Bulbil initiation: a comprehensive review on resources, development, and utilisation, with emphasis on molecular mechanisms, advanced technologies, and future prospects

Bulbil is an important asexual reproductive structure of bulbil plants. It mainly grows in leaf axils, leaf forks, tubers and the upper and near ground ends of flower stems of plants. They play a significant role in the reproduction of numerous herbaceous plant species by serving as agents of plant propagation, energy reserves, and survival mechanisms in adverse environmental conditions. Despite extensive research on bulbil-plants regarding their resources, development mechanisms, and utilisation, a comprehensive review of bulbil is lacking, hindering progress in exploiting bulbil resources. This paper provides a systematic overview of bulbil research, including bulbil-plant resources, identification of development stages and maturity of bulbils, cellular and molecular mechanisms of bulbil development, factors influencing bulbil development, gene research related to bulbil development, multi-bulbil phenomenon and its significance, medicinal value of bulbils, breeding value of bulbils, and the application of plant tissue culture technology in bulbil production. The application value of the Temporary Immersion Bioreactor System (TIBS) and Terahertz (THz) in bulbil breeding is also discussed, offering a comprehensive blueprint for further bulbil resource development. Additionally, additive, seven areas that require attention are proposed: (1) Utilization of modern network technologies, such as plant recognition apps or websites, to collect and identify bulbous plant resources efficiently and extensively; (2) Further research on cell and tissue structures that influence bulb cell development; (3) Investigation of the network regulatory relationship between genes, proteins, metabolites, and epigenetics in bulbil development; (4) Exploration of the potential utilization value of multiple sprouts, including medicinal, ecological, and horticultural applications; (5) Innovation and optimization of the plant tissue culture system for bulbils; (6) Comprehensive application research of TIBS for large-scale expansion of bulbil production; (7) To find out the common share genetics between bulbils and flowers.

Genotyping-by-Sequencing Reveals Population Differentiation and Linkage Disequilibrium in Alternaria linariae from Tomato

Alternaria linariae is an economically important foliar pathogen that causes early blight disease in tomatoes. Understanding genetic diversity, population genetic structure, and evolutionary potential is crucial to contemplating effective disease management strategies. We leveraged genotyping-by-sequencing (GBS) technology to compare genome-wide variation in 124 isolates of Alternaria spp. (A. alternata, A. linariae, and A. solani) for comparative genome analysis and to test the hypotheses of genetic differentiation and linkage disequilibrium (LD) in A. linariae collected from tomatoes in western North Carolina. We performed a pangenome-aware variant calling and filtering with GBSapp and identified 53,238 variants conserved across the reference genomes of three Alternaria spp. The highest marker density was observed on chromosome 1 (7 Mb). Both discriminant analysis of principal components and Bayesian model-based STRUCTURE analysis of A. linariae isolates revealed three subpopulations with minimal admixture. The genetic differentiation coefficients (FST) within A. linariae subpopulations were similar and high (0.86), indicating that alleles in the subpopulations are fixed and the genetic structure is likely due to restricted recombination. Analysis of molecular variance indicated higher variation among populations (89%) than within the population (11%). We found long-range LD between pairs of loci in A. linariae, supporting the hypothesis of low recombination expected for a fungal pathogen with limited sexual reproduction. Our findings provide evidence of a high level of population genetic differentiation in A. linariae, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. linariae.

The eco-evolutionary importance of reproductive system variation in the macroalgae: Freshwater reds as a case study

The relative frequency of sexual versus asexual reproduction governs the distribution of genetic diversity within and among populations. Most studies on the consequences of reproductive variation focus on the mating system (i.e., selfing vs. outcrossing) of diploid-dominant taxa (e.g., angiosperms), often ignoring asexual reproduction. Although reproductive systems are hypothesized to be correlated with life-cycle types, variation in the relative rates of sexual and asexual reproduction remains poorly characterized across eukaryotes. This is particularly true among the three major lineages of macroalgae (green, brown, and red). The Rhodophyta are particularly interesting, as many taxa have complex haploid-diploid life cycles that influence genetic structure. Though most marine reds have separate sexes, we show that freshwater red macroalgae exhibit patterns of switching between monoicy and dioicy in sister taxa that rival those recently shown in brown macroalgae and in angiosperms. We advocate for the investigation of reproductive system evolution using freshwater reds, as this will expand the life-cycle types for which these data exist, enabling comparative analyses broadly across eukaryotes. Unlike their marine cousins, species in the Batrachospermales have macroscopic gametophytes attached to filamentous, often microscopic sporophytes. While asexual reproduction through monospores may occur in all freshwater reds, the Compsopogonales are thought to be exclusively asexual. Understanding the evolutionary consequences of selfing and asexual reproduction will aid in our understanding of the evolutionary ecology of all algae and of eukaryotic evolution generally.

Genetic and Phenotypic Consequences of Local Transitions between Sexual and Parthenogenetic Reproduction in the Wild

AbstractTransitions from sexual to asexual reproduction have occurred in numerous lineages, but it remains unclear why asexual populations rarely persist. In facultatively parthenogenetic animals, all-female populations can arise when males are absent or become extinct, and such populations could help to understand the genetic and phenotypic changes that occur in the initial stages of transitions to asexuality. We investigated a naturally occurring spatial mosaic of mixed-sex and all-female populations of the facultatively parthenogenetic Australian phasmid Megacrania batesii. Analysis of single-nucleotide polymorphisms indicated multiple independent transitions between reproductive modes. All-female populations had much lower heterozygosity and allelic diversity than mixed-sex populations, but we found few consistent differences in fitness-related traits between population types. All-female populations exhibited more frequent and severe deformities in their (flight-incapable) wings but did not show higher rates of appendage loss. All-female populations also harbored more ectoparasites in swamp (but not beach) habitats. Reproductive mode explained little variation in female body size, fecundity, or egg hatch rate. Our results suggest that transitions to parthenogenetic reproduction can lead to dramatic genetic changes with little immediate effect on performance. All-female M. batesii populations appear to consist of high-fitness genotypes that might be able to thrive for many generations in relatively constant and benign environments but could be vulnerable to environmental challenges, such as increased parasite abundance.

A Network of Sporogenesis-Responsive Genes Regulates the Growth, Asexual Sporogenesis, Pathogenesis and Fusaric Acid Production of Fusarium oxysporum f. sp. cubense

The conidia produced by Fusarium oxysporum f. sp. cubense (Foc), the causative agent of Fusarium Wilt of Banana (FWB), play central roles in the disease cycle, as the pathogen lacks a sexual reproduction process. Until now, the molecular regulation network of asexual sporogenesis has not been clearly understood in Foc. Herein, we identified and functionally characterized thirteen (13) putative sporulation-responsive genes in Foc, namely FocmedA(a), FocmedA(b), abaA-L, FocflbA, FocflbB, FocflbC, FocflbD, FocstuA, FocveA, FocvelB, wetA-L, FocfluG and Foclae1. We demonstrated that FocmedA(a), abaA-L, wetA-L, FocflbA, FocflbD, FocstuA, FocveA and Foclae1 mediate conidiophore formation, whereas FocmedA(a) and abaA-L are important for phialide formation and conidiophore formation. The expression level of abaA-L was significantly decreased in the ΔFocmedA(a) mutant, and yeast one-hybrid and ChIP-qPCR analyses further confirmed that FocMedA(a) could bind to the promoter of abaA-L during micro- and macroconidiation. Moreover, the transcript abundance of the wetA-L gene was significantly reduced in the ΔabaA-L mutant, and it not only was found to function as an activator of micro- and macroconidium formation but also served as a repressor of chlamydospore production. In addition, the deletions of FocflbB, FocflbC, FocstuA and Foclae1 resulted in increased chlamydosporulation, whereas FocflbD and FocvelB gene deletions reduced chlamydosporulation. Furthermore, FocflbC, FocflbD, Foclae1 and FocmedA(a) were found to be important regulators for pathogenicity and fusaric acid synthesis in Foc. The present study therefore advances our understanding of the regulation pathways of the asexual development and functional interdependence of sporulation-responsive genes in Foc.

