Quick, practical selection of effective seeds for homology search.

It has been observed that in homology search gapped seeds have better sensitivity than ungapped ones for the same cost (weight). In this paper, we propose a probability leakage model (a dissipative Markov system) to elucidate the mechanism that confers power to spaced seeds. Based on this model, we identify desirable features of gapped search seeds and formulate an extremely efficient procedure for seed design: it samples from the set of spaced seed exhibiting those features, evaluates their sensitivity, and then selects the best. The sensitivity of the constructed seeds is negligibly less than that of the corresponding known optimal seeds. While the challenging mathematical question of characterizing optimal search seeds remains open, we believe that our eminently efficient and effective approach represents a satisfactory solution from a practitioner's viewpoint.     

On Subset Seeds for Protein Alignment

We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We propose several different design methods and use them to construct several alphabets. We then perform a comparative analysis of seeds built over those alphabets and compare them with the standard Blastp seeding method [2], [3], as well as with the family of vector seeds proposed in [4]. While the formalism of subset seeds is less expressive (but less costly to implement) than the cumulative principle used in Blastp and vector seeds, our seeds show a similar or even better performance than Blastp on Bernoulli models of proteins compatible with the common BLOSUM62 matrix. Finally, we perform a large-scale benchmarking of our seeds against several main databases of protein alignments. Here again, the results show a comparable or better performance of our seeds versus Blastp.     

Designing sensitive and specific spaced seeds for cross-species mRNA-to-genome alignment.

As the demand for accurately aligning gene sequences to the genome of a related species grows with the sequencing of new genomes, spaced seeds emerge as a promising vehicle for increasing alignment sensitivity. We extend the existing {0, 1} match-mismatch models for sensitivity evaluation to take into account the compositional structure of coding sequences and ultimately produce seeds better suited to this particular application. Designing seeds for alignment programs, however, needs to balance sensitivity and specificity.We assess the effects of seed variations on both sensitivity and specificity in an extended model that incorporates transitions and differentiates among the three codon positions, and show that spaced seeds with transitions offer a better sensitivity-specificity tradeoff. Furthermore, we propose a theoretical formulation for rigorously assessing seed specificity, starting from Bernoulli and Markov models of the mRNA and genomic sequences. Within this framework, we perform the first comprehensive analysis of seeds to serve as a blueprint for selecting sensitive and specific seeds for practical applications. Our analyses show that specificity is relatively constant for seeds of a given weight, while sensitivity varies widely, with the highest values attained by seeds allowing a small (2-6) number of transitions.A strategy for designing seeds, therefore, is to first select the weight of the seed by identifying the desired sensitivity-specificity tradeoff, then choose the most sensitive seed(s) within that weight group. We illustrate our methods with the alignment of chicken coding sequences against the human genome assembly version HG17.     

Spicing up restoration: can chili peppers improve restoration seeding by reducing seed predation?

Seed predation by rodents presents a significant barrier to native plant recruitment and can impede restoration seeding efforts. In nature, some plants contain secondary defense compounds that deter seed predators. If these natural defense compounds can be applied to unprotected seeds to inhibit rodent granivores, this approach could improve restoration seeding. Capsaicin is the active ingredient in chili pepper (Capsicum spp.) seeds that creates the burning sensation associated with human consumption of hot peppers. This compound has a similar effect on other mammals and is believed to have evolved as a deterrent to rodent seed predators. We used seed‐coating techniques to attach powder ground from Bhut Jolokia (Capsicum chinense) peppers to native plant seeds and evaluated the efficacy of these seed coatings for deterring rodent seed predation and enhancing native plant recruitment using laboratory and field experiments. Laboratory feeding trials demonstrated that native deer mice (Peromyscus maniculatus) consumed far fewer pepper‐coated seeds compared to untreated control seeds. Field seed‐addition experiments consistently demonstrated that rodent seed predation reduced native plant recruitment over the 4‐year study. Coating techniques used in the first 3 years were not persistent enough to reduce rodent seed predation effects on plant recruitment. However, a more persistent coating applied in conjunction with late‐winter sowing negated rodent seed predation effects on recruitment in year 4. Our results demonstrate that coating seeds with natural plant defense compounds may provide an effective, economical way to improve the efficacy of plant restoration by deterring seed predation by ubiquitous rodent granivores.     

