Phylogenetic Relationships and Evolutionary Trends in the Cactus Family

Ecological and metabolic implications of the nurse effect of Maihueniopsis camachoi in the Atacama Desert

Plant-plant positive interactions are key drivers of community structure. Yet, the underlying molecular mechanisms of facilitation processes remain unexplored. We investigated the 'nursing' effect of Maihueniopsis camachoi, a cactus that thrives in the Atacama Desert between c. 2800 and 3800 m above sea level. We hypothesised that an important protective factor is thermal amelioration of less cold-tolerant species with a corresponding impact on molecular phenotypes. To test this hypothesis, we compared plant cover and temperatures within the cactus foliage with open areas and modelled the effect of temperatures on plant distribution. We combined eco-metabolomics and machine learning to test the molecular consequences of this association. Multiple species benefited from the interaction with M. camachoi. A conspicuous example was the extended distribution of Atriplex imbricata to colder elevations in association with M. camachoi (400 m higher as compared to plants in open areas). Metabolomics identified 93 biochemical markers predicting the interaction status of A. imbricata with 79% accuracy, independently of year. These findings place M. camachoi as a key species in Atacama plant communities, driving local biodiversity with an impact on molecular phenotypes of nursed species. Our results support the stress-gradient hypothesis and provide pioneer insights into the metabolic consequences of facilitation.

Taxonomic dissection based on molecular evidence of the Eriosycecurvispina complex (Cactaceae): identifying nine endemic species from Central Chile

Chile's distinctive flora, geographical isolation, and complex topography collectively contribute to a notable endemic species diversity, particularly within central regions identified as critical areas for biodiversity conservation. The cactus genus Eriosyce, as currently circumscribed, encompasses seven sections, with Eriosycesect.Horridocatus presenting a notably complex species group. This study investigates the E.curvispina complex, a member of the Notocacteae tribe common in central Chile, by incorporating new populations and examining phylogenetic relationships using four plastid and one nuclear molecular marker. The phylogenetic analysis of sampled individuals identified nine independent lineages, each warranting recognition at the species rank. Despite minimal morphological differences among taxa, morphological characters were utilized to support and stabilize the DNA-based phylogenetic hypothesis. The results highlight the high taxonomic diversity in these cactus lineages and have implications for the classification of the E.curvispina complex, including new combinations and proposals of conservation status.

Unravelling phylogenetic relationships of the tribe Cereeae using target enrichment sequencing

BACKGROUND AND AIMS

Cactaceae are succulent plants, quasi-endemic to the American continent, and one of the most endangered plant groups in the world. Molecular phylogenies have been key to unravelling phylogenetic relationships among major cactus groups, previously hampered by high levels of morphological convergence. Phylogenetic studies using plastid markers have not provided adequate resolution for determining generic relationships within cactus groups. This is the case for the tribe Cereeae s.l., a highly diverse group from tropical America. Here we aimed to reconstruct a well-resolved phylogenetic tree of tribe Cereeae and update the circumscription of suprageneric and generic groups in this tribe.

METHODS

We integrated sequence data from public gene and genomic databases with new target sequences (generated using the customized Cactaceae591 probe set) across representatives of this tribe, with a denser taxon sampling of the subtribe Cereinae. We inferred concatenated and coalescent phylogenetic trees and compared the performance of both approaches.

KEY RESULTS

Six well-supported suprageneric clades were identified using different datasets. However, only genomic datasets, especially the Cactaceae591, were able to resolve the contentious relationships within the subtribe Cereinae.

CONCLUSIONS

We propose a new taxonomic classification within Cereeae based on well-resolved clades, including new subtribes (Aylosterinae subtr. nov., Uebelmanniinae subtr. nov. and Gymnocalyciinae subtr. nov.) and revised subtribes (Trichocereinae, Rebutiinae and Cereinae). We emphasize the importance of using genomic datasets allied with coalescent inference to investigate evolutionary patterns within the tribe Cereeae.

Tissue succulence in plants: Carrying water for climate change

Tissue succulence in plants involves the storage of water in one or more organs or tissues to assist in maintaining water potentials on daily or seasonal time scales. This drought-avoidance or drought-resistance strategy allows plants to occupy diverse environments including arid regions, regions with rocky soils, epiphytic habitats, and saline soils. Climate-resilient strategies are of increasing interest in the context of the global climate crisis, which is leading to hotter and drier conditions in many regions throughout the globe. Here, we describe a short history of succulent plants, the basic concepts of tissue succulence, the anatomical diversity of succulent morphologies and associated adaptive traits, the evolutionary, phylogenetic, and biogeographical diversity of succulent plants, extinction risks to succulents due to poaching from their natural environments, and the myriad uses and applications of economically important succulent species and the products derived from them. Lastly, we discuss current prospects for engineering tissue succulence to improve salinity and drought tolerance in crops.

Diverse signatures of convergent evolution in cacti-associated yeasts

Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently ~17 times. Using machine-learning, we further found that cactophily can be predicted with 76% accuracy from functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which is likely associated with duplication and altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved through disparate molecular mechanisms. Remarkably, multiple cactophilic lineages and their close relatives are emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-may preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.

Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae)

BACKGROUND

The cactus family (Cactaceae) has been reported to have evolved a minimal photosynthetic plastome size, with the loss of inverted-repeat (IR) regions and NDH gene suites. However, there are very limited genomic data on the family, especially Cereoideae, the largest subfamily of cacti.