Genetic and karyotype divergence between parents affect clonality and sterility in hybrids

Asexual reproduction can be triggered by interspecific hybridization, but its emergence is supposedly rare, relying on exceptional combinations of suitable genomes. To examine how genomic and karyotype divergence between parental lineages affect the incidence of asexual gametogenesis, we experimentally hybridized fishes (Cobitidae) across a broad phylogenetic spectrum, assessed by whole exome data. Gametogenic pathways generally followed a continuum from sexual reproduction in hybrids between closely related evolutionary lineages to sterile or inviable crosses between distant lineages. However, most crosses resulted in a combination of sterile males and asexually reproducing females. Their gametes usually experienced problems in chromosome pairing, but females also produced a certain proportion of oocytes with premeiotically duplicated genomes, enabling their development into clonal eggs. Interspecific hybridization may thus commonly affect cell cycles in a specific way, allowing the formation of unreduced oocytes. The emergence of asexual gametogenesis appears tightly linked to hybrid sterility and constitutes an inherent part of the extended speciation continuum.

Why do hybrids turn down sex?

Asexual reproduction is ancestral in prokaryotes; the switch to sexuality in eukaryotes is one of the major transitions in the history of life. The study of the maintenance of sex in eukaryotes has raised considerable interest for decades and is still one of evolutionary biology's most prominent question. The observation that many asexual species are of hybrid origin has led some to propose that asexuality in hybrids results from sexual processes being disturbed because of incompatibilities between the two parental species' genomes. However, in some cases, failure to produce asexual F1s in the lab may indicate that this mechanism is not the only road to asexuality in hybrid species. Here, we present a mathematical model and propose an alternative, adaptive route for the evolution of asexuality from previously sexual hybrids. Under some reproductive alterations, we show that asexuality can evolve to rescue hybrids' reproduction. Importantly, we highlight that when incompatibilities only affect the fusion of sperm and egg's genomes, the two traits that characterize asexuality, namely unreduced meiosis and the initiation of embryogenesis without the incorporation of the sperm's pronucleus, can evolve separately, greatly facilitating the overall evolutionary route. Taken together, our results provide an alternative, potentially complementary explanation for the link between asexuality and hybridization.

The Life Cycle of Aurelia aurita Depends on the Presence of a Microbiome in Polyps Prior to Onset of Strobilation

Aurelia aurita's intricate life cycle alternates between benthic polyp and pelagic medusa stages. The strobilation process, a critical asexual reproduction mechanism in this jellyfish, is severely compromised in the absence of the natural polyp microbiome, with limited production and release of ephyrae. Yet, the recolonization of sterile polyps with a native polyp microbiome can correct this defect. Here, we investigated the precise timing necessary for recolonization as well as the host-associated molecular processes involved. We deciphered that a natural microbiota had to be present in polyps prior to the onset of strobilation to ensure normal asexual reproduction and a successful polyp-to-medusa transition. Providing the native microbiota to sterile polyps after the onset of strobilation failed to restore the normal strobilation process. The absence of a microbiome was associated with decreased transcription of developmental and strobilation genes as monitored by reverse transcription-quantitative PCR. Transcription of these genes was exclusively observed for native polyps and sterile polyps that were recolonized before the initiation of strobilation. We further propose that direct cell contact between the host and its associated bacteria is required for the normal production of offspring. Overall, our findings indicate that the presence of a native microbiome at the polyp stage prior to the onset of strobilation is essential to ensure a normal polyp-to-medusa transition. IMPORTANCE All multicellular organisms are associated with microorganisms that play fundamental roles in the health and fitness of the host. Notably, the native microbiome of the Cnidarian Aurelia aurita is crucial for the asexual reproduction by strobilation. Sterile polyps display malformed strobilae and a halt of ephyrae release, which is restored by recolonizing sterile polyps with a native microbiota. Despite that, little is known about the microbial impact on the strobilation process's timing and molecular consequences. The present study shows that A. aurita's life cycle depends on the presence of the native microbiome at the polyp stage prior to the onset of strobilation to ensure the polyp-to-medusa transition. Moreover, sterile individuals correlate with reduced transcription levels of developmental and strobilation genes, evidencing the microbiome's impact on strobilation on the molecular level. Transcription of strobilation genes was exclusively detected in native polyps and those recolonized before initiating strobilation, suggesting microbiota-dependent gene regulation.

Vasa, Piwi, and Pl10 Expression during Sexual Maturation and Asexual Reproduction in the Annelid Pristina longiseta

Naidids are tiny, transparent freshwater oligochaetes, which are well known for their ability to propagate asexually. Despite the fact that sexually mature individuals and cocoons with embryos are sometimes found in nature, in long-period laboratory cultures, worms reproduce agametically only. In this paper, we showed, for the first time, the expression of Vasa, Piwi, and Pl10 homologs in mature Pristina longiseta worms with well-developed reproductive system structures and germ cells. Although the animals have been propagated asexually by paratomic fission for over 20 years in our lab, some individuals become sexualized under standard conditions for our laboratory culture and demonstrate various stages of maturation. The fully matured animals developed a complete set of sexual apparatus including spermatheca, atrium, seminal vesicles, and ovisac. They also had a clitellum and were able to form cocoons. The cues for the initiation of sexual maturation are still unknown for P. longiseta; nevertheless, our data suggest that the laboratory strain of P. longiseta maintains the ability to become fully sexually mature and to establish germline products even after a long period of agametic reproduction. On the other hand, many of the sexualized worms formed a fission zone and continued to reproduce asexually. Thus, in this species, the processes of asexual reproduction and sexual maturation do not preclude each other, and Vasa, Piwi, and Pl10 homologs are expressed in both somatic and germline tissue including the posterior growth zone, fission zone, nervous system, germline cells, and gametes.

Ploidy Variation and Its Implications for Reproduction and Population Dynamics in Two Sympatric Hawaiian Coral Species

Standing genetic variation is a major driver of fitness and resilience and therefore of fundamental importance for threatened species such as stony corals. We analyzed RNA-seq data generated from 132 Montipora capitata and 119 Pocillopora acuta coral colonies collected from Kāne'ohe Bay, O'ahu, Hawai'i. Our goals were to determine the extent of colony genetic variation and to study reproductive strategies in these two sympatric species. Surprisingly, we found that 63% of the P. acuta colonies were triploid, with putative independent origins of the different triploid clades. These corals have spread primarily via asexual reproduction and are descended from a small number of genotypes, whose diploid ancestor invaded the bay. In contrast, all M. capitata colonies are diploid and outbreeding, with almost all colonies genetically distinct. Only two cases of asexual reproduction, likely via fragmentation, were identified in this species. We report two distinct strategies in sympatric coral species that inhabit the largest sheltered body of water in the main Hawaiian Islands. These data highlight divergence in reproductive behavior and genome biology, both of which contribute to coral resilience and persistence.

Spatial Colinear but Broken Temporal Expression of Duplicated ParaHox Genes in Asexually Reproducing Annelids, Nais communis and Pristina longiseta

ParaHox genes are key developmental regulators involved in the patterning of the digestive tract along the anteroposterior axis and the development of the nervous system. Most studies have focused on the function of these genes in embryogenesis, while their expression patterns in postembryonic development often remain unknown. In this study, we identified for the first time all ParaHox orthologs in two naidid oligochaetes, N. communis and P. longiseta, and described their expression patterns during normal growth and fission in these animals. We showed that Gsx and Cdx are presented by two paralogs, while Xlox is a single copy gene in both species. Using whole-mount in situ hybridization, we also found that orthologs, except for the Xlox gene, have similar activity patterns with minor differences in details, while the expression patterns of paralogs can differ significantly. However, all these genes are involved in axial patterning and/or in tissue remodeling during growth and asexual reproduction in naidids. Moreover, during paratomic fission, these genes are expressed with spatial colinearity but temporal colinearity is broken. The results of this study may be evidence of the functional diversification of duplicated genes and suggest involvement of the ParaHox genes in whole-body patterning during growth and asexual reproduction in annelids.

