Phylogeny in Echinocereus (Cactaceae) based on combined morphological and molecular evidence: taxonomic implications

Identifying the multiple drivers of cactus diversification

Our understanding of the complexity of forces at play in the rise of major angiosperm lineages remains incomplete. The diversity and heterogeneous distribution of most angiosperm lineages is so extraordinary that it confounds our ability to identify simple drivers of diversification. Using machine learning in combination with phylogenetic modelling, we show that five separate abiotic and biotic variables significantly contribute to the diversification of Cactaceae. We reconstruct a comprehensive phylogeny, build a dataset of 39 abiotic and biotic variables, and predict the variables of central importance, while accounting for potential interactions between those variables. We use state-dependent diversification models to confirm that five abiotic and biotic variables shape diversification in the cactus family. Of highest importance are diurnal air temperature range, soil sand content and plant size, with lesser importance identified in isothermality and geographic range size. Interestingly, each of the estimated optimal conditions for abiotic variables were intermediate, indicating that cactus diversification is promoted by moderate, not extreme, climates. Our results reveal the potential primary drivers of cactus diversification, and the need to account for the complexity underlying the evolution of angiosperm lineages.

Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae

Rutaceae family comprises economically important plants due to their extensive applications in spices, food, oil, medicine, etc. The Rutaceae plants is able to better utilization through biotechnology. Modern biotechnological approaches primarily rely on the heterologous expression of functional proteins in different vectors. However, several proteins are difficult to express outside their native environment. The expression potential of functional genes in heterologous systems can be maximized by replacing the rare synonymous codons in the vector with preferred optimal codons of functional genes. Codon usage bias plays a critical role in biogenetic engineering-based research and development. In the current study, 727 coding sequences (CDSs) obtained from the chloroplast genomes of ten Rutaceae plant family members were analyzed for codon usage bias. The nucleotide composition analysis of codons showed that these codons were rich in A/T(U) bases and preferred A/T(U) endings. Analyses of neutrality plots, effective number of codons (ENC) plots, and correlations between ENC and codon adaptation index (CAI) were conducted, which revealed that natural selection is a major driving force for the Rutaceae plant family's codon usage bias, followed by base mutation. In the ENC vs. CAI plot, codon usage bias in the Rutaceae family had a negligible relationship with gene expression level. For each sample, we screened 12 codons as preferred and high-frequency codons simultaneously, of which GCU encoding Ala, UUA encoding Leu, and AGA encoding Arg were the most preferred codons. Taken together, our study unraveled the synonymous codon usage pattern in the Rutaceae family, providing valuable information for the genetic engineering of Rutaceae plant species in the future.

Morpho-palynological and anatomical studies in desert cacti (Opuntia dillenii and Opuntia monacantha) using light and scanning electron microscopy

Opuntia is the most diverse and widely distributed drought resistant promising genus of family Cactaceae. The cladodes were utilized to quantify the chemical composition of these plants helpful in lignocellulose conversion and their application towards biofuel production. The present study was aimed to evaluate and compare the taxonomic relationship based on morphology, stem anatomy and palynology of important desert cacti including Opuntia dillenii and Opuntia monacantha. This study also evaluates the potential usefulness of morphological, anatomical and pollen traits using light and scanning electron microscopy. The obtained microcharacters of stem and flowers are considered diagnostic at the generic and specific levels. Some distinguishing morphological features observed were elliptical to obovate cladodes, 1-7 spines per areole and presence of glochidia in O. dillenii. Pollen and stem anatomical characters of the studied taxa are considered highly diagnostic at the generic and species levels. The epidermis has irregular and wavy cells, with straight to sinuate wall pattern and paracytic stomata. Pollen grains appear as pantoporate and prolate spheroidal having reticulate to perforate-reticulate sculpturing while exine semi-tectate to tectate. The taxonomic features studied could be valuable to elaborate and helpful in correctly identification of Opuntia species. The methods of diverse microscopic examination also providing sufficient evidence about the taxonomy of the Opuntia species.