RESULTS

In the present study, we assembled and annotated 35 plastomes, 33 of which were representatives of Cereoideae, alongside 2 previously published plastomes. We analyzed the organelle genomes of 35 genera in the subfamily. These plastomes have variations rarely observed in those of other angiosperms, including size differences (with ~ 30 kb between the shortest and longest), dramatic dynamic changes in IR boundaries, frequent plastome inversions, and rearrangements. These results suggested that cacti have the most complex plastome evolution among angiosperms.

CONCLUSION

These results provide unique insight into the dynamic evolutionary history of Cereoideae plastomes and refine current knowledge of the relationships within the subfamily.

Supercritical Fluid Extraction of Oils from Cactus Opuntia ficus-indica L. and Opuntia dillenii Seeds

This study aimed to assess the capability of supercritical fluid extraction (SFE) as an alternative and green technique compared to Soxhlet extraction for the production of oils from Opuntia ficus-indica (OFI) seeds originating from Yemen and Italy and Opuntia dillenii (OD) seeds from Yemen. The following parameters were used for SFE extraction: a pressure of 300 bar, a CO₂ flow rate of 1 L/h, and temperatures of 40 and 60 °C. The chemical composition, including the fatty acids and tocopherols (vitamin E) of the oils, was determined using chromatographic methods. The highest yield was achieved with Soxhlet extraction. The oils obtained with the different extraction procedures were all characterized by a high level of unsaturated fatty acids. Linoleic acid (≤62% in all samples) was the most abundant one, followed by oleic and vaccenic acid. Thirty triacylglycerols (TAGs) were identified in both OFI and OD seed oils, with trilinolein being the most abundant (29-35%). Vanillin, 4-hydroxybenzaldehyde, vanillic acid, and hydroxytyrosol were phenols detected in both OFI and OD oils. The highest γ-tocopherol content (177 ± 0.23 mg/100 g) was obtained through the SFE of OFI seeds from Yemen. Overall, the results highlighted the potential of SFE as green technology to obtain oils suitable for functional food and nutraceutical products.

Phytochemical profiling, antimicrobial, and antioxidant activities of hydroethanolic extracts of prickly pear ( Opuntia ficus indica ) fruit and pulp

Phenolic compounds in prickly pear [Opuntia ficus indica (L.) Mill.] are known to contribute to the antioxidant and antimicrobial activities of the prickly pear. The present study aimed to evaluate the antioxidants and in vitro antimicrobial potential in the hydroethanolic extracts of different parts (fruit, cladode, and pulp) of prickly pear. Different polyphenolic compounds were analyzed by using high-performance liquid chromatography. The results indicated that cladode possessed a higher quantity of phenolics compared with that observed in fruit and pulp. The most important phenolic compound in high quantity was gallic acid (66.19 μg/g) in cladode. The 100% aqueous extract of cladode exhibited the highest antioxidant (92%) and antimicrobial activities against Salmonella typhi (3.40 mg/ml), Helicobacter pylori (1.37 mg/ml), Escherichia coli (1.41 mg/ml), and Staphylococcus aureus (1.41 mg/ml). Principal component analysis (PCA) indicated that antioxidant activity and minimum inhibitory concentration (MIC) responses had a significant negative correlation with each other. Overall, the current results provided basic data for choosing prickly pear cladode with high antioxidant capacity for the development and consumption of antioxidant-based alternative medicines and value addition of formulated foods.

Study on the Effectiveness of Two Biopolymer Coagulants on Turbidity and Chemical Oxygen Demand Removal in Urban Wastewater

The present study investigated the effectiveness of two biopolymer coagulants on turbidity and chemical oxygen demand removal in urban wastewater. The biopolymers were produced from vegetal biomass using the mucilage extracted from Opuntia robusta cladodes, and Uncaria tomentosa leaves. Opuntia robusta is an abundant species in Mexico, which is not edible. Uncaria tomentosa is an exotic invasive species in Mexico and other countries, which negatively affects the ecosystems where it is introduced. A combined experimental design of mixture-process was selected to evaluate the effectiveness of both biopolymer coagulants regarding aluminum sulfate (conventional chemical coagulant). Results showed turbidity and chemical oxygen demand removal efficiencies of 42.3% and 69.6% for Opuntia robusta and 17.2% and 39.4% for Uncaria tomentosa biopolymer coagulant, respectively, at a dose of 200 mg/L. Furthermore, optimum conditions from the experimental design to reach the maximum turbidity and chemical oxygen demand removal were obtained at an Opuntia robusta biopolymer coagulant concentration of 10 mg/L, showing removal efficiencies of 68.7 ± 1.7% and 86.1 ± 1.4%, respectively. These results support using Opuntia robusta as an alternative biopolymer coagulant in urban wastewater treatment.

