How important are transposons for plant evolution?

Construction of a comprehensive library of repeated sequences for the annotation of Citrus genomes

BACKGROUND

The comprehensive annotation of repeated sequences in genomes is an essential prerequisite for studying the dynamics of these sequences over time and their involvement in gene regulation. Currently, the diversity of repeated sequences in Citrus genomes is only partially characterized because the annotations have been performed using heterogeneous bioinformatics tools, each with its specificity and dedicated only to the annotation of transposable elements.

RESULTS

We combined complementary repeat-finding programs including REPET, CAULIFINDER, and TAREAN, to enable the identification of all types of repetitive sequences found in plant genomes, including transposable elements, endogenous caulimovirids, and satellite DNAs. A fine-grained annotation method was first developed to create a consensus sequence library of repeated sequences identified in the genome assemblies of C. medica, C. micrantha, C. reticulata, and C. maxima, the four ancestral parental species involved in the formation of economically valuable cultivated Citrus varieties. A second, faster annotation method was developed to enrich the dataset by adding new repeated sequences retrieved from genome assemblies of other Citrus species and closely related species belonging to the Aurantioideae subfamily. The final reference library contains 3,091 consensus sequences, of which 94.5% are transposable elements. The diversity of endogenous caulimovirids was characterized for the first time within the genus Citrus, contributing 160 consensus sequences to the final reference library. Finally, 10 satellite DNAs were also identified.

CONCLUSION

Combining multiple repeat detection methods enables the comprehensive annotation of all repeated sequences in Citrus genomes. Using the final reference library reported in this work will improve our understanding of the dynamics of repeated sequences during Citrus speciation, particularly following the genome duplication and hybridization events that led to modern cultivars. The exploration of repeat position insertions along chromosomes using the developed web interface, RepeatLoc Citrus, will also make it possible to further investigate the role of transposable elements and endogenous caulimovirids in genome structure and gene regulation in Citrus species.

Harnessing transposable elements for plant functional genomics and genome engineering

Transposable elements (TEs) constitute a large portion of many plant genomes and play important roles in regulating gene expression and in driving genome evolution and crop domestication. Despite advances in understanding the functions and mechanisms of TEs, a comprehensive review of their integrated knowledge and cutting-edge biotechnological applications of TEs is still needed. We provide a thorough overview that connects discoveries, mechanisms, and technologies associated with plant TEs. We discuss the identification and function of TEs driven by functional genomics, epigenetic regulation of TEs, and utilization of active TEs in plant functional genomics and genome engineering. In summary, expanding the knowledge and application of TEs will be beneficial to crop breeding and plant synthetic biology in the future.

Genome-wide comparison reveals large structural variants in cassava landraces

BACKGROUND

Structural variants (SVs) are critical for plant genomic diversity and phenotypic variation. This study investigates a large, 9.7 Mbp highly repetitive segment on chromosome 12 of TMEB117, a region not previously characterized in cassava (Manihot esculenta Crantz). We aim to explore its presence and variability across multiple cassava landraces, providing insights into its genomic significance and potential implications.

RESULTS

We validated the presence of the 9.7 Mbp segment in the TMEB117 genome, distinguishing it from other published cassava genome assemblies. By mapping short-read sequencing data from 16 cassava landraces to TMEB117 chromosome 12, we observed variability in read mapping, suggesting that while all genotypes contain the insertion region, some exhibit missing segments or sequence differences. Further analysis revealed two unique genes associated with deacetylase activity, HDA14 and SRT2, within the insertion. Additionally, the MUDR-Mutator transposable element was significantly overrepresented in this region.

CONCLUSIONS

This study uncovers a large structural variant in the TMEB117 cassava genome, highlighting its variability among different genotypes. The enrichment of HDA14 and SRT2 genes and the MUDR-Mutator elements within the insertion suggests potential functional significance, though further research is needed to explore this. These findings provide important insights into the role of structural variations in shaping cassava genomic diversity.

Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome

Transposon is the main component of the eukaryotic genome, and more and more plant genome data show that transposons are diverse in regulating genome structure, variation, function and evolution, with different transposition mechanisms in the genome. Hybridization and polyploidy play an important role in promoting plant speciation and evolution, and recent studies have shown that polyploidy is usually accompanied by the expansion of transposons, which affect the genome size and structure of polyploid plants. Transposons can insert into genes and intergenic regions, resulting in great differences in the overall genome structure of closely related plant species, and it can also capture gene segments in the genome to increase the copy number of genes. In addition, transposons influence the epigenetic modification state of the genome and regulate the expression of the gene, while plant phenotype, biological and abiotic stress response are also regulated by transposons. Overall, transposons play an important role in the plant genome, especially polyploid plant genome, adaptation and evolution.

