Morning glory as a powerful model in ecological genomics: tracing adaptation through both natural and artificial selection

Advancements in plant transformation: from traditional methods to cutting-edge techniques and emerging model species

The ability to efficiently genetically modify plant species is crucial, driving the need for innovative technologies in plant biotechnology. Existing plant genetic transformation systems include Agrobacterium-mediated transformation, biolistics, protoplast-based methods, and nanoparticle techniques. Despite these diverse methods, many species exhibit resistance to transformation, limiting the applicability of most published methods to specific species or genotypes. Tissue culture remains a significant barrier for most species, although other barriers exist. These include the infection and regeneration stages in Agrobacterium, cell death and genomic instability in biolistics, the creation and regeneration of protoplasts for protoplast-based methods, and the difficulty of achieving stable transformation with nanoparticles. To develop species-independent transformation methods, it is essential to address these transformation bottlenecks. This review examines recent advancements in plant biotechnology, highlighting both new and existing techniques that have improved the success rates of plant transformations. Additionally, several newly emerged plant model systems that have benefited from these technological advancements are also discussed.

The Boechera model system for evolutionary ecology

Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.

Diversification of ergot alkaloids and heritable fungal symbionts in morning glories

Heritable microorganisms play critical roles in life cycles of many macro-organisms but their prevalence and functional roles are unknown for most plants. Bioactive ergot alkaloids produced by heritable Periglandula fungi occur in some morning glories (Convolvulaceae), similar to ergot alkaloids in grasses infected with related fungi. Ergot alkaloids have been of longstanding interest given their toxic effects, psychoactive properties, and medical applications. Here we show that ergot alkaloids are concentrated in four morning glory clades exhibiting differences in alkaloid profiles and are more prevalent in species with larger seeds than those with smaller seeds. Further, we found a phylogenetically-independent, positive correlation between seed mass and alkaloid concentrations in symbiotic species. Our findings suggest that heritable symbiosis has diversified among particular clades by vertical transmission through seeds combined with host speciation, and that ergot alkaloids are particularly beneficial to species with larger seeds. Our results are consistent with the defensive symbiosis hypothesis where bioactive ergot alkaloids from Periglandula symbionts protect seeds and seedlings from natural enemies, and provide a framework for exploring microbial chemistry in other plant-microbe interactions.

Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed

Plastic phenotypic responses to environmental change are common, yet we lack a clear understanding of the fitness consequences of these plastic responses. Here, we use the evolution of herbicide resistance in the common morning glory (Ipomoea purpurea) as a model for understanding the relative importance of adaptive and maladaptive gene expression responses to herbicide. Specifically, we compare leaf gene expression changes caused by herbicide to the expression changes that evolve in response to artificial selection for herbicide resistance. We identify a number of genes that show plastic and evolved responses to herbicide and find that for the majority of genes with both plastic and evolved responses, plastic responses appear to be adaptive. We also find that selection for herbicide response increases gene expression plasticity. Overall, these results show the importance of adaptive plasticity for herbicide resistance in a common weed and that expression changes in response to strong environmental change can be adaptive.

Below-ground competition favors character convergence but not character displacement in root traits

Character displacement can play a major role in species ecology and evolution; however, research testing whether character displacement can influence the evolution of root traits in plant systems remains scarce in the literature. Here we investigated the potential that character displacement may influence the evolution of root traits using two closely related morning glory species, Ipomoea purpurea and Ipomoea hederacea. We performed a field experiment where we grew the common morning glory, I. purpurea, in the presence and absence of competition from I. hederacea and examined the potential that the process of character displacement could influence the evolution of root traits. We found maternal line variation in root phenotypes and evidence that below-ground competition acts as an agent of selection on these traits. Our test of character displacement, however, showed evidence of character convergence on our measure of root architecture rather than displacement. These results suggest that plants may be constrained by their local environments to express a phenotype that enhances fitness. Therefore, the conditions of the competitive environment experienced by a plant may influence the potential for character convergence or displacement to influence the evolution of root traits.

Belowground Competition Can Influence the Evolution of Root Traits

Although root traits play a critical role in mediating plant-plant interactions and resource acquisition from the soil environment, research examining whether and how belowground competition can influence the evolution of root traits remains largely unexplored. Here we examine the possibility that root traits may evolve as a target of selection from interspecific competition using Ipomoea purpurea and I. hederacea, two closely related morning glory species that commonly co-occur in the United States, as a model system. We show that belowground competitive interactions between the two species can alter the pattern of selection on root traits in each species. Specifically, competition with I. purpurea changes the pattern of selection on root angle in I. hederacea, and competitive interactions with I. hederacea change the pattern of selection on root size in I. purpurea. However, we did not uncover evidence that intraspecific competition altered the pattern of selection on any root traits within I. hederacea. Overall, our results suggest that belowground competition between closely related species can influence the phenotypic evolution of root traits in natural populations. Our findings provide a microevolutionary perspective of how competitive belowground interactions may impact plant fitness, potentially leading to patterns of plant community structure.