Sterol-Sensing Domain (SSD)-Containing Proteins in Sterol Auxotrophic Phytophthora capsici Mediate Sterol Signaling and Play a Role in Asexual Reproduction and Pathogenicity

Phytophthora species are devastating filamentous plant pathogens that belong to oomycetes, a group of microorganisms similar to fungi in morphology but phylogenetically distinct. They are sterol auxotrophic, but nevertheless exploit exogenous sterols for growth and development. However, as for now the mechanisms underlying sterol utilization in Phytophthora are unknown. In this study, we identified four genes in Phytophthora capsici that encode proteins containing a sterol-sensing domain (SSD), a protein domain of around 180 amino acids comprising five transmembrane segments and known to feature in sterol signaling in animals. Using a modified CRISPR/Cas9 system, we successfully knocked out the four genes named PcSCP1 to PcSCP4 (for P. capsici SSD-containing protein 1 to 4), either individually or sequentially, thereby creating single, double, triple, and quadruple knockout transformants. Results showed that knocking out just one of the four PcSCPs was not sufficient to block sterol signaling. However, the quadruple "all-four" PcSCPs knockout transformants no longer responded to sterol treatment in asexual reproduction, in contrast to wild-type P. capsici that produced zoospores under sterol treatment. Apparently, the four PcSCPs play a key role in sterol signaling in P. capsici with functional redundancy. Transcriptome analysis indicated that the expression of a subset of genes is regulated by exogenous sterols via PcSCPs. Further investigations showed that sterols could stimulate zoospore differentiation via PcSCPs by controlling actin-mediated membrane trafficking. Moreover, the pathogenicity of the "all-four" PcSCPs knockout transformants was significantly decreased and many pathogenicity related genes were downregulated, implying that PcSCPs also contribute to plant-pathogen interaction. IMPORTANCE Phytophthora is an important genus of oomycetes that comprises many destructive plant pathogens. Due to the incompleteness of the sterol synthesis pathway, Phytophthora spp. do not possess the ability to produce sterols. Therefore, these sterol auxotrophic oomycetes need to recruit sterols from the environment such as host plants to support growth and development, which seems crucial during pathogen-plant interactions. However, the mechanisms underlying sterol utilization by Phytophthora spp. remain largely unknown. Here, we show that a family of sterol-sensing domain-containing proteins (SCPs) consisting of four members in P. capsici plays a key role in sterol signaling with functional redundancy. Moreover, these SCPs play a role in different biological processes, including asexual reproduction and pathogenicity. Our study overall revealed the multiple functions of PcSCPs and addressed the question of how exogenous sterols regulate the development of heterothallic Phytophthora spp. via SSD-containing proteins.

Synthesis of aglycones, structure-activity relationships, and mode of action of lycosides as inhibitors of the asexual reproduction of Phytophthora

Phytophthora are plant pathogens that damage agricultural products. Lycosides (1a-d), found in vegetable juice, have the potential to curb the rapid outbreak and crop damage caused by the asexual reproduction of Phytophthora. Here, aglycones 2a, b with slightly higher activity than lycosides were synthesized as a diastereomeric mixture (mix-2) possessing activity (IC50 = 4.1 µm) comparable with that of lycosides. The importance of the cyclohexanone structure and side-chain length was demonstrated via structure-activity relationship analysis using synthetic intermediates. In addition, the action mechanism of lycosides was investigated using transcriptome analysis, which revealed a contribution to proline biosynthesis inhibition, a process crucial for the asexual reproduction of Phytophthora. These findings indicate that lycosides (and aglycone) are environmentally benign agents that can be used for protecting agricultural products from Phytophthora pathogens.

niveum

SUMOylation is an essential protein modification process that regulates numerous crucial cellular and biochemical processes in phytopathogenic fungi, and thus plays important roles in multiple biological functions. The present study characterizes the SUMOylation pathway components, including SMT3 (SUMO), AOS1 (an E1 enzyme), UBC9 (an E2 enzyme), and MMS21 (an E3 ligase), in Fusarium oxysporum f. sp. niveum (Fon), the causative agent of watermelon Fusarium wilt, in terms of the phylogenetic relationship, gene/protein structures, and basic biological functions. The SUMOylation components FonSMT3, FonAOS1, FonUBC9, and FonMMS21 are predominantly located in the nucleus. FonSMT3, FonAOS1, FonUBC9, and FonMMS21 are highly expressed in the germinating macroconidia, but their expression is downregulated gradually in infected watermelon roots with the disease progression. The disruption of FonUBA2 and FonSIZ1 seems to be lethal in Fon. The deletion mutant strains for FonSMT3, FonAOS1, FonUBC9, and FonMMS21 are viable, but exhibit significant defects in vegetative growth, asexual reproduction, conidial morphology, spore germination, responses to metal ions and DNA-damaging agents, and apoptosis. The disruption of FonSMT3, FonAOS1, FonUBC9, and FonMMS21 enhances sensitivity to cell wall-perturbing agents, but confers tolerance to digestion by cell wall-degrading enzymes. Furthermore, the disruption of FonSMT3, FonAOS1, and FonUBC9 negatively regulates autophagy in Fon. Overall, these results demonstrate that the SUMOylation pathway plays vital roles in regulating multiple basic biological processes in Fon, and, thus, can serve as a potential target for developing a disease management approach to control Fusarium wilt in watermelon.

Extraordinary high level of propagation of Babesia divergens in severe human babesiosis

Babesias are obligate apicomplexan parasites that affect the red blood cells (RBCs) of animals. Humans can serve as accidental hosts for them. Asexual reproduction of a parasite occurs in a vertebrate host through asynchronous binary fission, yielding a complex pleomorphic population of intraerythrocytic forms. In natural hosts (Bos taurus), paired pyriforms (‘figure 8’) of Babesia divergens are usual, but tetrads (‘Maltese Cross’) are very rare (only in 0.02% infected erythrocytes); in humans, however, up to 5% of infected erythrocytes show tetrads. The current study shows that B. divergens proliferating in an accidental human host can promote extraordinarily high level of fission. This phenomenon is expressed as the simultaneous division of the parasite into 6 and possibly a greater number of merozoites, forming a ‘daisy head’ (vs the usual 2, less often 4 merozoites). Reproduction is possible without egressing merozoites from the erythrocyte, which results in multi-occupancy of an RBC (≥5 parasites per RBC). An unusually high polyparasitism – up to 14 parasites developed in the affected erythrocytes – was observed. This phenomenon is rare in natural hosts (usually ≤5), but when B. divergens is cultured in vitro it can be 10–12.

[Seasonal differences in vegetative regeneration of three desiccation-tolerant mosses in the Loess Plateau and its mechanism]

Bryophytes have been used in many fields, such as landscaping and soil and water conservation. How-ever, few studies focused on moss regeneration and its influencing factors, which retards the application study. Three common desiccation-tolerant mosses (Barbula unguiculata, Didymodon vinealis, and Didymodon tectorum) in the Loess Plateau region were collected across four seasons. We measured vigor index of new shoots, representing vegetative regeneration capacity, and physiological indices, which included the contents of chlorophyll, soluble sugar, soluble protein and malondialdehyde (MDA), to determine seasonal differences in regeneration capacity and physiological characteristics of the three mosses, as well as their relationships. The results showed that, 1) vegetative regeneration of mosses showed significantly seasonal differences. The vigor index of the three mosses in summer were the lowest, averagely decreased by 56.1%, 48.4%, and 10.1% compared with that in autumn, winter, and spring, respectively. The vigor index of the three mosses in the same season showed interannual variation. 2) There were considerable differences in the regeneration capacity of mosses across species. D. tectorum and B. unguiculata had the highest and lowest vigor indices, respectively. In terms of regeneration capacity, B. unguiculata had the largest seasonal and interannual variations. 3) The physiological characteristics of mosses had seaonal variations. The mosses collected in the summer had the highest MDA content but the lowest contents of soluble sugar and soluble protein. 4) Seasonal variations in desiccation-tolerant moss regeneration were mostly due to soluble sugar. Our results showed seasonal variations of vegetative propagation capacity, and highlighted the role of soluble sugar as a critical factor influencing vegetative propagation of mosses. These findings could provide scientific support for moss protection and artificial cultivation.