Physical, Nutritional, and Bioactive Properties of Mandacaru Cladode Flour (Cereus jamacaru DC.): An Unconventional Food Plant from the Semi-Arid Brazilian Northeast

In this study, we evaluated the physical, nutritional, and bioactive properties of mandacaru cladode flour (Cereus jamacaru DC.). The granulometric profile revealed particles with non-uniform geometry, flakiness, a rectangular tendency, and a non-homogeneous surface, with particle sizes ranging from 20 to 60 µm. The flour presented low water activity (0.423), a moisture content of 8.24 g/100 g, high ash (2.82 g/100 g), protein (5.18 g/100 g), and total carbohydrate contents (74.48 g/100 g), and low lipid contents (1.88 g/100 g). Mandacaru flour is an excellent source of insoluble dietary fiber (48.08 g/100 g), calcium (76.33%), magnesium (15.21%), and potassium (5.94%). Notably, ¹H NMR analysis revealed the presence of N-methyltyramine. Using HPLC chromatography, glucose was identified as the predominant sugar (1.33 g/100 g), followed by four organic acids, especially malic acid (9.41 g/100 g) and citric acid (3.96 g/100 g). Eighteen phenolic compounds were detected, with relevant amounts of kaempferol (99.40 mg/100 g), myricetin (72.30 mg/100 g), and resveratrol (17.84 mg/100 g). The total phenolic compounds and flavonoids were 1285.47 mg GAE/100 g and 15.19 mg CE/100 g, respectively. The mean in vitro antioxidant activity values were higher using the FRAP method (249.45 µmol Trolox TEAC/100 g) compared to the ABTS^•+ method (0.39 µmol Trolox TEAC/g). Finally, the ascorbic acid had a content of 35.22 mg/100 g. The results demonstrate the value of mandacaru as a little-explored species and an excellent matrix for the development of flours presenting good nutritional value and bioactive constituents with excellent antioxidant potential.

Cactaceae plants as sources of active bioavailable phytochemicals

Arid-land plants from the Cactaceae family are endemic to the Americas and cultivated worldwide. Cactaceous plants and their fruits contain phenolic compounds, betalains, vitamins, carotenoids, minerals, and soluble fiber. Edible cactaceous matrices can be considered functional foods since their consumption may confer health benefits. These plants could be a source of novel bioactive compounds relevant to the area of phytomedicine. However, consumption of high concentrations of active molecules is not necessarily correlated to beneficial physiological effects because phytochemicals must be released from the food matrices under physiological conditions, resist digestion-associated chemical transformations, and remain in their active state in systemic circulation until the target tissues are reached. Notably, although digestion may either increase or decrease the bioactive phytochemicals' activity and stability, non-absorbed compounds may also be relevant for human health. Additionally, food matrices' type and composition and their technological processing operations may influence the compounds' release, stability, and accessibility. Thus, this review provides insights on the feasibility of using Cactaceae plants as sources of functional compounds. It is focused on compounds' bioactivity, bioaccessibility, and overall bioavailability after their metabolic transformation. Also, it addresses the influence of food processing on bioactive compounds. Many Cactaceae species are unexplored, and our understanding of how they confer health benefits is limited. To better understand the physiological relevance, nutraceutical potential, and therapeutic feasibility of cactaceous bioactive phytochemicals, future research should focus on the metabolic stability and safety of these compounds, as well as their assimilation mechanisms (absorption, distribution, and metabolic fate).

A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae

The molecular phylogenies of Cactaceae have enabled us to better understand their systematics, biogeography, and diversification ages. However, most of the phylogenetic relationships within Cactaceae major groups remain unclear, largely due to the lack of an appropriate set of molecular markers to resolve its contentious relationships. Here, we explored the genome and transcriptome assemblies available for Cactaceae and identified putative orthologous regions shared among lineages of the subfamily Cactoideae. Then we developed a probe set, named Cactaceae591, targeting both coding and noncoding nuclear regions for representatives from the subfamilies Pereskioideae, Opuntioideae, and Cactoideae. We also sampled inter- and intraspecific variation to evaluate the potential of this panel to be used in phylogeographic studies. We retrieved on average of 547 orthologous regions per sample. Targeting noncoding nuclear regions showed to be crucial to resolving inter- and intraspecific relationships. Cactaceae591 covers 13 orthologous genes shared with the Angiosperms353 kit and two plastid regions largely used in Cactaceae studies, enabling the phylogenies generated by our panel to be integrated with angiosperm and Cactaceae phylogenies, using these sequences. We highlighted the importance of using coalescent-based species tree approaches on the Cactaceae591 dataset to infer accurate phylogenetic trees in the presence of extensive incomplete lineage sorting in this family.

Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects

Here, we present a review of the studies of evolutionary genetics (phylogenetics, population genetics, and phylogeography) using genetic data as well as genome scale assemblies in Cactaceae (Caryophyllales, Angiosperms), a major lineage of succulent plants with astonishing diversity on the American continent. To this end, we performed a literature survey (1992–2021) to obtain detailed information regarding key aspects of studies investigating cactus evolution. Specifically, we summarize the advances in the following aspects: molecular markers, species delimitation, phylogenetics, hybridization, biogeography, and genome assemblies. In brief, we observed substantial growth in the studies conducted with molecular markers in the past two decades. However, we found biases in taxonomic/geographic sampling and the use of traditional markers and statistical approaches. We discuss some methodological and social challenges for engaging the cactus community in genomic research. We also stressed the importance of integrative approaches, coalescent methods, and international collaboration to advance the understanding of cactus evolution.

A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae

Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae, applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies.

