The application of high-throughput sequencing for taxonomy: The case of Plantago subg. Plantago (Plantaginaceae)

Plastid phylogenomics clarifies broad-level relationships in Bulbophyllum (Orchidaceae) and provides insights into range evolution of Australasian section Adelopetalum

The hyperdiverse orchid genus Bulbophyllum is the second largest genus of flowering plants and exhibits a pantropical distribution with a center of diversity in tropical Asia. The only Bulbophyllum section with a center of diversity in Australasia is sect. Adelopetalum. However, the phylogenetic placement, interspecific relationships, and spatio-temporal evolution of this section remain largely unclear. To infer broad-level relationships within Bulbophyllum, and interspecific relationships within sect. Adelopetalum, a genome skimming dataset was generated for 89 samples, which yielded 70 plastid coding regions and a nuclear ribosomal DNA cistron. For 18 additional samples, Sanger data from two plastid loci (matK and ycf1) and nuclear ITS were added using a supermatrix approach. The study provided new insights into broad-level relationships in Bulbophyllum, including phylogenetic evidence for the non-monophyly of sections Beccariana, Brachyantha, Brachypus, Cirrhopetaloides, Cirrhopetalum, Desmosanthes, Minutissima, Oxysepala, Polymeres, and Sestochilos. Section Adelopetalum and sect. Minutissima s.s. formed a highly supported clade that was resolved as a sister group to the remainder of the genus. Divergence time estimations based on a relaxed molecular clock model placed the origin of Bulbophyllum in the Early Oligocene (ca. 33.2 Ma) and sect. Adelopetalum in the Late Oligocene (ca. 23.6 Ma). Ancestral range estimations based on a BAYAREALIKE model identified the Australian continent as the ancestral area of the sect. Adelopetalum. The section underwent crown diversification from the mid-Miocene to the late Pleistocene, predominantly in continental Australia. At least two independent long-distance dispersal events were inferred eastward from the Australian continent to New Zealand and to New Caledonia from the early Pliocene onwards, likely mediated by predominantly westerly winds of the Southern hemisphere. Retraction and fragmentation of the eastern Australian rainforests from the early Miocene onwards are likely drivers of lineage divergence within sect. Adelopetalum facilitating allopatric speciation.

Effects of replacing of alfalfa hay with Plantago lanceolata hay on digestibility, methane production and microbial protein production of total mixed diet

The aim of current experiment was to determine the effect of replacement of alfalfa hay with ribwort plantain (Plantago lanceolata) hay in ruminant diets on the fermentation parameters such as gas production, methane (CH4) production, true digestible dry matter (TDDM), true digestibility (TD), partitioning factor, microbial protein, and efficiency of microbial protein using in vitro gas production technique. The alfalfa hay was replaced with P. lanceolata hay in a diets isocaloric (2650 kcal/kg DM) and nitrogenic (17% CP kg DM) at the ratio of 0, 5, 10 and 15%. Partial substitution of alfalfa hay with P. lanceolata hay had no significant effect on gas and methane (ml/incubated substrate or %) production whereas the partial substitution had a significant effect on TDDM, TD, gas (ml/digested DM), CH4 (ml ml/digested DM) and microbial MP of diets. The replacement of alfalfa hay with ribwort plantain hay shifted the fermentation pattern from gas and methane production to microbial protein production. Therefore alfalfa hay can be replaced with ribwort plantain hay with high digestibility and anti-methanogenic potential in ruminant diets up to 15% to decrease methane production and improve microbial protein production. However further in vivo experiments are required to determine the effect of replacement on feed intake and animal production.

Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data

The advent of high-throughput sequencing technologies has not only revolutionized the field of bioinformatics but has also heightened the demand for efficient taxonomic classification. Despite technological advancements, efficiently processing and analyzing the deluge of sequencing data for precise taxonomic classification remains a formidable challenge. Existing classification approaches primarily fall into two categories, database-based methods and machine learning methods, each presenting its own set of challenges and advantages. On this basis, the aim of our study was to conduct a comparative analysis between these two methods while also investigating the merits of integrating multiple database-based methods. Through an in-depth comparative study, we evaluated the performance of both methodological categories in taxonomic classification by utilizing simulated data sets. Our analysis revealed that database-based methods excel in classification accuracy when backed by a rich and comprehensive reference database. Conversely, while machine learning methods show superior performance in scenarios where reference sequences are sparse or lacking, they generally show inferior performance compared with database methods under most conditions. Moreover, our study confirms that integrating multiple database-based methods does, in fact, enhance classification accuracy. These findings shed new light on the taxonomic classification of high-throughput sequencing data and bear substantial implications for the future development of computational biology. For those interested in further exploring our methods, the source code of this study is publicly available on https://github.com/LoadStar822/Genome-Classifier-Performance-Evaluator. Additionally, a dedicated webpage showcasing our collected database, data sets, and various classification software can be found at http://lab.malab.cn/~tqz/project/taxonomic/.

Plantago asiatica L. polysaccharides: Physiochemical properties, structural characteristics, biological activity and application prospects: A review

Plantago asiatica L. (PAL), a traditional herb, has been used in East Asia for thousands of years. In recent years, polysaccharides extracted from PAL have garnered increased attention due to their outstanding pharmacological and biological properties. Previous research has established that PAL-derived polysaccharides exhibit antioxidant, anti-inflammatory, antidiabetic, antitumor, antimicrobial, immune-regulatory, intestinal health-promoting, antiviral, and other effects. Nevertheless, a comprehensive summary of the research related to Plantago asiatica L. polysaccharides (PALP) has not been reported to date. In this paper, we review the methods for isolation and purification, physiochemical properties, structural features, and biological activities of PALP. To provide a foundation for research and application in the fields of medicine and food, this review also outlines the future development prospects of plantain polysaccharides.

Genomic, spatial and morphometric data for discrimination of four species in the Mediterranean Tamus clade of yams (Dioscorea, Dioscoreaceae)

BACKGROUND AND AIMS

Among the numerous pantropical species of the yam genus, Dioscorea, only a small group occurs in the Mediterranean basin, including two narrow Pyrenean endemics (Borderea clade) and two Mediterranean-wide species (D. communis and D. orientalis, Tamus clade). However, several currently unrecognized species and infraspecific taxa have been described in the Tamus clade due to significant morphological variation associated with D. communis. Our overarching aim was to investigate taxon delimitation in the Tamus clade using an integrative approach combining phylogenomic, spatial and morphological data.

METHODS

We analysed 76 herbarium samples using Hyb-Seq genomic capture to sequence 260 low-copy nuclear genes and plastomes, together with morphometric and environmental modelling approaches.

KEY RESULTS

Phylogenomic reconstructions confirmed that the two previously accepted species of the Tamus clade, D. communis and D. orientalis, are monophyletic and form sister clades. Three subclades showing distinctive geographic patterns were identified within D. communis. These subclades were also identifiable from morphometric and climatic data, and introgression patterns were inferred between subclades in the eastern part of the distribution of D. communis.

CONCLUSIONS

We propose a taxonomy that maintains D. orientalis, endemic to the eastern Mediterranean region, and splits D. communis sensu lato into three species: D. edulis, endemic to Macaronesia (Canary Islands and Madeira); D. cretica, endemic to the eastern Mediterranean region; and D. communis sensu stricto, widespread across western and central Europe. Introgression inferred between D. communis s.s. and D. cretica is likely to be explained by their relatively recent speciation at the end of the Miocene, disjunct isolation in eastern and western Mediterranean glacial refugia and a subsequent westward recolonization of D. communis s.s. Our study shows that the use of integrated genomic, spatial and morphological approaches allows a more robust definition of species boundaries and the identification of species that previous systematic studies failed to uncover.

Living on the edge: morphological, karyological and genetic diversity studies of the Hungarian Plantago maxima populations and established ex situ collection

BACKGROUND

The analysis of genetic diversity of protected plant species can greatly support conservation efforts. Plantago maxima Juss. ex Jacq. is a perennial species distributed along the Eurasian steppe. The westernmost range edge of the species' distribution is located in the Pannonian basin, in Hungary where it is represented by a few, fragmented and highly endangered populations. We studied population diversity of all Hungarian range edge, natural populations, and one established ex situ population. One population from the centre of distribution (Kazakhstan) was implemented in the cpDNA haplotype study to compare the peripheral vs. central populations. We performed morphometric trait-based analysis, chromosome studies (morphometric analyses and FISH) and genetic diversity evaluations using inter simple sequence repeats (ISSR) and cpDNA trnL-trnF to evaluate differences between the in situ and ex situ populations as well as central vs. peripheral populations.