Mitochondrial Genomes of Two Asexual Trichogramma (Hymenoptera: Trichogrammatidae) Strains and Comparison with Their Sexual Relatives

Simple Summary

Sexual reproduction is dominant in animals, while asexual lineages are rare and evolutionarily short-lived. However, sexual reproduction has substantial costs, such as male production, inputs to courtship and mating, increased risk of predator exposure, and sexually transmitted diseases. A large body of theories has been proposed to explain the paradox of sex. One favored explanation is that asexuals are more likely to accumulate a greater number of deleterious mutations, known as Muller’s ratchet. Trichogramma is a genus of egg parasitoid wasps and is widely used as a biological control agent for agricultural and forest pests. With asexual lineages in at least 16 species, Trichogramma provides an excellent model to investigate the causes and consequences of asexual reproduction. In this study, we sequenced and assembled two asexual Trichogramma mitogenomes, representing two divergent origins of asexual reproduction. The asexual T. pretiosum is induced by the endosymbiont Wolbachia, while T. cacoeciae presumably originates from interspecific hybridization. To test Muller’s ratchet hypothesis, we compared these two asexual mitogenomes with their sexual relatives and found no association between asexual reproduction and mutation accumulation. This study provides a basis for further investigation into mitochondrial evolution and asexual reproduction in Trichogramma.

Abstract

Despite its substantial costs, sexual reproduction dominates in animals. One popular explanation for the paradox of sex is that asexual reproduction is more likely to accumulate deleterious mutations than sexual reproduction. To test this hypothesis, we compared the mitogenomes of two asexual wasp strains, Trichogramma cacoeciae and T. pretiosum, to their sexual relatives. These two asexual strains represent two different transition mechanisms in Trichogramma from sexual to asexual reproduction. Asexual T. pretiosum is induced by Wolbachia, while T. cacoeciae presumably originated from interspecific hybridization. We sequenced and assembled complete mitochondrial genomes of asexual T. cacoeciae and T. pretiosum. Compared to four sexual relatives, we found no evidence of higher mutation accumulation in asexual Trichogramma mitogenomes than in their sexual relatives. We also did not detect any relaxed selection in asexual Trichogramma mitogenomes. In contrast, the intensified selection was detected in Nad1 and Nad4 of the asexual T. pretiosum mitogenome, suggesting more purifying selection. In summary, no higher mitochondrial mutation accumulation was detected in these two asexual Trichogramma strains. This study provides a basis for further investigating mitochondrial evolution and asexual reproduction in Trichogramma.

New Records of Azooxanthellate Scleractinian Corals (Cnidaria: Anthozoa) from Sagami Bay and Suruga Bay, Japan

Sagami Bay and Suruga Bay harbor a rich marine biodiversity; however, their outer-shelf scleractinian coral fauna has not been characterized to date. Scleractinian corals were collected by dredge sampling of the Japanese Association for Marine Biology (JAMBIO) Coastal Organisms Joint Surveys in 2015 to elucidate the diversity of azooxanthellate scleractinian corals from the outer shelf zones of Sagami Bay and Suruga Bay. In this study, a total of 1291 azooxanthellate scleractinian specimens were collected, corresponding to 23 genera and 18 species, five of which are new records for Sagami Bay and eight are new records for Suruga Bay. Moreover, in all localities, except sampling locality (SL) 8, more than 70% of the specimens showed asexual reproduction. This finding suggests that asexual reproduction may play an important role in increasing the coral population size in soft-substrate environments of the outer shelf.

New Insights of Transcriptional Regulator AflR in Aspergillus flavus Physiology

Aspergillus flavusaflR, a gene encoding a Zn(II)₂Cys₆ DNA-binding domain, is an important transcriptional regulator of the aflatoxin biosynthesis gene cluster. Our previous results of Gene ontology (GO) analysis for the binding sites of AflR in A. flavus suggest that AflR may play an integrative regulatory role. In this study the ΔaflR and overexpression (OE) strains based on the well-established double-crossover recombinational technique were constructed to investigate the integrative function of the aflR gene in A. flavus. The disruption of aflR severely affected the aflatoxin biosynthetic pathway, resulting in a significant decrease in aflatoxin production. The aflatoxin B₁ (AFB₁) of the ΔaflR strain was 180 ng/mL and aflatoxin B₂ (AFB₂) was 2.95 ng/mL on YES medium for 5 days, which was 1/1,000 of that produced by the wild-type strain (WT). In addition, the ΔaflR strain produced relatively sparse conidia and a very small number of sclerotia. On the seventh day, the sclerotia yield on each plate of the WT and OE strains exceeded 1,000, while the sclerotial formation of the ΔaflR strain was not detected until 14 days. However, the biosynthesis of cyclopiazonic acid (CPA) was not affected by aflR gene disruption. Transcriptomic analysis of the ΔaflR strain grown on potato dextrose agar (PDA) plates at 0 h, 24 h, and 72 h showed that expression of clustering genes involved in the biosynthesis of aflatoxin was significantly downregulated. Meanwhile, the ΔaflR strain compared with the WT strain showed significant expression differences in genes involved in spore germination, sclerotial development, and carbohydrate metabolism compared to the WT. The results demonstrated that the A. flavusaflR gene also played a positive role in the fungal growth and development in addition to aflatoxin biosynthesis.

IMPORTANCE Past studies of the A. flavusaflR gene and its orthologues in related Aspergillus species were solely focused on their roles in secondary metabolism. In this study, we used the ΔaflR and OE strains to demonstrate the role of aflR in growth and development of A. flavus. For the first time, we confirmed that the ΔaflR strain also was defective in production of conidia and sclerotia, asexual propagules of A. flavus. Our transcriptomic analysis further showed that genes involved in spore germination, sclerotial development, aflatoxin biosynssssthesis, and carbohydrate metabolism exhibited significant differences in the ΔaflR strain compared with the WT strain. Our study indicates that AflR not only plays an important role in regulating aflatoxin synthesis but also in playing a positive role in the conidial formation and sclerotial development in A. flavus. This study reveals the critical and positive role of the aflR gene in fungal growth and development, and provides a theoretical basis for the genetic studies of other aspergilli.

Trends in Apomixis Research: The 10 Most Cited Research Articles Published in the Pregenomic and Genomic Eras

Apomixis, or asexual reproduction by seed, represents an easy shortcut for life cycle renewal based on maternal embryo production without ploidy reduction (meiosis) and ploidy restitution (syngamy). Although the first studies officially published on this topic in scientific journals date back to the early 1930s, the identification and introduction of genes involved in asexual reproduction in species of agronomic interest still represent a major challenge. Through a bibliometric analysis of the research programs implemented in apomixis over the last 40 years, the present study was aimed to discuss not only the main findings achieved but also the investigational methods and model species used. We split the critical survey of the most cited original articles into pregenomic and genomic eras to identify potential trends and depict scenarios that have emerged in the scientific community working on apomixis, as well as to determine any correlation between the exponential increase in acquired basic knowledge and the development of advanced analytical technologies. This review found a substantial stagnation in the use of the same model species, with few exceptions, for at least 40 years. In contrast, the development of new molecular techniques, genomic platforms, and repositories has directly affected the approaches used in research, which has been directed toward an increasingly focused study of the genetic and epigenetic determinants of apomixis.

Evidence from automixis with inverted meiosis for the maintenance of sex by loss of complementation

The adaptive value of sexual reproduction is still debated. A short-term disadvantage of asexual reproduction is loss of heterozygosity, which leads to the unmasking of recessive deleterious mutations. The cost of this loss of complementation is predicted to be higher than the twofold cost of meiosis for most types of asexual reproduction. Automixis with terminal fusion of sister nuclei is especially vulnerable to the effect of loss of complementation. It is found, however, in some taxa including oribatid mites, the most prominent group of ancient asexuals. Here, I show that automixis with terminal fusion is stable if it is associated with inverted meiosis and that this appears to be the case in nature, notably in oribatid mites. The existence of automixis with terminal fusion, and its co-occurrence with inverted meiosis, therefore, is consistent with the hypothesis that loss of complementation is important in the evolution of sexual reproduction.