FHY3/FAR1 transposable elements generate adaptive genetic variation in the Bassia scoparia genome

BACKGROUND

A nearly complete genome assembly consisting of 14 scaffolds, a total length of 969.6 Mb, and an N50 scaffold length of 99.88 Mb, was generated to better understand how transposable element activity has led to adaptive evolution in Bassia scoparia (kochia), an agronomically important weed.

RESULTS

The nine largest scaffolds correspond to the nine chromosomes of the close relative, Beta vulgaris. From this assembly, 54 387 protein-coding gene loci were annotated. We determined that genes containing Far-Red Elongated Hypocotyl 3 (FHY3) or Far-Red Impaired Response 1 (FAR1) functional domains have undergone a large, kochia-specific gene family expansion. We discovered that putative Mutator Don-Robertson (MuDR) transposable elements with detectable FHY3/FAR1 domains were tightly associated with segmental duplications of 5-enolpyruvylshikimate-3-phosphate synthase subsequently conferring resistance to the herbicide glyphosate. Further, we characterized a new MuDR subtype, named here as 'Muntjac', which contributes to the evolution of herbicide resistance in kochia through the process of transduplication.

CONCLUSION

Collectively, our study provides insights into the role FHY3/FAR1 genes as active transposable elements and contributes new perspectives on the interaction between transposons and herbicide resistance evolution. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

NUCLEAR RNA POLYMERASE D1 is essential for tomato embryogenesis and desiccation tolerance in seeds

Plant-unique RNA polymerase IV (RNA Pol IV) governs the establishment of small RNA (sRNA)-directed DNA methylation (RdDM). In dicotyledon, elevated RdDM activity is often associated with embryogenesis; however, the loss of RdDM frequently results in indiscernible phenotypes. Here, we report that the absence of SlNRPD1, encoding the largest subunit of RNA Pol IV, leads to diminished RdDM and abnormal embryogenesis in tomato (Solanum lycopersicum). Hypermethylation at pericentric transposable elements (TEs) and a burst of 21/22-nt siRNA from the distal and pericentric genes are observed in slnrpd1 embryos. The specific activation of endoribonuclease Dicer-like 2 (SlDCL2b/c/d) is correlated with 21/22-nt sRNA accumulation. Auxin and WUSCHEL-related homeobox (WOX) signaling gene expression is altered by mCHH hypomethylation, which may lead to defective embryos. Due to improper maturation, the slnrpd1 embryos cannot withstand post-harvest desiccation. This study provides insights into how DNA methylation regulates plant embryogenesis.

Tandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes

BACKGROUND

LTR-retrotransposons (LTR-RT) are a major component of plant genomes and important drivers of genome evolution. Most LTR-RT copies in plant genomes are defective elements found as truncated copies, nested insertions or as part of more complex structures. The recent availability of highly contiguous plant genome assemblies based on long-read sequences now allows to perform detailed characterization of these complex structures and to evaluate their importance for plant genome evolution.

RESULTS

The detailed analysis of two rice loci containing complex LTR-RT structures showed that they consist of tandem arrays of LTR copies sharing internal LTRs. Our analyses suggests that these LTR-RT tandems are the result of a single insertion and not of the recombination of two independent LTR-RT elements. Our results also suggest that gypsy elements may be more prone to form these structures. We show that these structures are highly polymorphic in rice and therefore have the potential to generate genetic variability. We have developed a computational pipeline (IDENTAM) that scans genome sequences and identifies tandem LTR-RT candidates. Using this tool, we have detected 266 tandems in a pangenome built from the genomes of 76 accessions of cultivated and wild rice, showing that tandem LTR-RT structures are frequent and highly polymorphic in rice. Running IDENTAM in the Arabidopsis, almond and cotton genomes showed that LTR-RT tandems are frequent in plant genomes of different size, complexity and ploidy level. The complexity of differentiating intra-element variations at the nucleotide level among haplotypes is very high, and we found that graph-based pangenomic methodologies are appropriate to resolve these structures.

CONCLUSIONS

Our results show that LTR-RT elements can form tandem arrays. These structures are relatively abundant and highly polymorphic in rice and are widespread in the plant kingdom. Future studies will contribute to understanding how these structures originate and whether the variability that they generate has a functional impact.

