Plant Evolution Research Articles

OGU: A Toolbox for Better Utilising Organelle Genomic Data

ABSTRACTOrganelle genomes serve as crucial datasets for investigating the genetics and evolution of plants and animals, genome diversity, and species identification. To enhance the collection, analysis, and visualisation of such data, we have developed a novel open‐source software tool named Organelle Genome Utilities (OGU). The software encompasses three modules designed to streamline the handling of organelle genome data. The data collection module is dedicated to retrieving, validating and organising sequence information. The evaluation module assesses sequence variance using a range of methods, including novel metrics termed stem and terminal phylogenetic diversity. The primer module designs universal primers for downstream applications. Finally, a visualisation pipeline has been developed to present comprehensive insights into organelle genomes across different lineages rather than focusing solely on individual species. The performance, compatibility and stability of OGU have been rigorously evaluated through benchmarking with four datasets, including one million mixed GenBank records, plastid genomic data from the Lamiaceae family, mitochondrial data from rodents, and 308 plastid genomes sourced from various angiosperm families. Based on software capabilities, we identified 30 plastid intergenic spacers. These spacers exhibit a moderate evolutionary rate and offer practical utility comparable to coding regions, highlighting the potential applications of intergenic spacers in organelle genomes. We anticipate that OGU will substantially enhance the efficient utilisation of organelle genomic data and broaden the prospects for related research endeavours.

Next‐Generation Directed Evolution in Plants

Next‐Generation Directed Evolution in Plants

Tracing the evolutionary and genetic footprints of atmospheric tillandsioids transition from land to air

Plant evolution is driven by key innovations of functional traits that enables their survivals in diverse ecological environments. However, plant adaptive evolution from land to atmospheric niches remains poorly understood. In this study, we use the epiphytic Tillandsioideae subfamily of Bromeliaceae as model plants to explore their origin, evolution and diversification. We provide a comprehensive phylogenetic tree based on nuclear transcriptomic sequences, indicating that core tillandsioids originated approximately 11.3 million years ago in the Andes. The geological uplift of the Andes drives the divergence of tillandsioids into tank-forming and atmospheric types. Our genomic and transcriptomic analyses reveal gene variations and losses associated with adaptive traits such as impounding tanks and absorptive trichomes. Furthermore, we uncover specific nitrogen-fixing bacterial communities in the phyllosphere of tillandsioids as potential source of nitrogen acquisition. Collectively, our study provides integrative multi-omics insights into the adaptive evolution of tillandsioids in response to elevated aerial habitats.

Evolution of Plant Genome Size and Composition.

The rapid development of sequencing technology has led to an explosion of plant genome data, opening up more opportunities for research in the field of comparative evolutionary analysis of plant genomes. In this review, we take changes in plant genome size and composition as a starting point and describe the effects of polyploidy, whole genome duplication and transposable elements changes on plant genome architecture and evolution, respectively. In addition, to address the lack of relevant information in some areas, we also collected and analyzed 234 representative plant genome data as a supplement. We aim to provide a global, up-to-date summary of information on plant genome architecture and evolution in this review.

Genome-wide comparative analysis of photosynthetic enzymatic genes provides novel insights into foxtail millet and other cereals

C4 crops have more efficient photosynthetic pathways that enable their higher photosynthetic capacities as well as nitrogen and water use efficiencies than C3 crops. Previous research has demonstrated that the genomes of C3 species include and express every gene needed for the C4 photosynthesis pathway. However, very little is known about the dynamics and evolutionary history of such genetic evolution in C4 plants. In this study, the genes encoding five key photosynthetic pathway enzymes in the genomes of C3 (rice), C4 (maize, sorghum, and foxtail millet), and CAM (pineapple) crops were identified and compared systematically. The numbers of genes in these photosynthetic enzymes were highest in the C4 crops like sorghum and foxtail millet, while only eight genes were identified in the CAM plant. However, 16 genes were identified in the C3 crop rice. Furthermore, we performed physical, chemical, gene structure and, cis-element analyses to obtain complete insights into these key genes. Tissue-specific expressions showed that most of the photosynthetic genes are expressed in the leaf tissues. Comparisons of the expression characteristics confirmed that the expression patterns of non-photosynthetic gene copies were relatively conserved among the species, while the C4 gene copies in the C4 species acquired new tissue expression patterns during evolution. Additionally, multiple sequence features that could affect C4 gene expressions and subcellular localization were found in the coding and promoter regions. Our research also highlights the variations in how different genes have evolved within the C4 photosynthetic pathway, and we confirmed that specific high expressions in the leaves and right distribution within the cells were crucial for the development of the C4 photosynthetic abilities. The findings of this study are expected to aid in understanding the evolutionary process of the C4 photosynthetic pathway in grasses as well as offer insights for modifying the C4 photosynthetic pathways in wheat, rice, and other significant C3 cereal crops.