Genome Fractionation and Loss of Heterozygosity in Hybrids and Polyploids: Mechanisms, Consequences for Selection, and Link to Gene Function

Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. The subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that opens up unexpected evolutionary pathways. To elucidate this problem, we compared published cytogenetic and RNAseq data with exome sequences of asexual diploid and polyploid hybrids between three fish species; Cobitis elongatoides, C. taenia, and C. tanaitica. Clonal genomes remained generally static at chromosome-scale levels but their heterozygosity gradually deteriorated at the level of individual genes owing to allelic deletions and conversions. Interestingly, the impact of both processes varies among animals and genomic regions depending on ploidy level and the properties of affected genes. Namely, polyploids were more tolerant to deletions than diploid asexuals where conversions prevailed, and genomic restructuring events accumulated preferentially in genes characterized by high transcription levels and GC-content, strong purifying selection and specific functions like interacting with intracellular membranes. Although hybrids were phenotypically more similar to C. taenia, we found that they preferentially retained C. elongatoides alleles. This demonstrates that favored subgenome is not necessarily the transcriptionally dominant one. This study demonstrated that subgenomes in asexual hybrids and polyploids evolve under a complex interplay of selection and several molecular mechanisms whose efficiency depends on the organism's ploidy level, as well as functional properties and parental ancestry of the genomic region.

Sex-Inducing Activities of the Land Planarian Bipalium nobile Extract Fractions, Obtained Using Bioassay-Guided Fractionation, in the Freshwater Planarian Dugesia ryukyuensis

Sexually mature planarians produce sex-inducing substances that induce postembryonic development of hermaphroditic reproductive organs in asexual freshwater planarians. Although the sex-inducing substances may be useful for elucidating the mechanism underlying this reproductive switch, the available information is limited. The potency of sex-inducing activity is conserved, at least at the order level. Recently, we showed that the sex-inducing activity in the land planarian Bipalium nobile was much higher than that in freshwater planarians. In the present study, we performed bioassay-guided fractionation of the sex-inducing substances produced by B. nobile and propose that crucial sex-inducing activity that triggers complete sexualization for asexual worms of the freshwater planarian Dugesia ryukyuensis is produced by additive and/or synergetic effects of various sex-inducing substances involved in ovarian development. The current study provided an isolation scheme for the minimum-required combination of sex-inducing substances for producing crucial sex-inducing activity.

Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis using genetic and clonal diversity

PREMISE

The distribution of genetic diversity on the landscape has critical ecological and evolutionary implications. This may be especially the case on a local scale for foundation plant species because they create and define ecological communities, contributing disproportionately to ecosystem function.

METHODS

We examined the distribution of genetic diversity and clones, which we defined first as unique multilocus genotypes (MLG), and then by grouping similar MLGs into multilocus lineages. We used 186 markers from inter-simple sequence repeats (ISSR) across 358 ramets from 13 patches of the foundation grass Leymus chinensis. We examined the relationship between genetic and clonal diversities, their variation with patch size, and the effect of the number of markers used to evaluate genetic diversity and structure in this species.

RESULTS

Every ramet had a unique MLG. Almost all patches consisted of individuals belonging to a single multilocus lineages. We confirmed this with a clustering algorithm to group related genotypes. The predominance of a single lineage within each patch could be the result of the accumulation of somatic mutations, limited dispersal, some sexual reproduction with partners mainly restricted to the same patch, or a combination of all three.

CONCLUSIONS

We found strong genetic structure among patches of L. chinensis. Consistent with previous work on the species, the clustering of similar genotypes within patches suggests that clonal reproduction combined with somatic mutation, limited dispersal, and some degree of sexual reproduction among neighbors causes individuals within a patch to be more closely related than among patches.

"Breeding on Mountains" Resulted in the Reorganization of Endophytic Fungi in Asexually Propagated Plants (Ligusticum chuanxiong Hort.)

"Breeding on mountains, cultivation in dam areas" is a unique propagation method for the vegetatively propagated plant Ligusticum chuanxiong, including two transplants between the mountain and the dam area. It is well known that the environment can influence the endophytic community structure of plants. However, the change of host endophytic flora caused by transplanting in different places and its influence on asexual reproduction are still poorly understood. We carried out three cycles of cultivation experiments on L. chuanxiong and collected stem nodes (LZ), immature rhizomes (PX), medicinal rhizomes (CX), and rhizosphere. High-throughput sequencing was performed to analyze the endophytic fungi in all samples. We observed that the diversity and richness of endophytic fungi in L. chuanxiong increased as a result of transplanting cultivation from dam areas to mountains. Local transplantation caused minor changes in the endophytic fungus structure of L. chuanxiong, while remote transplantation caused significant changes. Compared with LZ after breeding in the dam area, the LZ after breeding on mountains has more abundant Gibberella, Phoma, Pericona, Paraphoma, and Neocosmospora. The regular pattern of the relative abundance of endophytic fungi is consistent with that of the fungus in the soil, while there are also some cases that the relative abundance of endophytic fungi is the opposite of that of soil fungi. In addition, there is a significant correlation among certain kinds of endophytic fungi whether in the soil or the plants. We have isolated more gibberellin-producing and auxin-producing fungi in the LZ cultivated in the mountains than that in the LZ cultivated in the dam area. The results of pot experiments showed that the three fungi isolated from LZ cultivated in mountainous areas can promote the development of shoots, stem nodes, and internodes of LZ, and increase the activity of plant peroxidase, catalase, phenylalanine ammonia lyase, and other enzymes. We can conclude that transplantation leads to the recombination of the host endophytic fungus, the more significant the difference in the environment is, the greater the reorganization caused by transplanting. Reorganization is determined by the soil environment, hosts, and the interaction of microorganisms. Remote transplantation is a crucial opportunity to reshuffle the micro-ecological structure of the asexual reproduction of plants, and regulate the growth, development, and resistance of plants, and prevent germplasm degradation caused by asexual reproduction.

A pan-metazoan concept for adult stem cells: the wobbling Penrose landscape

Adult stem cells (ASCs) in vertebrates and model invertebrates (e.g. Drosophila melanogaster) are typically long‐lived, lineage‐restricted, clonogenic and quiescent cells with somatic descendants and tissue/organ‐restricted activities. Such ASCs are mostly rare, morphologically undifferentiated, and undergo asymmetric cell division. Characterized by ‘stemness’ gene expression, they can regulate tissue/organ homeostasis, repair and regeneration. By contrast, analysis of other animal phyla shows that ASCs emerge at different life stages, present both differentiated and undifferentiated phenotypes, and may possess amoeboid movement. Usually pluri/totipotent, they may express germ‐cell markers, but often lack germ‐line sequestering, and typically do not reside in discrete niches. ASCs may constitute up to 40% of animal cells, and participate in a range of biological phenomena, from whole‐body regeneration, dormancy, and agametic asexual reproduction, to indeterminate growth. They are considered legitimate units of selection. Conceptualizing this divergence, we present an alternative stemness metaphor to the Waddington landscape: the ‘wobbling Penrose’ landscape. Here, totipotent ASCs adopt ascending/descending courses of an ‘Escherian stairwell’, in a lifelong totipotency pathway. ASCs may also travel along lower stemness echelons to reach fully differentiated states. However, from any starting state, cells can change their stemness status, underscoring their dynamic cellular potencies. Thus, vertebrate ASCs may reflect just one metazoan ASC archetype.

Intensity and mode of Lindera melissifolia reproduction are affected by flooding and light availability

We studied the impact of flooding and light availability gradients on sexual and asexual reproduction in Lindera melissifolia (Walt.) Blume, an endangered shrub found in floodplain forests of the Mississippi Alluvial Valley (MAV), USA. A water impoundment facility was used to control the duration of soil flooding (0, 45, or 90 days), and shade houses were used to control light availability (high = 72%, intermediate = 33%, or low = 2% of ambient light) received by L. melissifolia established on native soil of the MAV. Sexual reproductive intensity, as measured by inflorescence bud count, fruit set, and drupe production, was greatest in the absence of soil flooding. Ninety days of soil flooding in the year prior to anthesis decreased inflorescence bud counts, and 45 days of soil flooding in the year of anthesis lessened fruit set and drupe production. Inflorescence bud development was the greatest in environments of intermediate light, decreased in high-light environments, and was absent in low light environments. But low fruit set diminished drupe production in intermediate light environments as compared to high light environments. Asexual reproduction, as measured by development of new ramets, was greatest in the absence of soil flooding and where plants were grown in high or intermediate light. Plants exhibited plasticity in reproductive mode such that soil flooding increased the relative importance of asexual reproduction. The high light environment was most favorable to sexual reproduction, and reproductive mode transitioned to exclusively asexual in the low light environment. Our results raise several implications important to active management for the conservation of this imperiled plant.