The Complete Chloroplast Genomes of Six Ipomoea Species and Indel Marker Development for the Discrimination of Authentic Pharbitidis Semen (Seeds of I. nil or I. purpurea)

Ipomoea L. is the largest genus within the Convolvulaceae and contains 600-700 species. Ipomoea species (morning glories) are economically valuable as horticultural species and scientifically valuable as ecological model plants to investigate mating systems, molecular evolution, and both plant-herbivore and plant-parasite interactions. Furthermore, the dried seeds of I. nil or I. purpurea are used in Korean traditional herbal medicines. In this study, chloroplast (cp) genomes were sequenced from six Ipomoea species, namely, I. nil and I. purpurea and, for the first time, I. triloba, I. lacunosa, I. hederacea, and I. hederacea var. integriuscula. The cp genomes were 161,354-161,750 bp in length and exhibited conserved quadripartite structures. In total, 112 genes were identified, including 78 protein-coding regions, 30 transfer RNA genes, and 4 ribosomal RNA genes. The gene order, content, and orientation of the six Ipomoea cp genomes were highly conserved and were consistent with the general structure of angiosperm cp genomes. Comparison of the six Ipomoea cp genomes revealed locally divergent regions, mainly within intergenic spacer regions (petN-psbM, trnI-CAU-ycf2, ndhH-ndhF, psbC-trnS, and ccsA-ndhD). In addition, the protein-coding genes accD, cemA, and ycf2 exhibited high sequence variability and were under positive selection (Ka/Ks > 1), indicating adaptive evolution to the environment within the Ipomoea genus. Phylogenetic analysis of the six Ipomoea species revealed that these species clustered according to the APG IV system. In particular, I. nil and I. hederacea had monophyletic positions, with I. purpurea as a sister. I. triloba and I. lacunosa in the section Batatas and I. hederacea and I. hederacea var. integriuscula in the section Quamoclit were supported in this study with strong bootstrap values and posterior probabilities. We uncovered high-resolution phylogenetic relationships between Ipomoeeae. Finally, indel markers (IPOTY and IPOYCF) were developed for the discrimination of the important herbal medicine species I. nil and I. purpurea. The cp genomes and analyses in this study provide useful information for taxonomic, phylogenetic, and evolutionary analysis of the Ipomoea genome, and the indel markers will be useful for authentication of herbal medicines.

Shifts in outcrossing rates and changes to floral traits are associated with the evolution of herbicide resistance in the common morning glory

Human-mediated selection can strongly influence the evolutionary response of natural organisms within ecological timescales. But what traits allow for, or even facilitate, adaptation to the strong selection humans impose on natural systems? Using a combination of laboratory and greenhouse studies of 32 natural populations of the common agricultural weed, Ipomoea purpurea, we show that herbicide-resistant populations self-fertilise more than susceptible populations. We likewise show that anther-stigma distance, a floral trait associated with self-fertilisation in this species, exhibits a nonlinear relationship with resistance such that the most and least resistant populations exhibit lower anther-stigma separation compared to populations with moderate levels of resistance. Overall, our results extend the general finding that plant mating can be impacted by human-mediated agents of selection to that of the extreme selection of the agricultural system. This work highlights the influence of human-mediated selection on rapid responses of natural populations that can lead to unexpected long-term evolutionary consequences.

An examination of fitness costs of glyphosate resistance in the common morning glory, Ipomoea purpurea

Fitness costs are frequently invoked to explain the presence of genetic variation underlying plant defense across many types of damaging agents. Despite the expectation that costs of resistance are prevalent, however, they have been difficult to detect in nature. To examine the potential that resistance confers a fitness cost, we examined the survival and fitness of genetic lines of the common morning glory, Ipomoea purpurea, that diverged in the level of resistance to the herbicide glyphosate. We planted a large field experiment and assessed survival following herbicide application as well as fitness of the divergent selection lines in the absence of the herbicide. We found that genetic lines selected for increased resistance exhibited lower death compared to control and susceptible lines in the presence of the herbicide, but no evidence that resistant lines produced fewer seeds in the absence of herbicide. However, susceptible lines produced more viable seeds than resistant or control lines, providing some evidence of a fitness cost in terms of seed germination, and thus potential empirical support for the expectation of trait trade-offs as a consequence of adaptation to novel environments.