The plastome of Melocactus glaucescens Buining & Brederoo reveals unique evolutionary features and loss of essential tRNA genes

The plastome of Melocactus glaucescens shows unique rearrangements, IR expansion, and unprecedented gene losses in Cactaceae. Our data indicate tRNA import from the cytosol to the plastids in this species. Cactaceae represents one of the richest families in keystone species of arid and semiarid biomes. This family shows various specific features comprehending morphology, anatomy, and metabolism, which allow them to grow under unfavorable environmental conditions. The subfamily Cactoideae contains the most divergence of species, which are highly variable in growth habit and morphology. This subfamily includes the endangered species Melocactus glaucescens (tribe Cereeae), which is a cactus endemic to the biome Caatinga in Brazil. Aiming to analyze the plastid evolution and develop molecular markers, we sequenced and analyzed in detail the plastome of M. glaucescens. Our analyses revealed that the M. glaucescens plastome is the most divergent among the species of the family Cactaceae sequenced so far. We characterized here unique rearrangements, expanded IRs containing an unusual set of genes, and several gene losses. Some genes related to the ndh complex were lost during the plastome evolution, while others have lost their functionality. Additionally, the loss of three tRNA genes (trnA-UGC, trnV-UAC, and trnV-GAC) suggests tRNA import from the cytosol to the plastids in M. glaucescens. Moreover, we identified high gene divergence, several putative positive signatures, and possible unique RNA-editing sites. Furthermore, we mapped 169 SSRs in the plastome of M. glaucescens, which are helpful to access the genetic diversity of natural populations and conservation strategies. Finally, our data provide new insights into the evolution of plastids in Cactaceae, which is an outstanding lineage adapted to extreme environmental conditions and a notorious example of the atypical evolution of plastomes.

Independent Evolutionary Lineages in a Globular Cactus Species Complex Reveals Hidden Diversity in a Central Chile Biodiversity Hotspot

Unraveling the processes involved in the origin of a substantial fraction of biodiversity can be a particularly difficult task in groups of similar, and often convergent, morphologies. The genus Eriosyce (Cactaceae) might present a greater specific diversity since much of its species richness might be hidden in morphological species complexes. The aim of this study was to investigate species delimitation using the molecular data of the globose cacti “E. curvispina”, which harbor several populations of unclear evolutionary relationships. We ran phylogenetic inferences on 87 taxa of Eriosyce, including nine E. curvispina populations, and by analyzing three plastid noncoding introns, one plastid and one nuclear gene. Additionally, we developed 12 new pairs of nuclear microsatellites to evaluate the population-level genetic structure. We identified four groups that originated in independent cladogenetic events occurring at different temporal depths; these groups presented high genetic diversity, and their populations were genetically structured. These results suggest a complex evolutionary history in the origin of globular cacti, with independent speciation events occurring at different time spans. This cryptic richness is underestimated in the Mediterranean flora of central Chile, and thus unique evolutionary diversity could be overlooked in conservation and management actions.

Evolution of flower allometry and pigmentation in Mammillaria haageana (Cactaceae)

BACKGROUND

A puzzle in evolution is the understanding of how the environment might drive subtle phenotypic variation, and whether this variation is adaptive. Under the neutral evolutionary theory, subtle phenotypes are almost neutral with little adaptive value. To test this idea, we studied the infraspecific variation in flower shape and color in Mammillaria haageana, a species with a wide geographical distribution and phenotypic variation, which populations are often recognized as infraspecific taxa.

RESULTS

We collected samples from wild populations, kept them in the greenhouse for at least one reproductive year, and collected newly formed flowers. Our first objective was to characterize tepal natural variation in M. haageana through geometric morphometric and multivariate pigmentation analyses. We used landmark-based morphometrics to quantify the trends of shape variation and tepal color-patterns in 20 M. haageana accessions, belonging to five subspecies, plus 8 M. albilanata accessions for comparison as the sister species. We obtained eight geometric morphometric traits for tepal shape and color-patterns. We found broad variation in these traits between accessions belonging to the same subspecies, without taxonomic congruence with those infraspecific units. Also the phenetic cluster analysis showed different grouping patterns among accessions. When we correlated these phenotypes to the environment, we also found that solar radiation might explain the variation in tepal shape and color, suggesting that subtle variation in flower phenotypes might be adaptive. Finally we present anatomical sections in M. haageana subsp. san-angelensis to propose some of the underlying tepal structural features that may give rise to tepal variation.

CONCLUSIONS

Our geometric morphometric approach of flower shape and color allowed us to identify the main trends of variation in each accession and putative subspecies, but also allowed us to correlate these variation to the environment, and propose anatomical mechanisms underlying this diversity of flower phenotypes.

A Systematic Review on Opuntia (Cactaceae; Opuntioideae) Flower-Visiting Insects in the World with Emphasis on Mexico: Implications for Biodiversity Conservation

Opuntia spp. are cacti with high ecological, economic and conservation interest in semiarid environments, particularly in Mexico. We conducted a systematic search of the existing peer-reviewed literature about the state of knowledge of pollination ecology on these plants. We documented the most studied Opuntia species worldwide with an emphasis on Mexico. We found that only 15% of Opuntia species described have been investigated so far, and studies were mainly focused on comprehension of the biology of a single species. Despite the economic and cultural importance of Opuntia, there is a significant lack of knowledge about the flower-visiting insects and their taxonomic identity. We provide a checklist of the insect species associated with Opuntia spp. Through a circular network, we visualize the complex Opuntia flower-visiting insect relationship, and we detected a set of key species constituting the generalist core of the networks constructed. Since pollination is crucial for crop production, a better understanding of ecological interactions would inform management measures to strengthen biodiversity and agriculture sustainability as well as productivity in arid and marginal lands. Further research on pollination ecology is needed to improve the conservation status of the insects associated with Opuntia species.