Integrative analysis of seed morphology, geographic origin, and genetic structure in Medicago with implications for breeding and conservation

BACKGROUND

Seed morphology and color are critical agronomic traits in Medicago spp., reflecting adaptations to diverse environments and influencing seedling establishment and vigor. Understanding the interplay between seed traits, geographic origin, and genetic diversity is crucial for effective germplasm conservation and breeding. This study presents a comprehensive analysis of these factors in a diverse collection of Medicago accessions, leveraging machine learning to illuminate these complex relationships.

RESULTS

We analyzed seed size, shape, and color data from 318 Medicago accessions representing 29 species/subspecies from 31 countries. Machine learning models, including Neural Boost, Bootstrap Forest, and Support Vector Machines, effectively classified accessions based on seed traits and geographic origin, achieving up to 80% accuracy. Seed size was accurately predicted (R-squared > 0.80) using a combination of species, geographic origin, and shape descriptors. Hierarchical clustering of 189 M. sativa accessions based on 8,565 SNP markers revealed 20 distinct genetic clusters, indicating substantial population structure. A machine learning-based genome-wide association (GWA) analysis identified SNPs on chromosomes 1, 6, and 8 with high importance for predicting geographic origin. Notably, the most significant SNPs were located in or near genes involved in stress response and genome stability, suggesting their potential role in local adaptation. Finally, we successfully imputed missing M. sativa SNP genotypes using multiple machine learning approaches, achieving over 70% accuracy overall and over 80% for individual nucleotides (A, T, C, G), enhancing the utility of genomic datasets with missing data.

CONCLUSIONS

Our integrated analysis of phenotypic, genetic, and geographic data, coupled with a machine learning-based GWAS approach, provides valuable insights into the diverse patterns within Medicago spp. We demonstrate the power of machine learning for germplasm characterization, trait prediction, and imputation of missing genomic data. These findings have significant implications for seed trait improvement, germplasm management, and understanding adaptation in Medicago and other diverse crop species. The identified candidate genes associated with geographic origin provide a foundation for future investigations into the functional mechanisms of local adaptation. Furthermore, our imputation method offers a valuable data for maximizing the utility of genomic resources in Medicago and other species.

Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis

Repetitive DNA contributes significantly to plant genome size, adaptation, and evolution. However, little is understood about the transcription of repeats. This is addressed here in the plant green foxtail millet (Setaria viridis). First, we used RepeatExplorer2 to calculate the genome proportion (GP) of all repeat types and compared the GP of long terminal repeat (LTR) retroelements against annotated complete and incomplete LTR retroelements (Ty1/copia and Ty3/gypsy) identified by DANTE in a whole genome assembly. We show that DANTE-identified LTR retroelements can comprise ∼0.75% of the inflorescence poly-A transcriptome and ∼0.24% of the stem ribo-depleted transcriptome. In the RNA libraries from inflorescence tissue, both LTR retroelements and DNA transposons identified by RepeatExplorer2 were highly abundant, where they may be taking advantage of the reduced epigenetic silencing in the germ line to amplify. Typically, there was a higher representation of DANTE-identified LTR retroelements in the transcriptome than RepeatExplorer2-identified LTR retroelements, potentially reflecting the transcription of elements that have insufficient genomic copy numbers to be detected by RepeatExplorer2. In contrast, for ribo-depleted libraries of stem tissues, the reverse was observed, with a higher transcriptome representation of RepeatExplorer2-identified LTR retroelements. For RepeatExplorer2-identified repeats, we show that the GP of most Ty1/copia and Ty3/gypsy families were positively correlated with their transcript proportion. In addition, guanine- and cytosine-rich repeats with high sequence similarity were also the most abundant in the transcriptome, and these likely represent young elements that are most capable of amplification due to their ability to evade epigenetic silencing.

S-RNase evolution in self-incompatibility: Phylogenomic insights into synteny with Class I T2 RNase genes

S-RNases are essential in the gametophytic self-incompatibility (GSI) system of many flowering plants, where they act as stylar-S determinants. Despite their prominence, the syntenic genomic origin and evolutionary trajectory of S-RNase genes in eudicots have remained largely unclear. Here, we performed large-scale phylogenetic and microsynteny network analyses of T2 RNase genes across 130 angiosperm genomes, encompassing 35 orders and 56 families. S-like RNase genes in Cucurbitaceae species phylogenetically grouped with functionally characterized S-RNases in various species. Additionally, Cucurbitaceae S-like RNase genes showed conserved synteny with Class I T2 RNase genes. From this, we inferred that the well-characterized S-RNase genes (belonging to Class III-A genes) and Class I T2 RNase genes (located on duplicated genomic blocks) likely derived from the gamma triplication event shared by core eudicots. Additionally, we identified frequent lineage-specific gene transpositions of S-RNases and S-like RNases across diverse angiosperm lineages, including Rosaceae, Solanaceae, and Rutaceae families, accompanied by a significant increase in transposable element activity near these genes. Our findings delineate the genomic origin and evolutionary path of eudicot S-RNase genes, enhancing our understanding of the evolution of the S-RNase-based GSI system.

