the mating-type locus. The nature of the vegetative incompatibility is deduced from parasexual diploid formation between wild isolates and tester strains of each mating type, examination of the frequency of formation of "escaped" diploids formed between vegetatively incompatible strains, and examination of the mating type and vegetative incompatibility of haploid segregants obtained from "escaped" diploids.     

Heterokaryon incompatibility function of barrage-associated vegetative incompatibility genes (vic) in Cryphonectria parasitica

Six vegetative incompatibility (vic) loci have been identified in Cryphonectria parasitica based on barrage formation during mycelial interactions. We used hygromycin B- and benomyl-resistance as forcing markers in C. parasitica strains to test whether heteroallelism at each vic locus prevents heterokaryon formation following mycelial interactions. Paired strains that had allelic differences at any of vic1, 2, 3, 6 or 7 but not vic4 displayed heterokaryon incompatibility function, as recognized by slow growth or aberrant morphology. While clearly forming barrages in mycelial interactions, paired strains with different alleles at vic4 formed stable heterokaryons. With examples from other fungi, this inconsistency at vic4 suggests that barrage formation and heterokaryon incompatibility are not different manifestations of the same process. Rather, the evidence indicates that heterokaryon incompatibility represents a component of a vegetative incompatibility system that may also use cell-surface or extracellular factors to trigger programmed cell death to modulate nonself recognition in fungi.     

Site-directed mutations in the repA C-terminal region of plasmid Rts1: pleiotropic effects on the replication and autorepressor functions.

We induced site-directed mutations near the 3' terminus of the gene repA, which encodes the protein of 288 amino acid residues essential for plasmid Rts1 replication, and obtained seven repA mutants. Three of them contained small deletions at the 3' terminus. Mutant repAz delta C4, which encodes a RepA protein that lacks the C-terminal four amino acids, expressed a high-copy-number phenotype and had lost both autorepressor and incompatibility functions. Deletion of one additional amino acid residue to form the RepAz delta C5 protein caused restoration of the wild-type copy number and strong incompatibility. Studies of the remaining four repA mutants, each of which contained a single amino acid substitution near the RepA C terminus, suggested that Lys-268 is involved in both ori(Rts1) activation and autorepressor-incompatibility activities and that Arg-279 contributes to ori(Rts1) activation but not to incompatibility. Lys-268 is part of a dual-lysine sequence with Lys-267 and is located 21 amino acids upstream of the RepA C terminus. A dual-lysine sequence is also found at a similar position in both mini-F RepE and mini-P1 RepA proteins.     

Incompatibility properties of the IncFIII/FIV haemolytic plasmid pSU316 when integrated in the Escherichia coli chromosome

The haemolytic plasmid pSU316 is incompatible with members of the IncFIII and IncFIV incompatibility groups. Plasmid pSU307 (pSU316 hlyC::Tn5) was inserted by integrative suppression into the chromosome of JW112, a temperature-sensitive dnaA mutant of Escherichia coli. The incompatibility properties of this strain (SU51) were studied and it was found that: (1) plasmid pSU306 (pSU316 hlyA::Tn802) was rapidly lost from strain SU51 both at 30 degrees C and 42 degrees C; (2) the IncFIII plasmid pSU397 (ColB-K98::Tn802) was lost from strain SU51 and at 42 degrees C but not at 30 degrees C; and (3) the IncFIV plasmid R124 was stably maintained in strain SU51 at both temperatures. Revertants of pSU307 to the autonomous state could be obtained from SU51. These revertants exerted incompatibility towards the prototype plasmids pSU306, pSU397 and R124 in the same way as pSU307 itself. Thus, strain SU51 provided a suitable method for distinguishing the three different incompatibility determinants of plasmid pSU316.     

Dence for a gene in rats affecting lymphocyte responsiveness to PHA

A gene controlling high responsiveness of lymphocytes to in vitro stimulation by PHA was transferred from the Lewis strain of rats to the BN background by ten generations of backcrossing. The high-responder phenotype was initially defined on the basis of incorporation of³H-thymidine, but we show that this trait also involves higher levels of mitotic activity than are observed with low responder lymphocytes. This gene is not closely linked to any histocompatibility locus which could be detected by skin grafting, and it does not appear to affect the proportion of T lymphocytes.     

Relationship of the replication and incompatibility genes of an IncFVI haemolysin plasmid with other F-like haemolysin plasmids

The replication and incompatibility region of the IncFVI plasmid pSU502 has been isolated by in vitro DNA manipulation as part of a 12.6 kb plasmid, denominated pSU503. Plasmid pSU503 was strongly incompatible with its parental plasmid, pSU1, but was fully compatible with the haemolytic plasmids pSU316 (IncFIII/IV), pHly152 (IncI2) and pSU233 (Inc-pSU233). Furthermore, the 6.9 kb EcoRI fragment of pSU503 which carries the replication and incompatibility determinants of pSU1 did not show any detectable homology (less than 70%) with any of the haemolysin-determining plasmids with which it is compatible. Thus, homologous haemolysin determinants have become linked to apparently unrelated replicons.     