RESULTS

Our results showed no obvious morphological differences among the in situ and ex situ populations in the period between 2018 and 2020. One ex situ subpopulation develops flowers three years in a row from 2019, which is a favourable indicator of the introduction success. Hungarian populations are exclusively diploids (2n = 2x = 12). The karyogram consists of 5 metacentric and 1 acrocentric chromosome pair. Plantago maxima has one 35S and two 5S rDNA loci, located on the acrocentric chromosome pair. Eight variable ISSR primers yielded 100 fragments, of which 74.6% were polymorphic (mean H_e = 0.220). A high level of genetic variation within population was observed (92%) while the genetic differentiation among the populations was only 8%. STRUCTURE analysis revealed that the largest Kunpeszér population separated from the rest of the Hungarian populations, indicating a high rate of admixture among the other ones. Based on the trnL-trnF sequence analysis the Hungarian populations represent a single haplotype, which can indicate a reduced diversity due to isolation and recent population decline. By contrast, Kazakh population represents a distinct haplotype compared to the Hungarian samples.

CONCLUSIONS

The present study draws the attention to the high conservation value of the Plantago maxima populations from the westernmost range edge of the species' distribution.

Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes

Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species' establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.

Improving phylogenetic resolution of the Lamiales using the complete plastome sequences of six Penstemon species

The North American endemic genus Penstemon (Mitchell) has a recent geologic origin of ca. 3.6 million years ago (MYA) during the Pliocene/Pleistocene transition and has undergone a rapid adaptive evolutionary radiation with ca. 285 species of perennial forbs and sub-shrubs. Penstemon is divided into six subgenera occupying all North American habitats including the Arctic tundra, Central American tropical forests, alpine meadows, arid deserts, and temperate grasslands. Due to the rapid rate of diversification and speciation, previous phylogenetic studies using individual and concatenated chloroplast sequences have failed to resolve many polytomic clades. We investigated the efficacy of utilizing the plastid genomes (plastomes) of 29 species in the Lamiales order, including five newly sequenced Penstemon plastomes, for analyzing phylogenetic relationships and resolving problematic clades. We compared whole-plastome based phylogenies to phylogenies based on individual gene sequences (matK, ndhF, psaA, psbA, rbcL, rpoC2, and rps2) and concatenated sequences. We also We found that our whole-plastome based phylogeny had higher nodal support than all other phylogenies, which suggests that it provides greater accuracy in describing the hierarchal relationships among taxa as compared to other methods. We found that the genus Penstemon forms a monophyletic clade sister to, but separate from, the Old World taxa of the Plantaginaceae family included in our study. Our whole-plastome based phylogeny also supports the rearrangement of the Scrophulariaceae family and improves resolution of major clades and genera of the Lamiales.

Complete Mitogenomes of Two Aragoa Species and Phylogeny of Plantagineae (Plantaginaceae, Lamiales) Using Mitochondrial Genes and the Nuclear Ribosomal RNA Repeat

Aragoa, comprising 19 high-altitude North Andean species, is one of three genera in the Plantagineae (Plantaginaceae, Lamiales), along with Littorella and Plantago. Based primarily on plastid data and nuclear ITS, Aragoa is sister to a clade of Littorella + Plantago, but Plantagineae relationships have yet to be assessed using multigene datasets from the nuclear and mitochondrial genomes. Here, complete mitogenomes were assembled for two species of Aragoa (A. abietina and A. cleefii). The mitogenomes of both species have a typical suite of genes for 34 proteins, 17 tRNAs, and three rRNAs. The A. abietina mitogenome assembled into a simple circular map, with no large repeats capable of producing alternative isoforms. The A. cleefii mitogenomic map was more complex, involving two circular maps bridged by a substoichiometric linear fragment. Phylogenetics of three mitochondrial genes or the nuclear rRNA repeat placed Aragoa as sister to Littorella + Plantago, consistent with previous studies. However, P. nubicola, the sole representative of subg. Bougueria, was nested within subg. Psyllium based on the mitochondrial and nuclear data, conflicting with plastid-based analyses. Phylogenetics of the nuclear rRNA repeat provided better resolution overall, whereas relationships from mitochondrial data were hindered by extensive substitution rate variation among lineages.