Pangeneric genome analyses reveal the evolution and diversity of the orchid genus Dendrobium

Orchids constitute one of the most diverse families of angiosperms, yet their genome evolution and diversity remain unclear. Here we construct and analyse chromosome-scale de novo assembled genomes of 17 representative accessions spanning 12 sections in Dendrobium, one of the largest orchid genera. These accessions represent a broad spectrum of phenotypes, lineages and geographical distributions. We first construct haplotype-resolved genomes for a Dendrobium hybrid and uncover haplotypic variations and allelic imbalance in the heterozygous genome, demonstrating the significance of diverse ancestry. At Dendrobium genus-wide scale, we further elucidate phylogenetic relationships, evolutionary dynamics, entire gene repertoire, and the mechanisms of preserving ancient genetic variants and rapid recent genome evolution for habitat adaption. We also showcase distinctive evolutionary trajectories in MADS-box and PEBP families over 28 Ma. These results considerably contribute to unearthing the mystery of orchid origin, evolution and diversification, laying the foundation for efficient use of genetic diversity in breeding.

Comparative analysis using a chromosome-scale genome assembly for Funaria hygrometrica suggests greater collinearity in mosses than in seed plants

Mosses, the largest lineage of seed-free plants, have smaller and less variable genome sizes than flowering plants. Nevertheless, whether this difference results from divergent genome dynamics is poorly known. Here, we use newly generated chromosome-scale genome assemblies for Funaria hygrometrica and comparative analysis with other moss and seed plant genomes to investigate moss genome dynamics. Although some aspects of moss genome dynamics are seed plant-like, such as the mechanism of genome size change and de novo gain/loss of genes, moss genomes retain higher synteny, and collinearity over evolutionary time than seed plant genomes. Furthermore, transposable elements and genes are more evenly distributed along chromosomes in mosses than in seed plants, a feature shared with other sequenced seed-free plant genomes. Overall, our findings support the hypothesis that large-scale genome structure and dynamics of mosses and seed plants differ. In particular, our data suggest a lower rate of gene order reshuffling along chromosomes in mosses compared to seed plants. We speculate that such lower rate of structural genomic variation and unique chromosome structure in mosses may contribute to their relatively smaller and less variable genome sizes.

Transposable Element Landscape in the Monotypic Species Barthea barthei (Hance) Krass (Melastomataceae) and Its Role in Ecological Adaptation

Transposable elements (TEs) are crucial for genome evolution and ecological adaptation, but their dynamics in non-model plants are poorly understood. Using genomic, transcriptomic, and population genomic approaches, we analyzed the TE landscape of Barthea barthei (Melastomataceae), a species distributed across tropical and subtropical southern China. We identified 64,866 TE copies (16.76% of a 235 Mb genome), dominated by Ty3/Gypsy retrotransposons (8.82%) and DNA/Mutator elements (2.7%). A genome-wide analysis revealed 13 TE islands enriched in genes related to photosynthesis, tryptophan metabolism, and stress response. We identified 3859 high-confidence TE insertion polymorphisms (TIPs), including 29 fixed insertions between red and white flower ecotypes, affecting genes involved in cell wall modification, stress response, and secondary metabolism. A transcriptome analysis of the flower buds identified 343 differentially expressed TEs between the ecotypes, 30 of which were near or within differentially expressed genes. The non-random distribution (primarily within 5 kb of genes) and association with adaptive traits suggest a significant role in B. barthei's successful colonization of diverse habitats. Our findings provide insights into how TEs contribute to plant genome evolution and ecological adaptation in tropical forests, particularly through their influence on regulatory networks governing stress response and development.