Differential expression of glycoside residues in the mammalian zona pellucida

The mammalian zona pellucida is an extracellular matrix surrounding the oocyte, and is composed of three major glycoproteins, ZP1, ZP2, and ZP3. Previous studies have suggested that the sperm receptor activity of the zona pellucida resides in specific oligosaccharide chains on the ZP3 glycoprotein. However, the nature of the terminal monosaccharide(s) on these glycosidic chains to which sperm bind is a matter of active debate. Evidence has been presented to support a role for at least three distinct monosaccharides in sperm binding, alpha-galactose, L-fucose on Lewis X structures, and beta-N-acetylglucosamine. Previous studies have shown that beta-N-acetylglucosamine is uniformly distributed throughout the zona matrix. In this study, we have investigated the expression and distribution of alpha-galactose and fucose moieties during the maturation of the zona pellucida in mouse, rat, and hamster. Interestingly, alpha-galactose residues are expressed only during later stages of zona secretion and, consequently, are confined to the inner portions of the mature zona pellucida in mouse and rat. In hamster, alpha-galactose residues are only detectable in the zona pellucida of ovulated eggs, and are not found in ovarian oocytes. Fucosyl residues linked to Lewis X glycosides are not detectable at any stage of zona maturation in these three species, whereas fucose linked to N-linked core oligosaccharides are present throughout the zona. These studies indicate a previously unappreciated heterogeneity in the composition of zona glycosides. The specific localization of alpha-galactose residues to the inner portions of the zona matrix suggest a role in the later stages of sperm penetration through the zona. Finally, due to their absence from the zona surface, alpha-galactose and Lewis X fucosyl residues are not likely to be mediators of primary sperm binding.     

Biological activities of human mannose-binding lectin bound to two different ligand sugar structures, Lewis A and Lewis B antigens and high-mannose type oligosaccharides.

The biological activities of mannose-binding lectin (MBL) which binds to different ligands on mammalian cells were examined using two types of Colo205 cells, a human colon adenocarcinoma cell line: one naturally expressing Lewis A and Lewis B antigens as ligands for MBL (NT-Colo205), and the other modified to express high-mannose type oligosaccharides by treatment with benzyl-2-acetamide-2-deoxy-alpha-galactopyranoside and 1-deoxymannojirimycin (Bz+dMM-Colo205). Although the final lysis was not observed, the deposition of C4 and C3 was observed on both types of Colo205 cells after treatment with MBL and complements as a result of complement activation by MBL. MBL bound to Bz+dMM-Colo205 could also activate human peripheral blood leukocytes and induce superoxide production; however, MBL bound to NT-Colo205 could not. This may be explained by the lower affinity of MBL to Lewis A and Lewis B antigens than to high-mannose type oligosaccharides under physiological conditions, since MBL bound to NT-Colo205 was more easily released from the cell surface than that bound to Bz+dMM-Colo205 at 37 degrees C. These findings suggest that the difference in the affinity of MBL to its ligands could influence the expression of some biological activities of MBL.     

Effects of changing temperature regimes on resistance to races of Melampsora medusae in a cultivar of poplar

Leaf discs of Populus deltoides cv. W-79/307 inoculated with race 4–C of Melampsora medusae, give a compatible reaction when incubated at 16°C (LT), but an incompatible reaction at 26°C (HT). When, over a 12–day period, sets of inoculated leaf discs were reciprocally transferred between the temperature regimes (LT to HT, or HT to LT), incubation for as short as 15 h at HT resulted in incompatibility which was not reversed by subsequent incubation at LT. In contrast, incubation of the inoculated discs at LT for at least 4 days was necessary for the development of a compatible reaction following transfer to HT. Further, incompatibility induced in discs by inoculation with race 4–C and incubation at HT is epistatic to expected compatibility following subsequent inoculation with race 4–M, a temperature non-sensitive biotype. The rapidity, irreversibility and epistatic nature of the temperature-induced incompatibility suggests that initial recognition in this pathosystem may be for incompatibility. The significance of these results in this host/pathogen system is discussed.     

Unusual heterostyly: style dimorphism and self-incompatibility are not tightly associated in Lithodora and Glandora (Boraginaceae)

Background and Aims

Heterostyly is a floral polymorphism characterized by the reciprocal position of stamens and stigmas in different flower morphs in a population. This reciprocal herkogamy is usually associated with an incompatibility system that prevents selfing and intra-morph fertilization, termed a heteromorphic incompatibility system. In different evolutionary models explaining heterostyly, it has been alternately argued that heteromorphic incompatibility either preceded or followed the evolution of reciprocal herkogamy. In some models, reciprocal herkogamy and incompatibility have been hypothesized to be linked together during the evolution of the heterostylous system.

Methods

We examine the incompatibility systems in species with different stylar polymorphisms from the genera Lithodora and Glandora (Boraginaceae). We then test whether evolution towards reciprocal herkogamy is associated with the acquisition of incompatibility. To this end, a phylogeny of these genera and related species is reconstructed and the morphological and reproductive changes that occurred during the course of evolution are assessed.

Key Results

Both self-compatibility and self-incompatibility are found within the studied genera, along with different degrees of intra-morph compatibility. We report for the first time extensive variability among members of the genus Glandora and related species in terms of the presence or absence of intraspecies polymorphism and heteromorphic incompatibility. Overall, our results do not support a tight link between floral polymorphism and incompatibility systems.

Conclusions

The independent evolution of stylar polymorphism and incompatibility appears to have occurred in this group of plants. This refutes the canonical view that there is strong linkage between these reproductive traits.