Elastic property and fracture mechanics of lateral branch-branch junctions in cacti: A case study of Opuntia ficus-indica and Cylindropuntia bigelovii

Species with various reproductive modes accompanied by different mechanical properties of their (lateral) branch-branch junctions have evolved in the cactus subfamily Opuntioideae. Older branches of Opuntia ficus-indica with fracture-resistant junctions often bear flowers and fruits for sexual reproduction, whereas younger branches break off easily and provide offshoots for vegetative propagation. Cylindropuntia bigelovii plants are known for their vegetative reproduction via easily detachable branches that can establish themselves as offshoots. We characterized the elastic and fracture behaviors of these lateral junctions by tensile testing and analyzed local strains during loading. Additionally, we carried out finite element analyses to quantify the influence of five relevant tissue layers on joint elastic behavior. Our fracture analysis revealed various fracture modes: (i) most young samples of Opuntia ficus-indica failed directly at the junction and had smooth fracture surfaces, and relative fracture strain was on median 4% of the total strain; (ii) most older samples of Opuntia ficus-indica failed at the adjacent branch and exhibited rough fracture surfaces, and relative fracture strain was on median 47%; (iii) most samples of Cylindropuntia bigelovii abscised directly at the junction and exhibited cup and cone surfaces, and relative fracture strain was on median 28%. Various geometric and mechanical properties such as junction area, fracture energy, and tensile strength were analyzed with respect to significant differences between species and age of sample. Interestingly, the abscission of lateral branches naturally triggered by wind, passing animals, or vibration showed the following differences in maximum force: 153 N (older Opuntia ficus-indica), 51 N (young Opuntia ficus-indica), and 14 N (Cylindropuntia bigelovii).

The role of ontogeny in wood diversity and evolution

Evolutionary developmental biology (evo-devo) explores the link between developmental patterning and phenotypic change through evolutionary time. In this review, we highlight the scientific advancements in understanding xylem evolution afforded by the evo-devo approach, opportunities for further engagement, and future research directions for the field. We review evidence that (1) heterochrony-the change in rate and timing of developmental events, (2) homeosis-the ontogenetic replacement of features, (3) heterometry-the change in quantity of a feature, (4) exaptation-the co-opting and repurposing of an ancestral feature, (5) the interplay between developmental and capacity constraints, and (6) novelty-the emergence of a novel feature, have all contributed to generating the diversity of woods. We present opportunities for future research engagement, which combine wood ontogeny within the context of robust phylogenetic hypotheses, and molecular biology.

Geometric Models for Seed Shape Description and Quantification in the Cactaceae

Seed shape in species of the Cactaceae is described by comparison with geometric models. Three new groups of models are presented, two for symmetric seeds, and a third group for asymmetric seeds. The first two groups correspond, respectively, to superellipses and the combined equations of two semi-ellipses. The third group contains models derived from the representation of polar equations of Archimedean spirals that define the shape of asymmetric seeds in genera of different subfamilies. Some of the new models are geometric curves, while others are composed with a part resulting from the average silhouettes of seeds. The application of models to seed shape quantification permits the analysis of variation in seed populations, as well as the comparison of shape between species. The embryos of the Cactaceae are of the peripheral type, strongly curved and in contact with the inner surface of the seed coat. A relationship is found between seed elongation and the models, in which the genera with elongated seeds are represented by models with longer trajectories of the spiral. The analysis of seed shape opens new opportunities for taxonomy and allows quantification of seed shape in species of the Cactaceae.

Coalescent-based species delimitation meets deep learning: Insights from a highly fragmented cactus system

Delimiting species boundaries is a major goal in evolutionary biology. An increasing volume of literature has focused on the challenges of investigating cryptic diversity within complex evolutionary scenarios of speciation, including gene flow and demographic fluctuations. New methods based on model selection, such as approximate Bayesian computation, approximate likelihoods, and machine learning are promising tools arising in this field. Here, we introduce a framework for species delimitation using the multispecies coalescent model coupled with a deep learning algorithm based on convolutional neural networks (CNNs). We compared this strategy with a similar ABC approach. We applied both methods to test species boundary hypotheses based on current and previous taxonomic delimitations as well as genetic data (sequences from 41 loci) in Pilosocereus aurisetus, a cactus species complex with a sky-island distribution and taxonomic uncertainty. To validate our method, we also applied the same strategy on data from widely accepted species from the genus Drosophila. The results show that our CNN approach has a high capacity to distinguish among the simulated species delimitation scenarios, with higher accuracy than ABC. For the cactus data set, a splitter hypothesis without gene flow showed the highest probability in both CNN and ABC approaches, a result agreeing with previous taxonomic classifications and in line with the sky-island distribution and low dispersal of P. aurisetus. Our results highlight the cryptic diversity within the P. aurisetus complex and show that CNNs are a promising approach for distinguishing complex evolutionary histories, even outperforming the accuracy of other model-based approaches such as ABC.