Structural Variants Contribute to Phenotypic Variation in Maize

Comprehensively identifying the loci shaping trait variation has been challenging, in part because standard approaches often miss many types of genetic variants. Structural variants (SVs), especially transposable elements (TEs), are likely to affect phenotypic variation but we lack methods that can detect polymorphic SVs and TEs using short-read sequencing data. Here, we used a whole genome alignment between two maize genotypes to identify polymorphic SVs and then genotyped a large maize diversity panel for these variants using short-read sequencing data. After characterising SV variation in the panel, we identified SV polymorphisms that are associated with life history traits and genotype-by-environment (GxE) interactions. While most of the SVs associated with traits contained TEs, only two of the SVs had boundaries that clearly matched TE breakpoints indicative of a TE insertion, while the other polymorphisms were likely caused by deletions. One of the SVs that appeared to be caused by a TE insertion had the most associations with gene expression compared to other trait-associated SVs. All of the SVs associated with traits were in linkage disequilibrium with nearby single nucleotide polymorphisms (SNPs), suggesting that the approach used here did not identify unique associations that would have been missed in a SNP association study. Overall, we have (1) created a technique to genotype SV polymorphisms across a large diversity panel using support from genomic short-read sequencing alignments and (2) connected this presence/absence SV variation to diverse traits and GxE interactions.

Decoding resilience: ecology, regulation, and evolution of biosynthetic gene clusters

Secondary metabolism is crucial for plant survival and can generate chemistry with nutritional, therapeutic, and industrial value. Biosynthetic genes of selected secondary metabolites cluster within localised chromosomal regions. The arrangement of these biosynthetic gene clusters (BGCs) challenges the long-held model of random gene order in eukaryotes, raising questions about their regulation, ecological significance, and evolution. In this review, we address these questions by exploring the contribution of BGCs to ecologically relevant plant-biotic interactions, while also evaluating the molecular-(epi)genetic mechanisms controlling their coordinated stress- and tissue-specific expression. Based on evidence that BGCs have distinct chromatin signatures and are enriched with transposable elements (TEs), we integrate emerging hypotheses into an updated evolutionary model emphasising how stress-induced epigenetic processes have shaped BGC formation.

Chromosome distribution of four LTR retrotransposons and 18 S rDNA in coffea eugenioides

Repetitive sequences are recognized for their roles in plant genome organization and function. Mobile elements are notable repeatome sequences due to their intrinsic mutagenic potential, which is related to the origin of adaptive novelties. Understanding the genomic organization and dynamics of the repeatome is fundamental to enlighten their role in plant genome evolution. We aimed to map and assemble the first karyogram for a Coffea species with a closer look at mobile elements. Four LTR-retrotransposons (LTR-RTs) and the 18S rDNA of Coffea eugenioides, a diploid progenitor of the allotetraploid Coffea arabica, were unprecedently mapped in prometaphase/metaphase chromosomes and interphase nuclei. The LTR-RTs included three Ty1/Copia (Bianca, TAR and Tork) and one Ty3/Gypsy (Athila) identified based on homology searches. The four LTR-RTs were mainly distributed in a clustered pattern throughout different portions of the 2n = 22 chromosomes. Athila showed the most intense fluorescence signals and co-located with the secondary constriction of chromosome 3. In addition, the 18S rDNA was mapped in the distal portions of the short arms of chromosome pairs 3 and 5. The obstacles related to obtaining high-quality chromosomes from Coffea species have long been hampering the cytogenomics, which associates in silico analysis with the in situ mapping. Thus, we hope that the results presented here enlighten not only the composition, but also the distribution of mobile elements in the C. eugenioides genome, providing background for further cytogenomic investigations regarding Coffea repeatome.

De novo assembly and characterization of the complete mitochondrial genome of Phellodendron amurense reveals three repeat-mediated recombination

Phellodendron amurense Rupr., a rare herb renowned for its medicinal and ecological significance, has remained genetically unexplored at the mitochondrial level until now. This study presents the first-ever systematic assembly and annotation of the complete mitochondrial genome of P. amurense, achieved through a hybrid strategy combining Illumina and Nanopore sequencing data. The mitochondrial genome spans 566,285 bp with a GC content of 45.51 %, structured into two circular molecules. Our comprehensive analysis identified 32 protein-coding genes (PCGs), 33 tRNA genes, and 3 rRNA genes, alongside 181 simple sequence repeats, 19 tandem repeats, and 310 dispersed repeats. Notably, multiple genome conformations were predicted due to repeat-mediated homologous recombination. Additionally, we assembled the chloroplast genome, identifying 21 mitochondrial plastid sequences that provide insights into organelle genome interactions. A total of 380 RNA-editing sites within the mitochondrial PCGs were predicted, enhancing our understanding of gene regulation and function. Phylogenetic analysis using mitochondrial PCGs from 30 species revealed evolutionary relationships, confirming the homology between P. amurense and Citrus species. This foundational study offers a valuable genetic resource for the Rutaceae family, facilitating further research into genetic evolution and molecular diversity in plant mitochondrial genomes.