A novel cellular automata approach: seed input/output of the alien species Leucaena leucocephala in the soil and the effects of climate changes

The potential impact of the soil seed bank of a given species and subsequent population persistence will depend on the robustness of the seeds against depletion. Invasiveness is frequently linked to this behavior and successful control of invasive species depends on reducing the size of their seed banks. We propose a hybrid model that simulates the seed bank dynamics in association with their physical dormancy (PD) based on experimental data on seed bank depletion of a Leucaena leucocephala population during the dispersal phase. The hybrid model uses cellular automata (CA) and Monte Carlo techniques. The sensitivity analysis revealed that the model delivers reproducible and reliable results. Then, we discuss the ability of the hybrid model to predict the effect of seasonal climate change. A 2.0 °C increase in temperature was enough to cause a considerable impact in the seed depletion curve, and after 1 year, ~?75% of the seeds had already disappeared from the seed bank. The proposed hybrid CA model can be used to study soil-stored seed banks with physical dormancy, and could be applied to other Fabaceae species with similar seed traits. We believe that this computational model contributes to a better understanding of seed bank dynamics and will aid in the control of invasive species and for testing different scenarios to reduce or eliminate seed banks that have already been formed.

     

A novel approach to an old problem: tracking dispersed seeds

Animals are the principal vectors of dispersal for a large number of plant species. Unfortunately it is not easy to discern their movement patterns or the fate of their dispersed seeds. Many animals transport seeds by consuming them and then, some time later, defecating them. Others gather seeds and then store them for later consumption. Both circumstances lead to a set of seeds that have been dispersed in a clumped pattern, which offers a unique opportunity to assess seed movements. We introduce a novel approach that uses maternally inherited seed tissue to quantify the genetic structure of dispersed seed pools. This direct approach measures the genetic variability within and among seed pools, and estimates the scale of seed movement, without requiring a highly polymorphic battery of markers or the location and genotypes of all possible seed parents. We demonstrate this approach with the specific case of seed transport of valley oak (Quercus lobata) acorns by acorn woodpeckers (Melanerpes formicivorus). These territorial birds store acorns in drilled holes in the bark of trees, called granaries. We sampled stored acorns from different granaries, extracted DNA from the maternally inherited pericarp, and then assessed individuals for three microsatellite markers. We found extremely high genetic structure among granaries, a low number of effective seed donors per granary, and restricted seed movement. A maternity analysis performed on the same sample with seven microsatellites confirms acorn transport is limited to approximately 100-m radius. Our findings provide insight into the foraging and seed-dispersal behaviour of acorn woodpeckers, with an approach that can be widely extended to other systems.     

Phospholipase Dα1‐mediated phosphatidic acid change is a key determinant of desiccation‐induced viability loss in seeds

High sensitivity of seeds to water loss is a widespread phenomenon in the world's plant species. The molecular basis of this trait is poorly understood but thought to be associated with critical changes in membrane function. We profiled membrane lipids of seeds in eight species with varying levels of desiccation tolerance and found a close association between reducing seed viability and increasing phosphatidic acid (PA). We applied hydration–dehydration cycles to Arabidopsis seeds, which are normally desiccation tolerant, to mimic the onset of desiccation sensitivity with progression towards germination and examined the role of phospholipase D (PLD) in desiccation stress‐induced production of PA. We found that PLDα1 became more abundant and migrated from the cytosol to the membrane during desiccation, whereas PLDδ did not change, and that all desiccation‐induced PA was derived from PLDα1 hydrolysis. When PLDα1 was suppressed, the germination level after each hydration–dehydration cycle improved significantly. We further demonstrated that PLDα1‐mediated PA formation modulates desiccation sensitivity as applying its inhibitor improved seed desiccation tolerance and its suppression in protoplasts enhanced survival under dehydration. The insights provided by comparative lipidomics enable us to propose a new membrane‐based model for seed desiccation stress and survival.     