The tetraploid Camellia oleifera genome provides insights into evolution, agronomic traits, and genetic architecture of oil Camellia plants

The tetraploid Camellia oleifera genome provides insights into evolution, agronomic traits, and genetic architecture of oil Camellia plants

Complete Chloroplast Genome of Crassula aquatica: Comparative Genomic Analysis and Phylogenetic Relationships

Background/Objectives: Crassula aquatica (L.) Schonl. is a very small annual plant growing along riverbanks. Chloroplast (cp) genomes, crucial for photosynthesis, are highly conserved and play a key role in understanding plant evolution. In this study, we conducted cp genome analysis of C. aquatica, aiming to elucidate its phylogenetic position and structural variations. We analyzed and described the features of the complete cp genome of C. aquatica and conducted comparative analysis with the cp genomes of closely related taxa. Rsults: The cp genome was 144,503 bp in length and exhibited the typical quadripartite structure, consisting of a large single-copy region (LSC; 77,993 bp), a small single-copy region (SSC; 16,784 bp), and two inverted repeats (24,863 bp). The cp genome of C. aquatica comprised 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs, and 4 rRNA genes. Comparative genomic analysis of 13 other Crassula species and six outgroups demonstrated highly conserved gene content and order among Crassula species. However, notable differences were observed, including the complete loss of the rpoC1 intron in C. aquatica and several closely related species, which may serve as a synapomorphic trait supporting the monophyly of the subgenus Disporocarpa. We analyzed the nucleotide diversity among 14 Crassula cp genomes and identified five highly variable regions (pi > 0.08) in the IGS regions. Phylogenetic analysis based on 78 PCGs confirmed the monophyly of Crassula and its division into two subgenera: Crassula and Disporocarpa. Although the phylogenetic tree supported the subgeneric classification system, the sectional classification system requires reassessment. Conclusions: In this study, we conducted a comparative analysis of the cp genome of the genus Crassula. We inferred evolutionary trends within the Crassula cp genome and provided molecular evidence supporting the integration of the genus Tillaea into the genus Crassula. However, as this study does not represent all species within the genus Tillaea, further comprehensive phylogenetic analyses are requrired.

The influence of plant genomics on plant evolution

With the increasing demand for high-quality tea, the genetic basis of ideal traits of tea plants has been widely concerned. The research on tea tree genomics, specifically focusing on “Longjing 43”, provides significant insights into plant evolution and breeding. “Longjing 43” was chosen due to its complex genome and economic importance. The study successfully assembled its genome to the chromosome level, revealing a large and heterogeneous genome with numerous repetitive sequences. Comparative genomics showed that hybridization has been a key driver of genetic diversity and adaptability in tea plants. These findings are crucial for developing marker-assisted selection (MAS) techniques, improving traits such as disease resistance, flavor, and stress response. Moreover, the research underscores the role of tea tree genomics in preserving cultural heritage and promoting economic benefits through enhanced tea quality. This study contributes to the broader understanding of plant genomics by illustrating the evolutionary processes and potential applications in agriculture, conservation, and industry, thus offering a comprehensive tool for future plant breeding and genetic improvement strategies.