RNA-seq between asexual archeospores and meiosis-related conchospores in Neopyropia yezoensis using Smart-seq2

In the life cycle of Neopyropia yezoensis, a potential model system for marine macroalgae, both asexual archeospores and meiosis-related conchospores develop into thalli (gametophyte). To understand this special life phenomenon in macroalgae, we picked out the two kinds of spores (10-30 cells in each sample) and conducted RNA-seq using Smart-seq2. Comparative analysis showed that light capture and carbon fixation associated differentially expressed genes (DEGs) were upregulated in archeospores, thus indicating that archeospores are in a state of rapid vegetative growth. In conchospores, protein synthesis and degradation, especially molecular chaperone, associated DEGs were up-regulated, indicating that complex life activities might be occurring in conchospores. There were 68 genes related to DNA replication and repair expressed in conchospores, showing that active DNA replication might occur in conchospores. Moreover, we found that one conchospore specifically expressed DEG (py04595: DNA helicase) only in diploid stages (conchocelis, sporangial filament) and three archeospores specifically expressed DEGs only in haploid stages (thalli). These molecular level results indicated that conchospores were closer to diploid, and might be the meiotic mother cells of N. yezoensis. In addition, we found that the knotted-like homeobox gene (PyKNOX), which might relate to the transition of gametophyte from sporophyte, was only expressed in sporophyte generation but not expressed in conchospores, archeospores and thalli, indicating the morphogenesis of gametophyte sin N. yezoensis might require the inactivation of PyKNOX.

Transitions to asexuality and evolution of gene expression in Artemia brine shrimp

While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.

Asexuality Associated with Marked Genomic Expansion of Tandemly Repeated rRNA and Histone Genes

How does asexual reproduction influence genome evolution? Although is it clear that genomic structural variation is common and important in natural populations, we know very little about how one of the most fundamental of eukaryotic traits-mode of genomic inheritance-influences genome structure. We address this question with the New Zealand freshwater snail Potamopyrgus antipodarum, which features multiple separately derived obligately asexual lineages that coexist and compete with otherwise similar sexual lineages. We used whole-genome sequencing reads from a diverse set of sexual and asexual individuals to analyze genomic abundance of a critically important gene family, rDNA (the genes encoding rRNAs), that is notable for dynamic and variable copy number. Our genomic survey of rDNA in P. antipodarum revealed two striking results. First, the core histone and 5S rRNA genes occur between tandem copies of the 18S-5.8S-28S gene cluster, a unique architecture for these crucial gene families. Second, asexual P. antipodarum harbor dramatically more rDNA-histone copies than sexuals, which we validated through molecular and cytogenetic analysis. The repeated expansion of this genomic region in asexual P. antipodarum lineages following distinct transitions to asexuality represents a dramatic genome structural change associated with asexual reproduction-with potential functional consequences related to the loss of sexual reproduction.

Heat-Stress Responses Differ among Species from Different 'Bangia' Clades of Bangiales (Rhodophyta)

The red alga ‘Bangia’ sp. ESS1, a ‘Bangia’ 2 clade member, responds to heat stress via accelerated asexual reproduction and acquires thermotolerance based on heat-stress memory. However, whether these strategies are specific to ‘Bangia’ 2, especially ‘Bangia’ sp. ESS1, or whether they are employed by all ‘Bangia’ species is currently unknown. Here, we examined the heat-stress responses of ‘Bangia’ sp. ESS2, a newly identified ‘Bangia’ clade 3 member, and Bangia atropurpurea. Intrinsic thermotolerance differed among species: Whereas ‘Bangia’ sp. ESS1 survived at 30 °C for 7 days, ‘Bangia’ sp. ESS2 and B. atropurpurea did not, with B. atropurpurea showing the highest heat sensitivity. Under sublethal heat stress, the release of asexual spores was highly repressed in ‘Bangia’ sp. ESS2 and completely repressed in B. atropurpurea, whereas it was enhanced in ‘Bangia’ sp. ESS1. ‘Bangia’ sp. ESS2 failed to acquire heat-stress tolerance under sublethal heat-stress conditions, whereas the acquisition of heat tolerance by priming with sublethal high temperatures was observed in both B. atropurpurea and ‘Bangia’ sp. ESS1. Finally, unlike ‘Bangia’ sp. ESS1, neither ‘Bangia’ sp. ESS2 nor B. atropurpurea acquired heat-stress memory. These findings provide insights into the diverse heat-stress response strategies among species from different clades of ‘Bangia’.

Mating Systems in True Morels (Morchella)

True morels (Morchella spp., Morchellaceae, Ascomycota) are widely regarded as a highly prized delicacy and are of great economic and scientific value. Recently, the rapid development of cultivation technology and expansion of areas for artificial morel cultivation have propelled morel research into a hot topic. Many studies have been conducted in various aspects of morel biology, but despite this, cultivation sites still frequently report failure to fruit or only low production of fruiting bodies. Key problems include the gap between cultivation practices and basic knowledge of morel biology. In this review, in an effort to highlight the mating systems, evolution, and life cycle of morels, we summarize the current state of knowledge of morel sexual reproduction, the structure and evolution of mating-type genes, the sexual process itself, and the influence of mating-type genes on the asexual stages and conidium production. Understanding of these processes is critical for improving technology for the cultivation of morels and for scaling up their commercial production. Morel species may well be good candidates as model species for improving sexual development research in ascomycetes in the future.

Sperm motility analysis of Cobitis hankugensis, Iksookimia longicorpa (Teleostei, Cypriniformes, Cobitidae) and their unisexual natural hybrids

Hybrid sterility is an inevitable phenomenon in the speciation process to avoid indiscriminate increases in species, but it is not always unconditional. We used computer assisted sperm analysis (CASA) to analyze sperm motility of Cobitis hankugensis, Iksookimia longicorpa, and their unisexual natural hybrids. In parental species, the sperm concentrations of C. hankugensis and I. longicorpa were 11.6 ± 4.8 × 10⁹ and 16.5 ± 6.8 × 10⁹ , respectively. For sperm motility, the total motility was higher in the parental species (C. hankugensis, 91.3%; I. longicorpa, 87.5%) than other hybrids. After 1 min, the motility duration was reduced to 14% in C. hankugensis and 3.3% in I. longicorpa. This result could indicate that the duration of sperm motility of C. hankugensis is longer than that of I. longicorpa up to 1 min after spermatozoa activation. All of the hybrids had a low concentration and it was distinct from their parent species. Total motility and other velocity parameters also showed significantly lower values except for the HHL (one from the C. hankugensis genome with two from the I. longicorpa genome) type motility measurement (13.6%). These results suggest that the hybrids derived from C. hankugensis and I. longicorpa, are not completely infertile, contrary to histological observations.

Asexual Experimental Evolution of Yeast Does Not Curtail Transposable Elements

Compared with asexual reproduction, sex facilitates the transmission of transposable elements (TEs) from one genome to another, but boosts the efficacy of selection against deleterious TEs. Thus, theoretically, it is unclear whether sex has a positive net effect on TE’s proliferation. An empirical study concluded that sex is at the root of TE’s evolutionary success because the yeast TE load was found to decrease rapidly in approximately 1,000 generations of asexual but not sexual experimental evolution. However, this finding contradicts the maintenance of TEs in natural yeast populations where sexual reproduction occurs extremely infrequently. Here, we show that the purported TE load reduction during asexual experimental evolution is likely an artifact of low genomic sequencing coverages. We observe stable TE loads in both sexual and asexual experimental evolution from multiple yeast data sets with sufficient coverages. To understand the evolutionary dynamics of yeast TEs, we turn to asexual mutation accumulation lines that have been under virtually no selection. We find that both TE transposition and excision rates per generation, but not their difference, tend to be higher in environments where yeast grows more slowly. However, the transposition rate is not significantly higher than the excision rate and the variance of the TE number among natural strains is close to its neutral expectation, suggesting that selection against TEs is at best weak in yeast. We conclude that the yeast TE load is maintained largely by a transposition–excision balance and that the influence of sex remains unclear.