Phylogenetic Relationships and Evolutionary Trends in the Cactus Family

Members of the cactus family are keystone species of arid and semiarid biomes in the Americas, as they provide shelter and resources to support other members of ecosystems. Extraordinary examples are the several species of flies of the genus Drosophila that lay eggs and feed in their rotting stems, which provide a model system for studying evolutionary processes. Although there is significant progress in understanding the evolution of Drosophila species, there are gaps in our knowledge about the cactus lineages hosting them. Here, we review the current knowledge about the evolution of Cactaceae, focusing on phylogenetic relationships and trends revealed by the study of DNA sequence data. During the last several decades, the availability of molecular phylogenies has considerably increased our understanding of the relationships, biogeography, and evolution of traits in the family. Remarkably, although succulent cacti have very low growth rates and long generation times, they underwent some of the fastest diversifications observed in the plant kingdom, possibly fostered by strong ecological interactions. We have a better understanding of the reproductive biology, population structure and speciation mechanisms in different clades. The recent publication of complete genomes for some species has revealed the importance of phenomena such as incomplete lineage sorting. Hybridization and polyploidization are common in the family, and have been studied using a variety of phylogenetic methods. We discuss potential future avenues for research in Cactaceae, emphasizing the need of a concerted effort among scientists in the Americas, together with the analyses of data from novel sequencing techniques.

Splitting Echinocactus: morphological and molecular evidence support the recognition of Homalocephala as a distinct genus in the Cacteae

Molecular phylogenetic studies of the six currently accepted species in the genus Echinocactus have partially clarified certain aspects of its phylogeny. Most of the studies lack a complete sampling of Echinocactus and are based only in one source of data. Phylogenetic uncertainties in Echinocactus, such as the recognition of Homalocephala as a different genus from Echinocactus, the exclusion of E.grusonii or the affinities of E.polycephalus, are here resolved. Phylogenetic relationships of Echinocactus were reconstructed with a maximum parsimony, a maximum likelihood and a Bayesian approach including 42 morphological characters, four chloroplast markers (atpB-rbcL, trnH-psbA, trnL-trnF and trnK/matK) and two nuclear genes. The utility of these two nuclear regions related to the betalain cycles (DODA and 5GT) are explored and discussed in relation to their potential as phylogenetic markers. Concatenated analyses with morphological and molecular data sets, plus 13 indels (2847 characters and 26 taxa), show general agreement with previous independent phylogenetic proposals but with strong support in order to propose the recognition of a reduced Echinocactus and the recognition of Homalocephala at the generic level. These results recovered a polyphyletic Echinocactus as currently defined. The here-named HEA clade, recovers the species of Homalocephala, Echinocacuts and Astrophytum as a monophyletic group with strong internal support. The Homalocephala (H.texensis, H.parryi and H.polycephala), was recovered as sister to the Echinocactus clade (E.platyacanthus and E.horizonthalonius), plus the Astrophytum clade. Consequently, we propose here to recognise a monophyletic Echinocactus and a monophyletic Homalocephala as two distinct genera with their own molecular and morphological synapomorphies. The evolution of some morphological characters supporting these clades are discussed, the necessary new taxonomic combinations for Homalocephala are proposed and an identification key for the genera, the species and the subspecies of the HEA clade are presented.

Chemical Composition of Cacti Wood and Comparison with the Wood of Other Taxonomic Groups

The aims of this study were to determine the wood chemical composition of 25 species of Cactaceae and to relate the composition to their anatomical diversity. The hypothesis was that wood chemical components differ in relationship to their wood features. The results showed significant differences in wood chemical compounds across species and genera (P < 0.05). Pereskia had the highest percentage of lignin, whereas species of Coryphantha had the lowest; extractive compounds in water were highest for Echinocereus, Mammillaria, and Opuntia. Principal component analysis showed that lignin proportion separated the fibrous, dimorphic, and non-fibrous groups; additionally, the differences within each type of wood occurred because of the lignification of the vascular tissue and the type of wall thickening. Compared with other groups of species, the Cactaceae species with fibrous and dimorphic wood had a higher lignin percentage than did gymnosperms and Acer species. Lignin may confer special rigidity to tracheary elements to withstand desiccation without damage during adverse climatic conditions.