Lineage‐specific duplication of a CYCLOIDEA2 gene and the diversification of capitula in the tribe Anthemideae (Asteraceae)

AbstractGene duplications have contributed to the innovation of morphological traits during plant evolution. An outstanding example is the role of CYCLOIDEA2 (CYC2) gene duplications in the formation of the complex structure of Asteraceae capitula. Previous studies have shown that Chrysanthemum lavandulifolium (Fischer ex Trautv.) Makino and a few other species of the Asteraceae harbor two copies of CYC2e. Here, we identified a lineage‐specific CYC2e duplication event at the root of the phylogeny of the tribe Anthemideae by analyzing the evolutionary history of CYC2 genes across the Asteraceae. Although the gene expression patterns of CYC2e1 and CYC2e2 were similar in most of floral organs, CYC2e1 promoted ligule elongation by promoting cell expansion, whereas CYC2e2 showed a weak inhibiting effect on the ray‐floret development, and overexpression of CYC2e2 resulted in the maldevelopment of stamens in disc florets. These results indicated differentiated functions of CYC2e1 and CYC2e2 in the capitulum development of the Anthemideae. Given the previous data that identified CYC2g and CYC2d as main regulators in ligule morphogenesis, we comparatively analyzed 10 Asteraceae genomic data, and identified tandem arrays of CYC2g, CYC2d, and CYC2e. We further investigated the regulatory relationships between CYC2g/CYC2d and CYC2e genes, and found that CYC2g can activate the expression of CYC2e1. The findings of this study elucidate the synergistic roles of CYC2 genes in regulating the formation of the Asteraceae capitula and enhance understanding of the mechanism of duplicated gene retention during plant evolution.

Ancient large-scale gene duplications and diversification in bryophytes illuminate the plant terrestrialization.

Large-scale gene duplications (LSGDs) are crucial for evolutionary adaptation and recurrent in vascular plants. However, the role of ancient LSGDs in the terrestrialization and diversification of bryophytes, the second most species-rich group of land plants, remains largely elusive due to limited sampling in bryophytes. Employing the most extensive nuclear gene dataset in bryophytes to date, we reconstructed a time-calibrated phylogenetic tree from 209 species, covering virtually all key bryophyte lineages, for phylogenomic analyses of LSGDs and diversification. We newly identified two ancient LSGDs: one in the most recent common ancestor (MRCA) of extant bryophytes and another in the MRCA of the majority of Jungermanniales s.lato.Duplicated genes from these two LSGDs show significant enrichment in photosynthesis-related processes and structures. Rhizoid-responsive ROOTHAIR DEFECTIVE SIX-LIKE (RSL) genes from ancient LSGDs are present in rhizoidless bryophytes, challenging assumptions about rhizoid absence mechanisms. We highlighted four major diversification rate upshifts, two of which slightly postdated LSGDs, potentially linked to the flourishing of gymnosperms and angiosperms and explaining over 80% of bryophyte diversity. Our findings, supported by extensive bryophyte sampling, highlight the significance of LSGDs in the early terrestrialization and diversification of bryophytes, offering new insights into land plant evolution.

Phylogenetic analysis of selected species of Asteraceae on the basis of RPS 11 Gene

The Asteraceae family is a prominent group of flowering plants found across the globe, with the exception of Antarctica. The Asteraceae family is a largest flowering family pivotal group in plant evolution and diversification. Despite its importance, the genetic diversity within this family remains understudied. We focused on the rps-11 gene, a chloroplast marker previously utilized in phylogenetic studies, to investigate its potential in resolving Asteraceae relationships. The focus was on examining genetic diversity within sixteen specifically chosen species from the Asteraceae family. This assessment was based on an analysis of a chloroplast gene responsible for encoding the ribosomal protein of the smaller subunit 11 (rps 11). Nearly 417 bp of rps 11 gene was amplified, sequenced, computationally translated into amino acid sequence and the data was used for phylogenetic analysis as well as for rps 11 protein structure predictions. Based on nucleotide and amino acid sequences phylograms were drawn with the help of Molecular Evolutionary Genetic Analysis (MEGA 6), which exhibited clear genetic relationship among species under investigation. The observed genetic distance was 0.02 for Maximum likelihood tree based on nucleotide sequences whereas it was 0.05 for phylogram based on amino acid sequences. These values revealed that amino acid-based tree has demonstrated greater diversity among selected species in comparison to nucleotides-based tree. On the basis of pair wise distance calculations, genetic divergence values were found within the range of 0.015–0.309. Moreover, 3D protein modeling for rps 11 protein of sixteen selected species was also carried out by iterative threading assembly refinement (I-Tasser) software. The models exhibiting the highest C-score were picked with satisfactory plot statistics (> 90%) and structurally validated by PROCHECK. Furthermore, Ramachandran plots displayed that the rps 11 protein structures of Tagetes minuta, Xanthium strumarium, Lactuca sativa and Chrysanthemum indicum have best feature models with > 90% of residues in the allowed region and ≤ 2% in the disallowed region. The research is not enough to stand alone to validate the viability of the rps11 gene as a prospective contender for phylogenetic analysis. İn future we will focus on the maximum genetic diversity theory for phylogenetic analysis of this family.