High Azole Resistance in Aspergillus fumigatus Isolates from Strawberry Fields, China, 2018

In 2018, we conducted a cross-sectional study to investigate azole resistance in environmental Aspergillus fumigatus isolates obtained from different agricultural fields in China. Using 63 soil cores, we cultured for azole-resistant A. fumigatus and characterized isolates by their cyp51A gene type, short tandem repeat genotype, and mating type. Of 206 A. fumigatus isolates, 21 (10.2%) were azole resistant. Nineteen of 21 had mutations in their cyp51A gene (5 TR34/L98H, 8 TR34/L98H/S297T/F495I, 6 TR46/Y121F/T289A). Eighteen were cultured from soil samples acquired from strawberry fields, suggesting this soil type is a potential hotspot for azole resistance selection. Twenty resistant isolates were mating type MAT1-1, suggesting asexual sporulation contributed to their evolution. Prochloraz, difenoconazole, and tebuconazole were the most frequently detected fungicides in soil samples with azole-resistant fungus. Our study results suggest that managing the fungicides used in agriculture will help contain the problem of antifungal drug resistance in clinics.

ESS1

The ebb tide causes calm stress to intertidal seaweeds in tide pools; however, little is known about their physiological responses to loss of water movement. This study investigated the effects of static culture of ‘Bangia’ sp. ESS1 at 15 °C on tolerance to temperature fluctuation. The freezing of aer-obically cultured thalli at −80 °C for 10 min resulted in the death of most cells. By contrast, statically cultured thalli acquired freezing tolerance that increased cell viability after freeze–thaw cycles, although they did not achieve thermotolerance that would enable survival at the lethal temperature of 32 °C. Consistently, the unsaturation of membrane fatty acids occurred in static culture. Notably, static culture of thalli enhanced the release of asexual spores after freeze-and-thaw treatment. We conclude that calm stress triggers both the acquisition of freezing tolerance and the promotion of freezing-dependent asexual reproduction. These findings provide novel insights into stress toler-ance and the regulation of asexual reproduction in Bangiales.

Molecular Aspects of Regeneration Mechanisms in Holothurians

Holothurians, or sea cucumbers, belong to the phylum Echinodermata. They show good regenerative abilities. The present review provides an analysis of available data on the molecular aspects of regeneration mechanisms in holothurians. The genes and signaling pathways activated during the asexual reproduction and the formation of the anterior and posterior parts of the body, as well as the molecular mechanisms that provide regeneration of the nervous and digestive systems, are considered here. Damage causes a strong stress response, the signs of which are recorded even at late regeneration stages. In holothurian tissues, the concentrations of reactive oxygen species and antioxidant enzymes increase. Furthermore, the cellular and humoral components of the immune system are activated. Extracellular matrix remodeling and Wnt signaling play a major role in the regeneration in holothurians. All available morphological and molecular data show that the dedifferentiation of specialized cells in the remnant of the organ and the epithelial morphogenesis constitute the basis of regeneration in holothurians. However, depending on the type of damage, the mechanisms of regeneration may differ significantly in the spatial organization of regeneration process, the involvement of different cell types, and the depth of reprogramming of their genome (dedifferentiation or transdifferentiation).

Mating Type Idiomorphs, Heterothallism, and High Genetic Diversity in Venturia carpophila, Cause of Peach Scab

Scab (caused by Venturia carpophila) is a major disease affecting peach in the eastern United States. The aims of the study were to characterize the mating-type loci in V. carpophila, determine whether they are in equilibrium, and assess the population genetic diversity and structure of the pathogen. The mating-type gene MAT1-1-1 was identified in isolate JP3-5 in an available genome sequence, and the MAT1-2-1 gene was PCR amplified from isolate PS1-1, thus indicating a heterothallic structure. Mating-type loci structures were consistent with those of other Venturia spp. (V. effusa and V. inaequalis): the mating-type gene is positioned between APN2 encoding a DNA lyase and a gene encoding a Pleckstrin homology domain. Primers designed to each of the mating-type genes and a reference gene TUB2 were used as a multiplex PCR to screen a population (n = 81) of V. carpophila from various locations in the eastern United States. Mating types in five of the nine populations studied were in equilibrium. Among the 81 isolates, there were 69 multilocus genotypes. A population genetic analysis of the populations with >10 individuals (four populations) showed them to be genetically diverse. Linkage disequilibrium was found in five of nine populations with ≥4 isolates. A discriminant analysis of principal components indicated three genetic clusters, although extensive admixture was observed. Mating-type identification in V. carpophila provides a basis for understanding reproductive methods of the pathogen and can be a basis for further studies of the genetics of the peach scab pathogen.

A Small Number of Gametophytes with Gametangia and Stunted Sporophytes of Antrophyum obovatum Baker (Pteridaceae): The Suppression of Functional Sporophyte Production by Prezygotic and Postzygotic Sterility

Ferns have conspicuous sporophytes as the dominant phase in their life cycle; however, the gametophytes are completely separated from the sporophytes and supply their own nutrition, unlike in bryophytes and seed plants. Among the gametophytes, some maintain their populations in the gametophyte phase without progressing to sporophyte production and are known as independent gametophytes. Independent gametophytes of Antrophyum obovatum Baker were recently reported in one population on Jeju Island, Korea. In the present study, we surveyed more places to find new independent gametophyte populations of A. obovatum using the rbcL gene sequence-based DNA barcoding technique. We identified two new sites inhabited by independent gametophytes. Archegonia and juvenile sporophytes were independently observed in each location under slightly different environmental conditions. Consequently, in the case of this species, functional sporophyte production is likely suppressed by prezygotic and postzygotic sterility, depending on microenvironmental factors.

Geo-Climatic Changes and Apomixis as Major Drivers of Diversification in the Mediterranean Sea Lavenders (Limonium Mill.)

The Mediterranean realm, comprising the Mediterranean and Macaronesian regions, has long been recognized as one of the world's biodiversity hotspots, owing to its remarkable species richness and endemism. Several hypotheses on biotic and abiotic drivers of species diversification in the region have been often proposed but rarely tested in an explicit phylogenetic framework. Here, we investigate the impact of both species-intrinsic and -extrinsic factors on diversification in the species-rich, cosmopolitan Limonium, an angiosperm genus with center of diversity in the Mediterranean. First, we infer and time-calibrate the largest Limonium phylogeny to date. We then estimate ancestral ranges and diversification dynamics at both global and regional scales. At the global scale, we test whether the identified shifts in diversification rates are linked to specific geological and/or climatic events in the Mediterranean area and/or asexual reproduction (apomixis). Our results support a late Paleogene origin in the proto-Mediterranean area for Limonium, followed by extensive in situ diversification in the Mediterranean region during the late Miocene, Pliocene, and Pleistocene. We found significant increases of diversification rates in the "Mediterranean lineage" associated with the Messinian Salinity Crisis, onset of Mediterranean climate, Plio-Pleistocene sea-level fluctuations, and apomixis. Additionally, the Euro-Mediterranean area acted as the major source of species dispersals to the surrounding areas. At the regional scale, we infer the biogeographic origins of insular endemics in the oceanic archipelagos of Macaronesia, and test whether woodiness in the Canarian Nobiles clade is a derived trait linked to insular life and a biotic driver of diversification. We find that Limonium species diversity on the Canary Islands and Cape Verde archipelagos is the product of multiple colonization events followed by in situ diversification, and that woodiness of the Canarian endemics is indeed a derived trait but is not associated with a significant shift to higher diversification rates. Our study expands knowledge on how the interaction between abiotic and biotic drivers shape the uneven distribution of species diversity across taxonomic and geographical scales.