Extensive genome evolution distinguishes maize within a stable tribe of grasses

Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species, including maize, show a history of polyploidy - a condition that, while offering the evolutionary advantage of multiple gene copies, poses challenges to basic cellular processes, gene expression, and epigenetic regulation. Genomic studies of polyploidy have been limited by sparse sampling of taxa in groups with multiple polyploidy events. Here, we present 33 genome assemblies from 27 species, including chromosome-scale assemblies of maize relatives Zea and Tripsacum. In maize, the after-effects of polyploidy have been widely studied, showing reduced chromosome number, biased fractionation of duplicate genes, and transposable element (TE) expansions. While we observe these patterns within the genus Zea, 12 other polyploidy events deviate significantly. Those tetraploids and hexaploids retain elevated chromosome number, maintain nearly complete complements of duplicate genes, and have only stochastic TE amplifications. These genomes reveal variable outcomes of polyploidy, challenging simple predictions and providing a foundation for understanding its evolutionary implications in an ecologically and economically important clade.

Miniature-inverted-repeat transposable elements contribute to phenotypic variation regulation of rice induced by space environment

Introduction

Rice samples exposed to the space environment have generated diverse phenotypic variations. Miniature-inverted-repeat transposable elements (MITEs), often found adjacent to genes, play a significant role in regulating the plant genome. Herein, the contribution of MITEs in regulating space-mutagenic phenotypes was explored.

Methods

The space-mutagenic phenotype changes in the F3 to F5 generations of three space-mutagenic lines from the rice varieties Dongnong423 (DN423) and Dongnong (DN416) were meticulously traced. Rice leaves samples at the heading stage from three space-mutagenic lines were subjected to high coverage whole-genome bisulfite sequencing and whole-genome sequencing. These analyses were conducted to investigate the effects of MITEs related epigenetic and genetic variations on space-mutagenic phenotypes.

Results and discussion

Studies have indicated that MITEs within gene regulatory regions might contribute to the formation and differentiation of space-mutagenic phenotypes. The space environment has been shown to induce the transposable elements insertion polymorphisms of MITEs (MITEs-TIPs), with a notable preference for insertion near genes involved in stress response and phenotype regulation. The space-induced MITEs-TIPs contributed to the formation of space-mutagenic phenotype by modulating the expression of gene near the insertion site. This study underscored the pivotal role of MITEs in modulating plant phenotypic variation induced by the space environment, as well as the transgenerational stability of these phenotypic variants.

OsCYCBL1 and OsHTR702 positively regulate rice tolerance to cold stress

Chaling wild rice (Oryza rufipogon Griff.) can survive winter due to its extreme cold tolerance, whereas cultivated rice (Oryza sativa L.) cannot. Here, we found that the expression level of OsCYCBL1 decreased relatively less at low temperatures in Chaling wild rice compared with cultivated rice. Transgenic assays of OsCYCBL1 in Nipponbare (Nip) showed that overexpression of OsCYCBL1 promoted cold tolerance. Transcriptome profiling, RT-qPCR analysis, and physiological parameters measurement indicated that overexpression of OsCYCBL1 maintained better DNA damage repair capacity, balanced the cell cycle, enhanced reactive oxygen species (ROS) homeostasis, and increased wax content, directly affecting the ICE-CBF-COR cascade. Moreover, OsHTR702, a gene that interacts with OsCYCBL1, also positively regulates rice cold tolerance by affecting the ICE-CBF-COR cascade and increasing ROS homeostasis at low temperatures. In addition, overexpression of OsCYCBL1 and OsHTR702 enabled rice to survive through winter. Taken together, the current results indicate that OsCYCBL1 and OsHTR702 are related to cold tolerance in rice, making them potential targets for enhancing crop resilience to cold stress.

The smallest angiosperm genomes may be the price for effective traps of bladderworts

BACKGROUND

Species of the carnivorous family Lentibulariaceae exhibit the smallest genomes in flowering plants. We explored the hypothesis that their minute genomes result from the unique mitochondrial cytochrome c oxidase (COX) mutation. The mutation may boost mitochondrial efficiency, which is especially useful for suction-bladder traps of Utricularia, but also increase DNA-damaging reactive oxygen species, leading to genome shrinkage through deletion-biased DNA repair. We aimed to explore the impact of this mutation on genome size, providing insights into genetic mutation roles in plant genome evolution under environmental pressures.

METHODS

We compiled and measured genome and mean chromosome sizes for 127 and 67 species, respectively, representing all three genera (Genlisea, Pinguicula and Utricularia) of Lentibulariaceae. We also isolated and analysed COX sequences to detect the mutation. Through phylogenetic regressions and Ornstein-Uhlenbeck models of trait evolution, we assessed the impact of the COX mutation on the genome and chromosome sizes across the family.