Spatial and host related genomic variation in partially sympatric cactophagous moth species

Surveys of patterns of genetic variation in natural sympatric and allopatric populations of recently diverged species are necessary to understand the processes driving intra- and interspecific diversification. The South American moths Cactoblastis cactorum, Cactoblastis doddi and Cactoblastis bucyrus are specialized in the use of cacti as host plants. These species have partially different geographic ranges and differ in patterns of host plant use. However, there are areas that overlap, particularly, in northwestern Argentina, where they are sympatric. Using a combination of genome-wide SNPs and mitochondrial data we assessed intra and interspecific genetic variation and investigated the relative roles of geography and host plants on genetic divergence. We also searched for genetic footprints of hybridization between species. We identified three well delimited species and detected signs of hybridization in the area of sympatry. Our results supported a hypothetical scenario of allopatric speciation in the generalist C. cactorum and genetic interchange during secondary geographic contact with the pair of specialists C. bucyrus and C. doddi that probably speciated sympatrically. In both cases, adaptation to new host plants probably played an important role in speciation. The results also suggested the interplay of geography and host plant use as drivers of divergence and limiting gene flow at intra and interspecific levels.

Development of novel SSR molecular markers using a Next-Generation Sequencing approach (ddRADseq) in Stetsonia coryne (Cactaceae)

The Cactaceae family is native to the American continent with several centers of diversity. In South America, one of these centers is the Central Andes and many species are considered to be threatened or vulnerable according to the International Union for Conservation of Nature (IUCN). Stetsonia coryne is an emblematic giant columnar cacti of the Chaco phytogeographic province. It has an extensive geographical distribution in many countries of the continent. However, to date there are no specific molecular markers for this species, neither reports of population genetic variability studies, such as for many cactus species. The lack of information is fundamentally due to the lack of molecular markers that allow these studies. In this work, by applying a Genotyping by Sequencing (GBS) technique, we developed polymorphic SSR markers for the Stetsonia coryne and evaluated their transferability to phylogenetically close species, in order to account for a robust panel of molecular markers for multispecies-studies within Cactaceae.

New World Cactaceae Plants Harbor Diverse Geminiviruses

The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infects them. We previously identified a highly divergent geminivirus that is the first known to infect cacti. Recent research efforts in non-cultivated and asymptomatic plants have shown that the diversity of this viral family has been under-sampled. As a consequence, little is known about the effects and interactions of geminiviruses in many plants, such as cacti. With the objective to expand knowledge on the diversity of geminiviruses infecting cacti, we used previously acquired high-throughput sequencing results to search for viral sequences using BLASTx against a viral RefSeq protein database. We identified two additional sequences with similarity to geminiviruses, for which we designed abutting primers and recovered full-length genomes. From 42 cacti and five scale insects, we derived 42 complete genome sequences of a novel geminivirus species that we have tentatively named Opuntia virus 2 (OpV2) and 32 genomes of an Opuntia-infecting becurtovirus (which is a new strain of the spinach curly top Arizona virus species). Interspecies recombination analysis of the OpV2 group revealed several recombinant regions, in some cases spanning half of the genome. Phylogenetic analysis demonstrated that OpV2 is a novel geminivirus more closely related to viruses of the genus Curtovirus, which was further supported by the detection of three recombination events between curtoviruses and OpV2. Both OpV2 and Opuntia becurtoviruses were identified in mixed infections, which also included the previously characterized Opuntia virus 1. Viral quantification of the co-infected cactus plants compared with single infections did not show any clear trend in viral dynamics that might be associated with the mixed infections. Using experimental Rhizobium-mediated inoculations, we found that the initial accumulation of OpV2 is facilitated by co-infection with OpV1. This study shows that the diversity of geminiviruses that infect cacti is under-sampled and that cacti harbor diverse geminiviruses. The detection of the Opuntia becurtoviruses suggests spill-over events between viruses of cultivated species and native vegetation. The threat this poses to cacti needs to be further investigated.

The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes

Dragon fruits are tropical fruits economically important for agricultural industries. As members of the family of Cactaceae, they have evolved to adapt to the arid environment. Here we report the draft genome of Hylocereus undatus, commercially known as the white-fleshed dragon fruit. The chromosomal level genome assembly contains 11 longest scaffolds corresponding to the 11 chromosomes of H. undatus. Genome annotation of H. undatus found ~29,000 protein-coding genes, similar to Carnegiea gigantea (saguaro). Whole-genome duplication (WGD) analysis revealed a WGD event in the last common ancestor of Cactaceae followed by extensive genome rearrangements. The divergence time between H. undatus and C. gigantea was estimated to be 9.18 MYA. Functional enrichment analysis of orthologous gene clusters (OGCs) in six Cactaceae plants found significantly enriched OGCs in drought resistance. Fruit flavor-related functions were overrepresented in OGCs that are significantly expanded in H. undatus. The H. undatus draft genome also enabled the discovery of carbohydrate and plant cell wall-related functional enrichment in dragon fruits treated with trypsin for a longer storage time. Lastly, genes of the betacyanin (a red-violet pigment and antioxidant with a very high concentration in dragon fruits) biosynthetic pathway were found to be co-localized on a 12 Mb region of one chromosome. The consequence may be a higher efficiency of betacyanin biosynthesis, which will need experimental validation in the future. The H. undatus draft genome will be a great resource to study various cactus plants.

Pleistocene aridification underlies the evolutionary history of the Caribbean endemic, insular, giant Consolea (Opuntioideae)

PREMISE

The Caribbean islands are in the top five biodiversity hotspots on the planet; however, the biogeographic history of the seasonally dry tropical forest (SDTF) there is poorly studied. Consolea consists of nine species of dioecious, hummingbird-pollinated tree cacti endemic to the West Indies, which form a conspicuous element of the SDTF. Several species are threatened by anthropogenic disturbance, disease, sea-level rise, and invasive species and are of conservation concern. However, no comprehensive phylogeny yet exists for the clade.