海草种子特性与海草床修复

海草床面积的急剧减少已引起人们对海草床生态修复的重视, 种子在海草床修复中具有较大的应用潜力。该文系统归纳了近年来有关海草种子的研究概况及其应用进展: 从种子生物学和生态学角度对海草种子的形态结构、发育、散布、休眠和萌发进行了归纳比较; 提出了在研究天然海草种子库的同时, 有必要建立人工海草种子库的观点, 并指出建立和完善人工海草种子库需基于种子生物学和生态学研究, 以指导种子的采集和保存; 对海草种子的播种方式和利用种子修复海草床的途径进行了阐述, 并指出了目前研究和应用中存在的一系列问题。最后对海草种子的研究和应用前景进行了展望, 提出海草种子生态学将成为今后的研究热点, 在应用方面, 仍然需要以提高种子萌发率和成苗率为研究重点, 并指出如果利用由种子获得的人工幼苗进行海草床修复, 需首先解决幼苗成活率低的难题。     

Pollen and seed dispersal inferred from seedling genotypes: the Bayesian revolution has passed here too

Understanding precisely how plants disperse their seeds and pollen in their neighbourhood is a central question for both ecologists and evolutionary biologists because seed and pollen dispersal governs both the rate of spread of an expanding population and gene flow within and among populations. The concept of a 'dispersal kernel' has become extremely popular in dispersal ecology as a tool that summarizes how dispersal distributes individuals and genes in space and at a given scale. In this issue of Molecular Ecology, the study by Moran & Clark (2011) (M&C in the following) shows how genotypic and spatial data of established seedlings can be analysed in a Bayesian framework to estimate jointly the pollen and seed dispersal kernels and finally derive a parentage analysis from a full-probability approach. This approach applied to red oak shows important dispersal of seeds (138 m on average) and pollen (178 m on average). For seeds, this estimate contrasts with previous results from inverse modelling on seed trap data (9.3 m). This research gathers several methodological advances made in recent years in two research communities and could become a cornerstone for dispersal ecology.     

Dynamic distribution and the role of abscisic acid during seed development of a lady’s slipper orchid,Cypripedium formosanum

Background and Aims Although abscisic acid (ABA) is commonly recognized as a primary cause of seed dormancy, there is a lack of information on the role of ABA during orchid seed development. In order to address this issue, the localization and quantification of ABA were determined in developing seeds of Cypripedium formosanum.Methods The endogenous ABA profile of seeds was measured by enzyme-linked immunosorbent assay (ELISA). Temporal and spatial distributions of ABA in developing seeds were visualized by immunohistochemical staining with monoclonal ABA antibodies. Fluoridone was applied to test the causal relationship between ABA content and seed germinability.Key Results ABA content was low at the proembryo stage, then increased rapidly from 120 to 150 days after pollination (DAP), accompanied by a progressive decrease in water content and seed germination. Immunofluorescence signals indicated an increase in fluorescence over time from the proembryo stage to seed maturation. From immunogold labelling, gold particles could be seen within the cytoplasm of embryo-proper cells during the early stages of seed development. As seeds approached maturity, increased localization of gold particles was observed in the periplasmic space, the plasmalemma between embryo-proper cells, the surface wall of the embryo proper, and the inner walls of inner seed-coat cells. At maturity, gold particles were found mainly in the apoplast, such as the surface wall of the embryo proper, and the shrivelled inner and outer seed coats. Injection of fluoridone into capsules resulted in enhanced germination of mature seeds.Conclusions The results indicate that ABA is the key inhibitor of germination in C. formosanum. The distinct accumulation pattern of ABA suggests that it is synthesized in the cytosol of embryo cells during the early stages of seed development, and then exported to the apoplastic region of the cells for subsequent regulatory processes as seeds approach maturity.     

Linking traits of foraging animals to spatial patterns of plants: social and solitary ants generate opposing patterns of surviving seeds

Foraging traits of seed predators are expected to impact the spatial structure of plant populations, community dynamics and diversity. Yet, many of the key mechanisms governing distance- or density-dependent seed predation are poorly understood. We designed an extensive set of field experiments to test how seed predation by two harvester ant species interact with seed dispersal in shaping the spatial patterns of surviving seeds. We show that the Janzen–Connell establishment pattern can be generated by central-place foragers even if their focal point is located away from the seed source. Furthermore, we found that differences in the social behaviour of seed predators influence their sensitivity to seed density gradients and yield opposing spatial patterns of surviving seeds. Our results support the predictions of a recent theoretical framework that unifies apparently opposing plant establishment patterns, and suggest that differences in foraging traits among seed predators can drive divergent pathways of plant community dynamics.     

Designing multiple simultaneous seeds for DNA similarity search.