Current update on psyllium and alginate incorporate for interpenetrating polymer network (IPN) and their biomedical applications

Natural polysaccharides and their designed structures are extremely valuable due to their intrinsic pharmacological properties and are also used as pharmaceutical aids. These naturally occurring polysaccharides (e.g., psyllium and alginate) are gaining popularity for their use in the preparation of interpenetrating polymer network (IPN) materials with improved swelling ability, biodegradability, stability, non-cytotoxic, biocompatibility, and cost-effectiveness. IPN is prepared sequentially or simultaneously by microwave irradiation, casting evaporation, emulsification cross-linking, miniemulsion/inverse miniemulsion technique, and radiation polymerization methods. In addition, the prepared IPNs have has been extensively characterized using various analytical and imaging techniques before sustainable deployment for multiple applications. Regardless of these multi-characteristic attributes, the current literature lacks a detailed overview of the biomedical aspects of psyllium, alginate, and their engineered IPN structures. Herein, we highlight the unique synthesis, structural, and biomedical considerations of psyllium, alginate, and engineered IPN structures. In this review, a wide range of biomedical applications, such as role as a drug carrier for sustain delivery, wound dressing, tissue engineering, and related miscellaneous application of psyllium, alginate, and their IPN structures described with appropriate examples. Further research will be carried out for the development of IPN using psyllium and alginate, which will be a smart and active carrier for drugs used in the treatment of life-threatening diseases due to their inherent pharmacological potential such as hypoglycemic, immunomodulatory, antineoplastic, and antimicrobial.

Molecular and Morphological Data Improve the Classification of Plantagineae (Lamiales)

The tribe Plantagineae (Lamiales) is a group of plants with worldwide distribution, notorious for its complicated taxonomy and still unresolved natural history. We describe the result of a broadly sampled phylogenetic study of tribe. The expanded sampling dataset is based on the trnL-F spacer, rbcL, and ITS2 markers across all three included genera (Aragoa, Littorella and Plantago) and makes this the most comprehensive study to date. The other dataset uses five markers and provides remarkably good resolution throughout the tree, including support for all of the major clades. In addition to the molecular phylogeny, a morphology database of 114 binary characters was assembled to provide comparison with the molecular phylogeny and to develop a means to assign species not sampled in the molecular analysis to their most closely related species that were sampled. Based on the molecular phylogeny and the assignment algorithm to place unsampled species, a key to sections is presented, and a revised classification of the tribe is provided. We also include the description of new species from North America.

Plantago campestris (Plantaginaceae), a rare new species from southern Brazil, supported by phylogenomic and morphological evidence

High-throughput sequencing, when combined with taxonomic expertise, is a powerful tool to refine and advance taxonomic classification, including at the species level. In the present work, a new species, Plantago campestris, is described out of the P. commersoniana species complex, based on phylogenomic and morphological evidence. The main morphological characters that distinguish the new species from P. commersoniana are the glabrous posterior sepals and the slightly broader leaves. The new species is known from only three localities, all in natural high-elevation grasslands in Paraná and Santa Catarina states, southern Brazil. According to the IUCN criteria new species should be assessed as Endangered (EN). We present field photographs of P. campestris and related species, and we provide an identification key to the species previously included within the circumscription of P. commersoniana.

Responses to Salinity in Four Plantago Species from Tunisia

The genus Plantago is particularly interesting for studying the mechanisms of salt tolerance in plants, as it includes both halophytes and glycophytes, as well as species adapted to xeric environments. In this study, the salt stress responses of two halophytes, P. crassifolia and P. coronopus, were compared with those of two glycophytes, P. ovata and P. afra. Plants obtained by seed germination of the four species, collected in different regions of Tunisia, were subjected to increasing salinity treatments for one month under greenhouse conditions. Morphological traits and biochemical parameters, such as ion accumulation and the leaf contents of photosynthetic pigments, osmolytes, oxidative stress markers and antioxidant metabolites, were measured after the treatments. Salt-induced growth inhibition was more pronounced in P. afra, and only plants subjected to the lowest applied NaCl concentration (200 mM) survived until the end of the treatments. The biochemical responses were different in the two groups of plants; the halophytes accumulated higher Na+ and proline concentrations, whereas MDA levels in their leaves decreased, indicating a lower level of oxidative stress. Overall, the results showed that P. coronopus and P. crassifolia are the most tolerant to salt stress, and P. afra is the most susceptible of the four species. Plantago ovata is also quite resistant, apparently by using specific mechanisms of tolerance that are more efficient than in the halophytes, such as a less pronounced inhibition of photosynthesis, the accumulation of higher levels of Cl- ions in the leaves, or the activation of K+ uptake and transport to the aerial part under high salinity conditions.