METHODS

We reconstructed the phylogeny of Consolea, sampling all species using plastomic data to determine relationships, understand the evolution of key morphological characters, and test their biogeographic history. We estimated divergence times to determine the role climate change may have played in shaping the current diversity of the clade.

RESULTS

Consolea appears to have evolved very recently during the latter part of the Pleistocene on Cuba/Hispaniola likely from a South American ancestor and, from there, moved into the Bahamas, Jamaica, Puerto Rico, Florida, and the Lesser Antilles. The tree growth form is a synapomorphy of Consolea and likely aided in the establishment and diversification of the clade.

CONCLUSIONS

Pleistocene aridification associated with glaciation likely played a role in shaping the current diversity of Consolea, and insular gigantism may have been a key innovation leading to the success of these species to invade the often-dense SDTF. This in-situ Caribbean radiation provides a window into the generation of species diversity and the complexity of the SDTF community within the Antilles.

The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae

The reconstruction of relationships within recently radiated groups is challenging even when massive amounts of sequencing data are available. The use of restriction site-associated DNA sequencing (RAD-Seq) to this end is promising. Here, we assessed the performance of RAD-Seq to infer the species-level phylogeny of the rapidly radiating genus Cereus (Cactaceae). To examine how the amount of genomic data affects resolution in this group, we used datasets and implemented different analyses. We sampled 52 individuals of Cereus, representing 18 of the 25 species currently recognized, plus members of the closely allied genera Cipocereus and Praecereus, and other 11 Cactaceae genera as outgroups. Three scenarios of permissiveness to missing data were carried out in iPyRAD, assembling datasets with 30% (333 loci), 45% (1440 loci), and 70% (6141 loci) of missing data. For each dataset, Maximum Likelihood (ML) trees were generated using two supermatrices, i.e., only SNPs and SNPs plus invariant sites. Accuracy and resolution were improved when the dataset with the highest number of loci was used (6141 loci), despite the high percentage of missing data included (70%). Coalescent trees estimated using SVDQuartets and ASTRAL are similar to those obtained by the ML reconstructions. Overall, we reconstruct a well-supported phylogeny of Cereus, which is resolved as monophyletic and composed of four main clades with high support in their internal relationships. Our findings also provide insights into the impact of missing data for phylogeny reconstruction using RAD loci.

Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies

Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (∼25 kb) and the ndh gene suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address (1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and (2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeat and the presence of all the ndh gene suite. An expansion of the large single copy unit and a reduction of the small single copy unit was observed, including translocations and inversion of genes, as well as the putative pseudogenization of some loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in resolving three tribes with high support within Opuntioideae: Cylindropuntieae, Tephrocacteae and Opuntieae. However, conflicting topologies were recovered among major clades when exploring different assemblies of markers. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.

A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants

Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensively studied, little research has focused on cactus-associated viral communities. While only single-stranded RNA viruses had ever been reported in cacti, here we report the discovery of cactus-infecting single-stranded DNA viruses. These viruses all apparently belong to a single divergent species of the family Geminiviridae and have been tentatively named Opuntia virus 1 (OpV1). A total of 79 apparently complete OpV1 genomes were recovered from 31 different cactus plants (belonging to 20 different cactus species from both the Cactoideae and Opuntioideae clades) and from nine cactus-feeding cochineal insects (Dactylopius sp.) sampled in the USA and Mexico. These 79 OpV1 genomes all share > 78.4% nucleotide identity with one another and < 64.9% identity with previously characterized geminiviruses. Collectively, the OpV1 genomes display evidence of frequent recombination, with some genomes displaying up to five recombinant regions. In one case, recombinant regions span ~40% of the genome. We demonstrate that an infectious clone of an OpV1 genome can replicate in Nicotiana benthamiana and Opuntia microdasys. In addition to expanding the inventory of viruses that are known to infect cacti, the OpV1 group is so distantly related to other known geminiviruses that it likely represents a new geminivirus genus. It remains to be determined whether, like its cactus hosts, its geographical distribution spans the globe.

Prospects for the Study and Improvement of Abiotic Stress Tolerance in Date Palms in the Post-genomics Era

Date palm (Phoenix dactylifera L.) is a socio-economically important crop in the Middle East and North Africa and a major contributor to food security in arid regions of the world. P. dactylifera is both drought and salt tolerant, but recent water shortages and increases in groundwater and soil salinity have threatened the continued productivity of the crop. Recent studies of date palm have begun to elucidate the physiological mechanisms of abiotic stress tolerance and the genes and biochemical pathways that control the response to these stresses. Here we review recent studies on tolerance of date palm to salinity and drought stress, the role of the soil and root microbiomes in abiotic stress tolerance, and highlight recent findings of omic-type studies. We present a perspective on future research of abiotic stress in date palm that includes improving existing genome resources, application of genetic mapping to determine the genetic basis of variation in tolerances among cultivars, and adoption of gene-editing technologies to the study of abiotic stress in date palms. Development of necessary resources and application of the proposed methods will provide a foundation for future breeders and genetic engineers aiming to develop more stress-tolerant cultivars of date palm.