The challenge of similarity search in massive DNA sequence databases has inspired major changes in BLAST-style alignment tools, which accelerate search by inspecting only pairs of sequences sharing a common short "seed," or pattern of matching residues. Some of these changes raise the possibility of improving search performance by probing sequence pairs with several distinct seeds, any one of which is sufficient for a seed match. However, designing a set of seeds to maximize their combined sensitivity to biologically meaningful sequence alignments is computationally difficult, even given recent advances in designing single seeds. This work describes algorithmic improvements to seed design that address the problem of designing a set of n seeds to be used simultaneously. We give a new local search method to optimize the sensitivity of seed sets. The method relies on efficient incremental computation of the probability that an alignment contains a match to a seed pi, given that it has already failed to match any of the seeds in a set Pi. We demonstrate experimentally that multi-seed designs, even with relatively few seeds, can be significantly more sensitive than even optimized single-seed designs.     

Systemic spread of downy mildew in basil plants and detection of the pathogen in seed and plant samples

Downy mildew on sweet basil (Ocimum basilicum L.) occurs worldwide. Contaminated seeds are considered as the primary inoculum source. So far no strategy to control the disease is available. Hence, the use of pathogen-free seeds is the only alternative to prevent disease outbreaks. Therefore, a rapid diagnostic method for seed testing is urgently needed. The sensitivity of a specific PCR method for direct detection of the downy mildew pathogen Peronospora belbahrii on basil samples, particularly on seeds, was evaluated. The applied PCR method proved to be very sensitive for direct detection of the pathogen on seeds and plant samples. The PCR detection limit of P. belbahrii in artificially infested seeds corresponded to the DNA amount of a single spore per seed. Additionally, the systemic spread of the pathogen from naturally infected seeds was investigated. The experiments showed that outgrowing basil plants were latently infected with the downy mildew pathogen, and the infection continued within the plant. Contaminated seeds were harvested from symptomless latently infected plants. These results support the implementation of PCR-based detection in a seed certification scheme and the necessity to control the pathogen on seeds. The PCR method can also be used for evaluation of pathogen control on seeds based on detection of the pathogen in outgrowing plants.     

Imprinting of the Polycomb Group Gene MEDEA Serves as a Ploidy Sensor in Arabidopsis

Balanced maternal and paternal genome contributions are a requirement for successful seed development. Unbalanced contributions often cause seed abortion, a phenomenon that has been termed “triploid block.” Misregulation of imprinted regulatory genes has been proposed to be the underlying cause for abnormalities in growth and structure of the endosperm in seeds with deviating parental contributions. We identified a mutant forming unreduced pollen that enabled us to investigate direct effects of unbalanced parental genome contributions on seed development and to reveal the underlying molecular mechanism of dosage sensitivity. We provide evidence that parent-of-origin–specific expression of the Polycomb group (PcG) gene MEDEA is causally responsible for seed developmental aberrations in Arabidopsis seeds with increased paternal genome contributions. We propose that imprinted expression of PcG genes is an evolutionary conserved mechanism to balance parental genome contributions in embryo nourishing tissues.     

What we don’t seed: the role of long-lived seed banks as hidden legacies of invasive plants

Acacia dealbata is an invasive south-eastern Australian tree that produces a persistent soil seed bank. In order to characterize the seed bank in plots invaded by A. dealbata and to understand its implications for management and re-invasion risk, density, germinability, and viability of the seed bank were evaluated in five sites in central Portugal. Soil samples were collected in A. dealbata invaded plots and adjacent areas and screened for seeds, which were then quantified and germinated at 25 °C. A subset of seeds was first exposed to 60 °C to assess the effect of high soil temperature on dormancy breaking. Variables influencing differences between sites were explored with generalized linear mixed models with a Poisson distribution. Inside A. dealbata invaded plots the seed bank averaged 4608 seeds/m², reaching up to 62,747 seeds/m²; in adjacent areas, up to 14 m from the plots, only 9 seeds/m² were found. Seed bank densities were mostly influenced by stoniness, number of fires in the last 10 years, and density of trees and roots. Almost 90% of seeds were viable, but only 8.6% germinated without treatment. Nearly 70% of seeds exposed to 60 °C germinated without any physical stimulation, suggesting that high soil temperatures can effectively break seed dormancy. The high density and viability of A. dealbata’s seed bank and its ability to disperse seeds far from the parent plants contribute to the species’ invasive success. These features combined with heat events that can overcome seed dormancy need to be considered in the management of this species.     