Temporal host–symbiont dynamics in community contexts: Impacts of host fitness and vertical transmission efficiency on symbiosis prevalence

Abstract Symbiotic associations play a role in plant ecology and evolution, but the outcome of the interaction depends on the life‐history traits of the partners and the environmental context. Although symbiosis with vertically transmitted microorganisms should result in mutualism, it is not clear how the transmission process aligns with the outcome of the context‐dependent symbiosis. For 3 years, we sampled individuals of an annual plant species that forms symbiosis with a vertically transmitted fungal endophyte, in paired stands of two contrasting vegetation communities (humid mesophytic meadows [HMM]: productive/low stress, and humid prairies [HP]: less productive/high stress). We estimated the prevalence of symbiosis at the population level, and the fitness of the plant, the symbiotic status and vertical transmission efficiency at the individual level. Over 3 years, the prevalence of symbiosis was ≈100% in HMM and ≈75% in HP. Plant fitness was very low and high in years with precipitation below and above the yearly mean, respectively. The higher fitness of endophyte‐symbiotic plants was evident in the HMM and high precipitation years. Vertical transmission of endophytes was higher in HMM (≈96%) compared to HP (≈93%) and was not related to plant fitness. Despite transmission inefficiencies in HP, changes in prevalence within the growing season (from seeds to the final plant stand) suggest a fitness advantage for symbiotic plants. Vertical transmission is expected to promote mutualism as it aligns partners' fitness. Although symbiotic plants showed higher fitness and the probability of transmission failures was higher among low‐fitness plants, the variation in transmission efficiency between plants and vegetation communities was not related to the fitness of the individual host. Our study provides evidence that context‐dependent vertical transmission efficiency and endophyte‐mediated fitness advantages interact complexly to determine the prevalence of symbiosis in populations that occur in contrasting vegetation communities. Read the free Plain Language Summary for this article on the Journal blog.

Expression and functional divergence of a type-A response regulator paralog pair formed by dispersed duplication during Populus deltoides evolution

Gene duplication and divergence are essential to plant evolution. The Arabidopsis type-A response regulator (ARR) family, negative regulators in cytokinin signaling, exemplifies gene expansion and differential retention. Despite extensive research, the understanding of type-A RR homologs in woody plants remains limited. In this study, the evolution history of type-A RR gene families across four rosids and one monocot has been comprehensively investigated. Focusing on Populus deltoides, a unique pair of dispersed duplicates, PdRR8 and PdFERR, is identified, and their duplication is estimated to have occurred in the common ancestor of the four rosids. The duplication remnants corresponding to PdRR8 have been retained in all rosids but the counterpart of PdFERR has been lost. In poplar, PdRR8 shows the highest expression levels in leaves, while PdFERR is specifically expressed in female floral buds. Among various external stimuli, cold strongly represses PdRR8 promoter activity, whereas 6-BA markedly inhibits that of PdFERR. Overexpression of PdRR8 in the Arabidopsis arr16arr17 double-mutant fully complements the reduced hydrotropic response. In contrast, PdFERR fails to rescue the hydrotropic defects of the mutant. Results of evolutionary, expression and functional analyses indicate that PdRR8, rather than PdFERR, is the true ortholog of the ARR16-ARR17 paralogs. Though PdRR8 and PdFERR originate from a common ancestral gene and evolve under strong negative selection, these two dispersed duplicates have exhibited differential expression and some degree of functional divergence.