RESULTS

Our findings reveal significant correlations between the COX mutation and smaller genome and chromosome sizes. Specifically, species carrying the ancestral COX sequence exhibited larger genomes and chromosomes than those with the novel mutation. This evidence supports the notion that the COX mutation contributes to genome downsizing, with statistical analyses confirming a directional evolution towards smaller genomes in species harbouring these mutations.

CONCLUSIONS

Our study confirms that the COX mutation in Lentibulariaceae is associated with genome downsizing, probably driven by increased reactive oxygen species production and subsequent DNA damage requiring deletion-biased repair mechanisms. While boosting mitochondrial energy output, this genetic mutation compromises genome integrity and may potentially affect recombination rates, illustrating a complex trade-off between evolutionary advantages and disadvantages. Our results highlight the intricate processes by which genetic mutations and environmental pressures shape genome size evolution in carnivorous plants.

Centromere drive may propel the evolution of chromosome and genome size in plants

BACKGROUND

Genome size is influenced by natural selection and genetic drift acting on variations from polyploidy and repetitive DNA sequences. We hypothesized that centromere drive, where centromeres compete for inclusion in the functional gamete during meiosis, may also affect genome and chromosome size. This competition occurs in asymmetric meiosis, where only one of the four meiotic products becomes a gamete. If centromere drive influences chromosome size evolution, it may also impact post-polyploid diploidization, where a polyploid genome is restructured to function more like a diploid through chromosomal rearrangements, including fusions. We tested if plant lineages with asymmetric meiosis exhibit faster chromosome size evolution compared to those with only symmetric meiosis, which lack centromere drive as all four meiotic products become gametes. We also examined if positive selection on centromeric histone H3 (CENH3), a protein that can suppress centromere drive, is more frequent in these asymmetric lineages.

METHODS

We analysed plant groups with different meiotic modes: asymmetric in gymnosperms and angiosperms, and symmetric in bryophytes, lycophytes and ferns. We selected species based on available CENH3 gene sequences and chromosome size data. Using Ornstein-Uhlenbeck evolutionary models and phylogenetic regressions, we assessed the rates of chromosome size evolution and the frequency of positive selection on CENH3 in these clades.

RESULTS

Our analyses showed that clades with asymmetric meiosis have a higher frequency of positive selection on CENH3 and increased rates of chromosome size evolution compared to symmetric clades.

CONCLUSIONS

Our findings support the hypothesis that centromere drive accelerates chromosome and genome size evolution, potentially also influencing the process of post-polyploid diploidization. We propose a model which in a single framework helps explain the stability of chromosome size in symmetric lineages (bryophytes, lycophytes and ferns) and its variability in asymmetric lineages (gymnosperms and angiosperms), providing a foundation for future research in plant genome evolution.

Near-complete telomere-to-telomere de novo genome assembly in Egyptian clover (Trifolium alexandrinum)

Egyptian clover (Trifolium alexandrinum L.), also known as berseem clover, is an important forage crop to semi-arid conditions that was domesticated in ancient Egypt in 5,5000 BCE and introduced and well adapted to numerous countries including India, Pakistan, Turkey, and Mediterranean region. Despite its agricultural importance, genomic research on Egyptian clover has been limited to developing efficient modern breeding programs. In the present study, we constructed near-complete telomere-to-telomere-level genome assemblies for 2 Egyptian clover cultivars, Helaly and Fahl. Initial assemblies were established by using highly fidelity long-read technology. To extend sequence contiguity, we developed a gap-targeted sequencing (GAP-Seq) method, in which contig ends are targeted for sequencing to obtain long reads bridging 2 contigs. The total length of the resultant chromosome-level assemblies was 547.7 Mb for Helaly and 536.3 Mb for Fahl. These differences in sequence length can be attributed to the expansion of DNA transposons. Population genomic analysis using single-nucleotide polymorphisms revealed genomic regions highly differentiated between 2 cultivars and increased genetic uniformity within each cultivar. Gene ontologies associated with metabolic and biosynthetic processes and developmental processes were enriched in these genomic regions, indicating that these genes may determine the unique characteristics of each cultivar. Comprehensive genomic resources can provide valuable insights into genetic improvements in Egyptian clover and legume genomics.