De novo assembly and annotation of the transcriptome of the agricultural weed Ipomoea purpurea uncovers gene expression changes associated with herbicide resistance

Human-mediated selection can lead to rapid evolution in very short time scales, and the evolution of herbicide resistance in agricultural weeds is an excellent example of this phenomenon. The common morning glory, Ipomoea purpurea, is resistant to the herbicide glyphosate, but genetic investigations of this trait have been hampered by the lack of genomic resources for this species. Here, we present the annotated transcriptome of the common morning glory, Ipomoea purpurea, along with an examination of whole genome expression profiling to assess potential gene expression differences between three artificially selected herbicide resistant lines and three susceptible lines. The assembled Ipomoea transcriptome reported in this work contains 65,459 assembled transcripts, ~28,000 of which were functionally annotated by assignment to Gene Ontology categories. Our RNA-seq survey using this reference transcriptome identified 19 differentially expressed genes associated with resistance-one of which, a cytochrome P450, belongs to a large plant family of genes involved in xenobiotic detoxification. The differentially expressed genes also broadly implicated receptor-like kinases, which were down-regulated in the resistant lines, and other growth and defense genes, which were up-regulated in resistant lines. Interestingly, the target of glyphosate-EPSP synthase-was not overexpressed in the resistant Ipomoea lines as in other glyphosate resistant weeds. Overall, this work identifies potential candidate resistance loci for future investigations and dramatically increases genomic resources for this species. The assembled transcriptome presented herein will also provide a valuable resource to the Ipomoea community, as well as to those interested in utilizing the close relationship between the Convolvulaceae and the Solanaceae for phylogenetic and comparative genomics examinations.

Phylogenetics and diversification of morning glories (tribe Ipomoeeae, Convolvulaceae) based on whole plastome sequences

PREMISE OF THE STUDY

Morning glories are an emerging model system, and resolving phylogenetic relationships is critical for understanding their evolution. Phylogenetic studies demonstrated that the largest morning glory genus, Ipomoea, is not monophyletic, and nine other genera are derived from within Ipomoea. Therefore, systematic research is focused on the monophyletic tribe Ipomoeeae (ca. 650-900 species). We used whole plastomes to infer relationships across Ipomoeeae.

METHODS

Whole plastomes were sequenced for 29 morning glory species, representing major lineages. Phylogenies were estimated using alignments of 82 plastid genes and whole plastomes. Divergence times were estimated using three fossil calibration points. Finally, evolution of root architecture, flower color, and ergot alkaloid presence was examined.

KEY RESULTS

Phylogenies estimated from both data sets had nearly identical topologies. Phylogenetic results are generally consistent with prior phylogenetic hypotheses. Higher-level relationships with weak support in previous studies were recovered here with strong support. Molecular dating analysis suggests a late Eocene divergence time for the Ipomoeeae. The two clades within the tribe, Argyreiinae and Astripomoeinae, diversified at similar times. Reconstructed most recent common ancestor of the Ipomoeeae had blue flowers, an association with ergot-producing fungi, and either tuberous or fibrous roots.

CONCLUSIONS

Phylogenetic results provide confidence in relationships among Ipomoeeae lineages. Divergence time estimation results provide a temporal context for diversification of morning glories. Ancestral character reconstructions support previous findings that morning glory morphology is evolutionarily labile. Taken together, our study provides strong resolution of the morning glory phylogeny, which is broadly applicable to the evolution and ecology of these fascinating species.

Tracing the geographic origins of weedy Ipomoea purpurea in the southeastern United States

Ipomoea purpurea (common morning glory) is an annual vine native to Mexico that is well known for its large, showy flowers. Humans have spread morning glories worldwide, owing to the horticultural appeal of morning glory flowers. Ipomoea purpurea is an opportunistic colonizer of disturbed habitats including roadside and agricultural settings, and it is now regarded as a noxious weed in the Southeastern US. Naturalized populations in the Southeastern United States are highly polymorphic for a number of flower color morphs, unlike native Mexican populations that are typically monomorphic for the purple color morph. Although I. purpurea was introduced into the United States from Mexico, little is known about the specific geographic origins of US populations relative to the Mexican source. We use resequencing data from 11 loci and 30 I. purpurea accessions collected from the native range of the species in Central and Southern Mexico and 8 accessions from the Southeastern United States to infer likely geographic origins in Mexico. Based on genetic assignment analysis, haplotype composition, and the degree of shared polymorphism, I. purpurea samples from the Southeastern United States are genetically most similar to samples from the Valley of Mexico and Veracruz State. This supports earlier speculation that I. purpurea in the Southeastern United States was likely to have been introduced by European colonists from sources in Central Mexico.

The promise of genomics in the study of plant-pollinator interactions

Flowers exist in exceedingly complex fitness landscapes, in which subtle variation in each trait can affect the pollinators, herbivores and pleiotropically linked traits in other plant tissues. A whole-genome approach to flower evolution will help our understanding of plant-pollinator interactions.

Molecular spandrels: tests of adaptation at the genetic level

Although much progress has been made in identifying the genes (and, in rare cases, mutations) that contribute to phenotypic variation, less is known about the effects that these genes have on fitness. Nonetheless, genes are commonly labelled as 'adaptive' if an allele has been shown to affect a phenotype with known or suspected functional importance or if patterns of nucleotide variation at the locus are consistent with positive selection. In these cases, the 'adaptive' designation may be premature and may lead to incorrect conclusions about the relationships between gene function and fitness. Experiments to test targets and agents of natural selection within a genomic context are necessary for identifying the adaptive consequences of individual alleles.