Label-free quantitative phase imaging and analysis of airborne pollen

Abstract Pollen morphology, involving the physical characteristics of pollen grains from seed plants during reproduction, plays an important role in plant biology, ecology, and evolution. High pollen concentrations in the air can degrade air quality and exacerbate respiratory conditions such as asthma. Understanding pollen morphology and its implications for air quality is significant for mitigating respiratory health risks. Conventionally, fluorescence microscopy is used for pollen imaging, but photobleaching, quenching, and phototoxicity affect the surface morphology and do not provide quantitative data on the pollen grains. For this study, we used bright field (BF) imaging and quantitative phase imaging (QPI), a label-free interferometric microscopy method, to look at differences in the shape of pollen. BF imaging provides information about the shape and size of the different pollens but has a limitation of low contrast. To obtain high-contrast images and quantitative data on the pollen grains without any exogenous agents, we employed QPI and BF imaging in the present study. QPI enables the extraction of detailed information regarding the cell wall, aperture, and thickness of pollen while also maintaining their natural state without the need for chemical treatments. In the present work, we sampled the ambient air from May 2023 to January 2024 on the IIT Delhi campus. Subsequently, QPI and BF imaging have been done for pollen identification and phase analysis of arboreal and non-arboreal pollen. Further, by utilizing the information obtained from BF microscopy and QPI, different species of pollen have been identified, and a pollen calendar has been prepared for exhibiting pollen season throughout the year. To the best of the authors’ knowledge, they have conducted the QPI of airborne pollen grains for the first time; this technique holds great potential for characterizing airborne pollens without the need for staining or sample preparation.

Enhancers in Plant Development, Adaptation, and Evolution.

Understanding plant responses to developmental and environmental cues is crucial for studying morphological divergence and local adaptation. Gene expression changes, governed by cis-regulatory modules (CRMs) including enhancers, are a major source of plant phenotypic variation. However, while genome-wide approaches have revealed thousands of putative enhancers in mammals, far fewer have been identified and functionally characterized in plants. This review provides an overview of how enhancers function to control gene regulation, methods to predict DNA sequences that may have enhancer activity, methods utilized to functionally validate enhancers, and the current knowledge of enhancers in plants, including how they impact plant development, response to environment, and evolutionary adaptation.

Irradiance level and elevation shape the soil microbiome communities of Coffea arabica L.

BackgroundThe nexus plant-microbe-environment is essential to understand the ecosystem processes shaping plant health and fitness. Within this triangle, soils and associated microflora are among the key ecosystem’s drivers, underpinning plant productivity and evolution. In this study, we conducted a comprehensive analysis (physicochemical properties, enzyme activities, and taxonomic diversity) of soils under the canopy projection of Coffea arabica trees along a gradient of elevation (600, 800, and 900 m) and shade (0, 50, 100%).ResultsWhile shade had no influence on most parameters, altitude shaped the dynamics of microbial communities. Available phosphorus, soil organic carbon, and nitrate were significantly higher at 800 m, likely due to the higher activities of β-glucosidase and phosphatases at this altitude. Microbial biomass (carbon and nitrogen) and moisture were significantly higher at 600 and 900 m, which might be attributed to the abundance and richness of soil microorganisms. Indeed, metabarcoding analysis revealed a complex pattern of microbial consortia (bacteria, archaea, fungi) at the three altitudes, with the lowest index of richness recorded at 800 m. The highest number of Amplicon Sequence Variants was observed in bacteria, whose functional analysis revealed distinct metabolic adaptations across different altitudes. At 900 m, the main functional attributes favored the responses to environmental stimuli and microbial interactions; at 800 m, the predominant metabolic pathways were related to organic matter, fermentation, and bioremediation; and at the lower 600 m, the pathways shifted towards the breakdown of plant-derived compounds (e.g. geraniol, limonene, and pinene degradation).ConclusionOverall, the results indicate a higher effectiveness of the microbial consortium at 800 m, which might result in better nutrient cycling. The study highlights the importance of canopy shade species and elevation for the composition of microbial consortia in C. arabica, unveiling ecological functions beyond plant health, with implications for bio-based solutions and biotechnology.

An interview with Liam Dolan.

Liam Dolan is a Group Leader at the Gregor Mendel Institute of Molecular Plant Biology (GMI) in Vienna, Austria, interested in intersection of plant development, evolution and ecology using the emerging model system Marchantia polymorpha. We met with Liam at the GMI to learn more about his career so far, his views on biodiversity and the ecosystem, and why he became involved as a Guest Editor for Development's Special Issue: Uncovering Developmental Diversity.

The role of fossils for reconstructing the evolution of plant development.