Plastomes from tribe Plantagineae (Plantaginaceae) reveal infrageneric structural synapormorphies and localized hypermutation for Plantago and functional loss of ndh genes from Littorella

Tribe Plantagineae (Plantaginaceae) comprises ~ 270 species in three currently recognized genera (Aragoa, Littorella, Plantago), of which Plantago is most speciose. Plantago plastomes exhibit several atypical features including large inversions, expansions of the inverted repeat, increased repetitiveness, intron losses, and gene-specific increases in substitution rate, but the prevalence of these plastid features among species and subgenera is unknown. To assess phylogenetic relationships and plastomic evolutionary dynamics among Plantagineae genera and Plantago subgenera, we generated 25 complete plastome sequences and compared them with existing plastome sequences from Plantaginaceae. Using whole plastome and partitioned alignments, our phylogenomic analyses provided strong support for relationships among major Plantagineae lineages. General plastid features-including size, GC content, intron content, and indels-provided additional support that reinforced major Plantagineae subdivisions. Plastomes from Plantago subgenera Plantago and Coronopus have synapomorphic expansions and inversions affecting the size and gene order of the inverted repeats, and particular genes near the inversion breakpoints exhibit accelerated nucleotide substitution rates, suggesting localized hypermutation associated with rearrangements. The Littorella plastome lacks functional copies of ndh genes, which may be related to an amphibious lifestyle and partial reliance on CAM photosynthesis.

Plantago spp. as Models for Studying the Ecology and Evolution of Species Interactions across Environmental Gradients

AbstractA central challenge in ecology and evolutionary biology is to understand how variation in abiotic and biotic factors combine to shape the distribution, abundance, and diversity of focal species. Environmental gradients, whether natural (e.g., latitude, elevation, ocean proximity) or anthropogenic (e.g., land-use intensity, urbanization), provide compelling settings for addressing this challenge. However, not all organisms are amenable to the observational and experimental approaches required for untangling the factors that structure species along gradients. Here we highlight herbaceous plants in the genus Plantago as models for studying the ecology and evolution of species interactions along abiotic gradients. Plantago lanceolata and P. major are native to Europe and Asia but distributed globally, and they are established models for studying population ecology and interactions with herbivores, pathogens, and soil microbes. Studying restricted range congeners in comparison with those cosmopolitan species can provide insight into abiotic and biotic determinants of range size and population structure. We highlight one such species, P. rugelii, which is endemic to eastern North America. We give an overview of the literature on these focal Plantago species and explain why they are logical candidates for studies of species interactions across environmental gradients. Finally, we emphasize collaborative and community science approaches that can facilitate such research and note the amenability of Plantago for authentic research projects in science education.

Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region

With c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic and comparative analyses of 22 plastome sequences from all four recognized subgenera within Euphorbia revealed that plastome length in Euphorbia is labile, presenting a range of variation c. 42 kb. Large-scale expansions of the inverted repeat (IR) region were identified, and at the extreme opposite, the near-complete loss of the IR region (with only 355 bp left) was detected for the first time in Euphorbiaceae. Other structural variations, including gene inversion and duplication, and gene loss/pseudogenization, were also observed. We screened the most promising molecular markers from both intergenic and coding regions for phylogeny-based utilities, and estimated maximum likelihood and Bayesian phylogenies from four datasets including whole plastome sequences. The monophyly of Euphorbia is supported, and its four subgenera are recovered in a successive sister relationship. Our study constitutes the first comprehensive investigation on the plastome structural variation in Euphorbia and it provides resources for phylogenetic research in the genus, facilitating further studies on its taxonomy, evolution, and conservation.