Unraveling Reticulate Evolution in Opuntia (Cactaceae) From Southern Mexico

The process of hybridization occurs in approximately 40% of vascular plants, and this exchange of genetic material between non-conspecific individuals occurs unequally among plant lineages, being more frequent in certain groups such as Opuntia (Cactaceae). This genus is known for multiple taxonomic controversies due to widespread polyploidy and probable hybrid origin of several of its species. Southern Mexico species of this genus have been poorly studied despite their great diversity in regions such as the Tehuacán-Cuicatlán Valley which contains around 12% of recognized Mexico's native Opuntia species. In this work, we focus on testing the hybrid status of two putative hybrids from this region, Opuntia tehuacana and Opuntia pilifera, and estimate if hybridization occurs among sampled southern opuntias using two newly identified nuclear intron markers to construct phylogenetic networks with HyDe and Dsuite and perform invariant analysis under the coalescent model with HyDe and Dsuite. For the test of hybrid origin in O. tehuacana, our results could not recover hybridization as proposed in the literature, but we found introgression into O. tehuacana individuals involving O. decumbens and O. huajuapensis. Regarding O. pilifera, we identified O. decumbens as probable parental species, supported by our analysis, which sustains the previous hybridization hypothesis between Nopalea and Basilares clades. Finally, we suggest new hybridization and introgression cases among southern Mexican species involving O. tehuantepecana and O. depressa as parental species of O. velutina and O. decumbens.

Bees may drive the reproduction of four sympatric cacti in a vanishing coastal mediterranean-type ecosystem

Background

Sympatric congeneric plants might share pollinators, or each species might avoid competition by evolving specialized traits that generate partitions in pollinator assemblages. In both cases, pollen limitation (a decrease in the quality and quantity of compatible reproductive pollen) can occur, driving the plant mating system to autogamy as a mechanism of reproductive assurance. We assessed the relationships between pollinator assemblages and mating systems in a group of sympatric congeneric plants. We attempted to answer the following questions: (i) How similar are pollinator assemblages among sympatric cactus species? (ii) Which mating systems do sympatric cactus species use?

Methods

We studied sympatric Eriosyce taxa that inhabit a threatened coastal strip in a mediterranean-type ecosystem in central Chile. We performed field observations on four taxa and characterized pollinators during the years 2016 and 2017. We estimated differences in the pollinator assemblages using the Bray-Curtis index. To elucidate the mating systems, we conducted hand-pollination experiments using three treatments: manual cross-pollination, automatic self-pollination, and control (unmanipulated individuals). We tested differences in seed production for statistical significance using Kruskal-Wallis analysis.

Results

Eriosyce subgibbosa showed a distinctive pollinator assemblage among the sympatric species that we studied (similarity ranged from 0% to 8%); it was visited by small bees and was the only species that was visited by the giant hummingbird Patagona gigas. Pollinator assemblages were similar between E. chilensis (year 2016 = 4 species; 2017 = 8) and E. chilensis var. albidiflora (2016 = 7; 2017 = 4); however, those of E. curvispina var. mutabilis (2016 = 7; 2017 = 6) were less similar to those of the aforementioned species. E. curvispina var. mutabilis showed the highest interannual variation in its pollinator assemblage (18% similarity). Reproduction in E. subgibbosa largely depends on pollinators, although it showed some degree of autogamy. Autonomous pollination was unfeasible in E. chilensis, which depended on flower visitors for its reproductive success. Both E. chilensis var. albidiflora and E. curvispina var. mutabilis showed some degree of autogamy.

Discussion

We observed differences in pollinator assemblages between E. subgibbosa and the remaining Eriosyce taxa, which depend on hymenopterans for pollen transfer. Pollinator assemblages showed considerable interannual variation, especially those of E. subgibbosa (ornithophilous syndrome) and E. curvispina var. mutabilis (melitophilous syndrome). Autogamous reproduction in these taxa may act as a reproductive assurance mechanism when pollinator availability is unpredictable. Our study contributes to improving our understanding of the reproductive systems of ecological interactions between threatened species in a Chilean mediterranean-type ecosystem.

Phylogenomics in Cactaceae: A case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan and Sonoran deserts

PREMISE

Although numerous phylogenetic studies have been conducted in Cactaceae, whole-plastome datasets have not been employed. We used the chollas to develop a plastome dataset for phylogeny reconstruction to test species relationships, biogeography, clade age, and morphological evolution.

METHODS

We developed a plastome dataset for most known diploid members of the chollas (42 taxa) as well as for other members of Cylindropuntieae. Paired-end, raw reads from genome skimming were reference-mapped onto a de novo plastome assembly of one species of cholla, Cylindropuntia bigelovii, and were used to build our plastome dataset, which was analyzed using various methods.

RESULTS

Our plastome dataset resolved the phylogeny of the chollas, including most interspecific and intraspecific relationships. Tribe Cylindropuntieae arose ~18 mya, during the early Miocene in southern South America, and is supported as sister to the South American clade Tephrocacteae. The (Micropuntia (Cylindropuntia + Grusonia)) clade most likely originated in the Chihuahuan Desert region around 16 mya and then migrated into other North American desert regions. Key morphological characters for recognizing traditional taxonomic series in Cylindropuntia (e.g., spiny fruit) are mostly homoplasious.

CONCLUSIONS

This study provides the first comprehensive plastome phylogeny for any clade within Cactaceae. Although the chollas s.l. are widespread throughout western North American deserts, their most recent common ancestor likely arose in the Chihuahuan Desert region during the mid-Miocene, with much of their species diversity arising in the early to mid-Pliocene, a pattern strikingly similar to those found in other western North American desert groups.