Sex and Asex: A Clonal Lexicon

Organisms across the tree of life have complex life cycles that include both sexual and asexual reproduction or that are obligately asexual. These organisms include ecologically dominant species that structure many terrestrial and marine ecosystems, as well as many pathogens, pests, and invasive species. We must consider both the evolution and maintenance of these various reproductive modes and how these modes shape the genetic diversity, adaptive evolution, and ability to persist in the species that exhibit them. Thus, having a common framework is a key aspect of understanding the biodiversity that shapes our planet. In the 2019 AGA President's Symposium, Sex and Asex: The genetics of complex life cycles, researchers investigating a wide range of taxonomic models and using a variety of modes of investigation coalesced around a common theme-understanding not only how such complex life cycles may evolve, but how they are shaped by the evolutionary and ecological forces around them. In this introduction to the Special Issue from the symposium, we give an overview of some of the key ideas and areas of investigation (a common clonal lexicon, we might say) and introduce the breadth of work submitted by symposium participants.

DNA Content Variation and SNP Diversity Within a Single Population of Asexual Snails

A growing body of research suggests that many clonal populations maintain genetic diversity even without occasional sexual reproduction. The purpose of our study was to document variation in single-nucleotide polymorphism (SNP) diversity, DNA content, and pathogen susceptibility in clonal lineages of the New Zealand freshwater snail, Potamopyrgus antipodarum. We studied snails that were collected from multiple field sites around a single lake (Lake Alexandrina), as well as isofemale clonal lineages that had been isolated and maintained in the laboratory. We used the kompetitive allele specific PCR (KASP) method to genotype our samples at 46 nuclear SNP sites, and we used flow cytometry to estimate DNA content. We found high levels of SNP diversity, both in our field samples and in our clonal laboratory lines. We also found evidence of high variation in DNA content among clones, even among clones with identical genotypes across all SNP sites. Controlled pathogen exposures of the laboratory populations revealed variation in susceptibility among distinct clonal genotypes, which was independent of DNA content. Taken together, these results show high levels of diversity among asexual snails, especially for DNA content, and they suggest rapid genome evolution in asexuals.

The Evolution of Sex is Tempered by Costly Hybridization in Boechera (Rock Cress)

Despite decades of research, the evolution of sex remains an enigma in evolutionary biology. Typically, research addresses the costs of sex and asexuality to characterize the circumstances favoring one reproductive mode. Surprisingly few studies address the influence of common traits that are, in many organisms, obligately correlated with asexuality, including hybridization and polyploidy. These characteristics have substantial impacts on traits under selection. In particular, the fitness consequences of hybridization (i.e., reduced fitness due to interspecific reproductive isolation) will influence the evolution of sex. This may comprise a cost of either sex or asexuality due to the link between hybridity and asexuality. We examined reproductive isolation in the formation of de novo hybrid lineages between 2 widespread species in the ecological model system Boechera. Seventeen percent of 664 crosses produced F1 fruits, and only 10% of these were viable, suggesting that postmating prezygotic and postzygotic barriers inhibit hybrid success in this system. The postmating prezygotic barrier was asymmetrical, with 110 of 115 total F1 fruits produced when Boechera stricta acted as maternal parent. This asymmetry was confirmed in wild-collected lineages, using a chloroplast phylogeny of wild-collected B. stricta, Boechera retrofracta, and hybrids. We next compared fitness of F2 hybrids and selfed parental B. stricta lines, finding that F2 fitness was reduced by substantial hybrid sterility. Multiple reproductively isolating barriers influence the formation and fitness of hybrid lineages in the wild, and the costs of hybridization likely have profound impacts on the evolution of sex in the natural environment.

The Medical Triazole Voriconazole Can Select for Tandem Repeat Variations in Azole-Resistant Aspergillus Fumigatus Harboring TR34/L98H Via Asexual Reproduction

Azole-resistant Aspergillus fumigatus isolates recovered at high frequency from patients, harbor mutations that are associated with variation of promoter length in the cyp51A gene. Following the discovery of the TR₃₄/L98H genotype, new variations in tandem repeat (TR) length and number of repeats were identified, as well as additional single nucleotide polymorphisms (SNPs) in the cyp51A gene, indicating that the diversity of resistance mutations in A. fumigatus is likely to continue to increase. Investigating the development routes of TR variants is critical to be able to design preventive interventions. In this study, we tested the potential effects of azole exposure on the selection of TR variations, while allowing haploid A. fumigatus to undergo asexual reproduction. Through experimental evolution involving voriconazole (VOR) exposure, an isolate harboring TR₃₄³/L98H evolved from a clinical TR₃₄/L98H ancestor isolate, confirmed by whole genome sequencing. TR₃₄³/L98H was associated with increased cyp51A expression and high VOR and posaconazole MICs, although additional acquired SNPs could also have contributed to the highly azole-resistant phenotype. Exposure to medical azoles was found to select for TR₃₄³, thus supporting the possibility of in-host selection of TR₃₄ variants.

Gemma cup and gemma development in Marchantia polymorpha

The basal land plant Marchantia polymorpha efficiently propagates in favourable environments through clonal progeny called gemmae. Gemmae develop in cup-shaped receptacles known as gemma cups, which are formed on the gametophyte body. Anatomical studies have described the developmental processes involved over a century ago; however, little is known about the underlying molecular mechanisms. Recent studies have started to unravel the mechanism underlying genetic and hormonal regulation of gemma cup and gemma development, showing that it shares some regulatory mechanisms with several sporophytic organs in angiosperms. Further study of these specialized organs will contribute to our understanding of the core regulatory modules underlying organ development in land plants and how these became so diversified morphologically over the course of evolution.

Male phenotypes in a female framework: Evidence for degeneration in sperm produced by male snails from asexual lineages

How changes in selective regimes affect trait evolution is an important open biological question. We take advantage of naturally occurring and repeated transitions from sexual to asexual reproduction in a New Zealand freshwater snail species, Potamopyrgus antipodarum, to address how evolution in an asexual context-including the potential for relaxed selection on male-specific traits-influences sperm morphology. The occasional production of male offspring by the otherwise all-female asexual P. antipodarum lineages affords a unique and powerful opportunity to assess the fate of sperm traits in a context where males are exceedingly rare. These comparisons revealed that the sperm produced by 'asexual' males are markedly distinct from sexual counterparts. We also found that the asexual male sperm harboured markedly higher phenotypic variation and was much more likely to be morphologically abnormal. Together, these data suggest that transitions to asexual reproduction might be irreversible, at least in part because male function is likely to be compromised. These results are also consistent with a scenario where relaxed selection and/or mutation accumulation in the absence of sex translates into rapid trait degeneration.

Using asexual vertebrates to study genome evolution and animal physiology: Banded (Fundulus diaphanus) x Common Killifish (F. heteroclitus) hybrid lineages as a model system

Wild, asexual, vertebrate hybrids have many characteristics that make them good model systems for studying how genomes evolve and epigenetic modifications influence animal physiology. In particular, the formation of asexual hybrid lineages is a form of reproductive incompatibility, but we know little about the genetic and genomic mechanisms by which this mode of reproductive isolation proceeds in animals. Asexual lineages also provide researchers with the ability to produce genetically identical individuals, enabling the study of autonomous epigenetic modifications without the confounds of genetic variation. Here, we briefly review the cellular and molecular mechanisms leading to asexual reproduction in vertebrates and the known genetic and epigenetic consequences of the loss of sex. We then specifically discuss what is known about asexual lineages of Fundulus diaphanus x F. heteroclitus to highlight gaps in our knowledge of the biology of these clones. Our preliminary studies of F. diaphanus and F. heteroclitus karyotypes from Porter's Lake (Nova Scotia, Canada) agree with data from other populations, suggesting a conserved interspecific chromosomal arrangement. In addition, genetic analyses suggest that: (a) the same major clonal lineage (Clone A) of F. diaphanus x F. heteroclitus has remained dominant over the past decade, (b) some minor clones have also persisted, (c) new clones may have recently formed, and iv) wild clones still mainly descend from F. diaphanus ♀ x F. heteroclitus ♂ crosses (96% in 2017-2018). These data suggest that clone formation may be a relatively rare, but continuous process, and there are persistent environmental or genetic factors causing a bias in cross direction. We end by describing our current research on the genomic causes and consequences of a transition to asexuality and the potential physiological consequences of epigenetic variation.