Many of the developmental innovations that underpin the diversity of plant form alive today, such as those facilitating apical growth, branching, leaves, roots, wood and seeds, all evolved over 360 million years ago. Fossils, as our only direct record of plant form in the past, are thus essential for interpreting the origin and evolution of these innovations. The focus of this Spotlight is to showcase the rich plant fossil record open for developmental interpretation and to cement the role that fossils play at a time when increases in genome sequencing and new model species make tackling major questions in the area of plant evolution and development tractable for the first time.

Polymeric phenylpropanoid derivatives crosslinked by hydroxyl fatty acids form the core structure of rape sporopollenin.

Sporopollenin, a critical innovation in the evolution of terrestrial plants, is the core building brick for the outer wall of land-plant spores and pollen. Despite its significance, the basic structure of sporopollenin remains elusive due to its extreme chemical inertness. In this study, we used ethanolamine to completely dissolve rape sporopollenin and successfully identified a total of 22 components, including fatty acids, p-coumaric acid, sterols and polymeric phenylpropanoid derivatives. After that, using NaOH treatment and partial dissolution, alongside Arabidopsis mutants analysis and spectroscopic methods, we determined that polymeric phenylpropanoid derivatives crosslinked by hydroxyl fatty acids serve as the core structure of sporopollenin. The free hydroxyl groups and carboxyl groups of the polymeric phenylpropanoid derivatives can be modified by other fatty acids (C16:0, C18:0 and C18:3) as well as alcohols/phenols (for example, naringenin, β-sitosterol), resulting in a structure that protects pollen from terrestrial stresses. This discovery provides a basis for further exploration of sporopollenin's role in plant reproduction and evolution.

Assessment of bi-metal paleo-redox proxies in the Bakken Formation black shales, Williston Basin, North Dakota, USA

The influence of paleoredox conditions and water-mass restriction on trace metal (TM) accumulation in the lower (LBS) and upper black shales (UBS) of the Devonian–Mississippian (D–M) Bakken Formation was assessed utilizing V/Cr, V/(V + Ni), Ni/Co, U/Th, and enrichment factors (EF) for Mo vs. U. These assessments were compared to previously published estimates based on degree of pyritization (DOPT), sulfur‑iron and C–S–Fe relationships, and sedimentological data. Bi–metal ratios suggest >80 % of samples were deposited under suboxic to anoxic/euxinic conditions, whereas DOPT results suggest >60 % of samples were deposited under dysoxic (0.42–0.75 DOPT) bottom–water conditions. DOPT results are in good agreement with C–S–Fe and total S vs. Fe assessments of paleoredox conditions and sedimentological evidence. Good agreement is also seen between Mo/TOC and Mo EF/U EF that both suggest the Bakken shales were deposited under a relatively unrestricted water mass conditions resulting in consistent renewal of TMs into the basin. With TM resupply outpacing drawdown, the basin could support enhanced primary productivity as well as high concentrations of TMs. Trace metal concentrations for the Bakken Fm. show considerable range for Co (0–10,324 ppm), Mo (0–2018 ppm), Ni (0–1574 ppm), U (0–1604 ppm), and V (0–3194 ppm), and bi–metal ratios for the Bakken Fm. are up to 5× greater than those reported for other D–M black shale formations. Bivariate and principal component analysis indicate Mo, Ni, U, and V accumulation was more closely associated with the organic fraction than with reducing conditions, thus accumulation of organic matter during deposition and generation, migration, and biodegradation of hydrocarbons during diagenesis may have influenced the accumulation and distribution of these TMs. Furthermore, changes in biogeochemical processes during the D–M transition may have fundamentally altered marine chemistry, with the evolution of vascular land plants and enhanced terrestrial weathering leading to an increased influx of nutrients into marine waters resulting in the Annulata, Dasberg, and Hangenberg black shale events. Factors controlling TM accumulation during time of deposition (e.g., TM availability, bottom-water redox conditions, adsorption onto organic matter) and during diagenesis and catagenesis (e.g., alteration and break down of organic matter, movement of fluid hydrocarbons or other basinal fluids) likely contribute to the lack of agreement between redox proxies, and subsequently, the lack of applicability of bi–metal ratios in assessing bottom–water conditions for the Bakken shales. Therefore, it is suggested that these bi-metal redox proxies are not an effective means to describe bottom-water conditions during the deposition of the Bakken shales.