Gibberellins are required for embryo growth and seed development in pea

The gibberellin (GA) biosynthesis mutants lh-1 and lh-2 have been used to examine the physiological role of GAs in pea seed development. The LH protein is required for the three-step oxidation of ent -kaurene to ent -kaurenoic acid early in the GA biosynthesis pathway. The allele-specific interaction of lh-1 and lh-2 with chemical inhibitors of these three steps suggests that LH encodes the multi-functional GA biosynthesis enzyme ent -kaurene oxidase. Unlike the lh-2 mutation which reduces seed weight and decreases seed survival by ∼50% compared with wild-type plants, the lh-1 allele has a transient effect on embryo and seed growth and only slightly increases seed abortion. These seed phenotypes parallel the effects of the two mutant alleles on GA levels in young seeds. Detailed examination of the growth of lh-1 seeds reveals homeostatic regulation of GA-promoted embryo and seed growth. Although GA-deficient seeds grow more slowly than WT seeds, decreased assimilate availability to the developing seeds is not the primary reason for the altered seed development. Instead, GAs act to promote some process(es) required for embryo and seed growth and only indirectly influence the distribution of assimilates. How GA deficiency causes seed abortion is not known but it may simply be a consequence of reduced seed or embryo growth rate. These results demonstrate that even relatively small changes in the levels of GAs in young seeds can alter seed development and suggest that the available GA-related mutants may represent only a subset of all possible mutants with reduced GA levels or GA signalling.     

壳斗科三种植物种子大小对昆虫寄生及种子存活率的影响

种子内的寄生昆虫可以严重影响种子的发育、损害种子活力。种子足余策略理论认为大种子有利于抵御和适应昆虫寄生取食,但动物最优觅食理论推测,大种子更易遭受昆虫寄生。为对这两种对立观点进行验证,本实验以青冈、苦槠和麻栎各2个种群的种子为材料,对昆虫寄生与完好种子间的体积和萌发率进行比较,并对寄生种子萌发率与种子体积的关系进行了分析。结果显示:(1)在6个种群的种子中,只有松阳麻栎和青冈种群的寄生种子体积大于完好种子,其余4个种群的寄生种子体积小于完好种子,但这种差异不显著;(2)所有寄生种子的整体萌发率(18%)显著低于完好种子(45.66%)(P<0.001),在不同种群内,寄生种子的萌发率也分别显著低于完好种子。(3)比较同种植物体积差异显著的寄生种子的萌发率发现,大种子总比小种子具有更高的萌发率,但差异不显著;在不同植物的寄生种子间比较时,体积最大的麻栎种子萌发率显著高于体积较小的青冈和苦槠种子。研究结果表明,象虫在种子上产卵时对大种子没有选择偏好,在昆虫寄生取食严重损害种子活力的压力下,大种子比小种子具有更强的耐受力。     

Self-pollen interference is absent in wild radish (Raphanus raphanistrum, Brassicaceae), a species with sporophytic self-incompatibility

Explaining the diversity of mating systems and floral forms in flowering plants is a long-standing concern of evolutionary biologists. One topic of interest is the conditions under which self-pollination can interfere with seed set for flowering plants with a self-incompatibility system. We investigated the effect of self-pollen interference for wild radish, Raphanus raphanistrum, which has sporophytic self-incompatibility. We performed pollinations and determined seed set for plants grown in the greenhouse, using pollen mixtures representing either self- with outcross-pollen or outcross-pollen alone. Stigmas were collected for a subset of pollinated flowers to determine the number of pollen grains applied. Average seed set for the self/cross (5.13 seeds/pollination) and cross treatments (5.09 seeds/pollination) did not differ significantly. Stigmatic pollen loads averaged around 700 grains, an amount close to observed natural pollen loads on R. raphanistrum. We concluded that for R. raphanistrum in natural populations, self-pollen is unlikely to interfere with outcross-pollen success. This study is the first to investigate effects of self-pollen interference on seed set for a homomorphic species with sporophytic self-incompatibility where rejection occurs at the stigmatic surface.     

Seed storage: maintaining seed viability and vigor for restoration use

Effective seed storage after sourcing (harvesting or purchasing) is critical to restoration practitioners and native seed producers, as it is key to maintaining seed viability. Inadequate seed storage can lead to a waste of both natural and economic resources when seeds of poor quality are sown. When working with native species with unknown storage behavior, general assumptions can be made based on studies on related species, and standard practices may be applied with caution; however, an investigation should be conducted to understand if specific storage requirements are needed and for how long seeds can be stored before they lose significant viability. In this paper of the Special Issue Standards for Native Seeds in Ecological Restoration, we provide an overview of the key concepts in seed storage and the steps to take for effective storage of native seeds for restoration use.