New estimates and synthesis of chromosome numbers, ploidy levels and genome size variation in Allium sect. Codonoprasum: advancing our understanding of the unresolved diversification and evolution of this section

BACKGROUND

The genus Allium is known for its high chromosomal variability, but most chromosome counts are based on a few individuals and genome size (GS) reports are limited in certain taxonomic groups. This is evident in the Allium sect. Codonoprasum, a species-rich (> 150 species) and taxonomically complex section with weak morphological differences between taxa, the presence of polyploidy and frequent misidentification of taxa. Consequently, a significant proportion of older karyological reports may be unreliable and GS data are lacking for the majority of species within the section. This study, using chromosome counting and flow cytometry (FCM), provides the first comprehensive and detailed insight into variation in chromosome number, polyploid frequency and distribution, and GS in section members, marking a step towards understanding the unresolved diversification and evolution of this group.

RESULTS

We analysed 1578 individuals from 316 populations of 25 taxa and reported DNA ploidy levels and their GS, with calibration from chromosome counts in 22 taxa. Five taxa had multiple ploidy levels. First estimates of GS were obtained for 16 taxa. A comprehensive review of chromosome number and DNA-ploidy levels in 129 taxa of the section revealed that all taxa have x = 8, except A. rupestre with two polyploid series (x = 8, descending dysploidy x = 7), unique for this section. Diploid taxa dominated (72.1%), while di- & polyploid (12.4%) and exclusively polyploid (15.5%) taxa were less common. Ploidy diversity showed that diploid taxa dominated in the eastern Mediterranean and decreased towards the west and north, whereas only polyploid cytotypes of di- & polyploid taxa or exclusively polyploid taxa dominated in northern and northwestern Europe. A 4.1-fold variation in GS was observed across 33 taxa analysed so far (2C = 22.3-92.1 pg), mainly due to polyploidy, with GS downsizing observed in taxa with multiple ploidy levels. Intra-sectional GS variation suggests evolutionary relationships, and intraspecific GS variation within some taxa may indicate taxonomic heterogeneity and/or historical migration patterns.

CONCLUSIONS

Our study showed advantages of FCM as an effective tool for detecting ploidy levels and determining GS within the section. GS could be an additional character in understanding evolution and phylogenetic relationships within the section.

A single dominant GLOBOSA allele accounts for repeated origins of hose-in-hose flowers in Sinningia (Gesneriaceae)

Plants bearing double flowers have long been cultivated as ornamental plants. Hose-in-hose flowers, bearing two-whorled corolla tubes in whorls 1 and 2, are uncommon but recur in Sinningia (Gesnerioideae, Gesneriaceae). In this study, we selected 15 hose-in-hose cultivars as materials to explore the underlying molecular and genetic mechanisms of this floral architecture. We found that they originated from different hybridization events within the Dircaea clade. Three B-class MADS-box genes were globally expressed in all floral whorls, but only GLOBOSA1 (GLO1) has accumulated a dominant mutation, i.e. the insertion of a hAT-like miniature inverted-repeat transposable element (MITE) into its promoter, that co-segregated with the hose-in-hose phenotype. In addition, all 15 hose-in-hose cultivars contained the same dominant GLO1 allele. Transient gene expression assays confirmed the role of this MITE insertion in upregulating the promoter activity of GLO1 by providing several cis-regulatory elements. Genetic transformation in heterologous Chirita pumila (Didymocarpoideae, Gesneriaceae) verified that this dominant GLO1 allele is sufficient to confer the hose-in-hose phenotype. We further demonstrated that both the GLO1 allele and the hAT-like MITE descended from wild S. cardinalis with single flowers. This study highlights the significance of wide hybridization in frequent gains of the dominant GLO1 allele and thereafter repeated occurrence of hose-in-hose flowers in Sinningia.

Tandemly duplicated Rubisco activase genes of cereals show differential evolution and response to heat stress

Heat stress affects various components of photosynthetic machinery of which Rubisco activation inhibition due to heat sensitive Rubisco activase (RCA) is the most prominent. Detailed comparison of RCA coding genes identified a tandem duplication event in the grass family lineage where the duplicated genes showed very different evolutionary pattern. One of the two genes showed high level of sequence conservation whereas the second copy, although present only 1.5 kb away, was highly variable among various plant species because of loss of introns, alternative splicing and loss of the last exon coding redox regulated C-terminal extension domain. Gene specific expression analysis, both at the transcription as well as the protein level, showed very different expression pattern of the two RCA copies. Expression of the highly conserved copy was higher under normal plant growing conditions that decreased many folds under heat stress with substantial genotypic variation, but the variable copy showed much higher expression under heat stress conditions across all grass species. The cultivated rice has only one functional gene as the second copy became nonfunctional due to multiple deletions but Oryza brachyantha and Oryza australiensis still have two functional Rca genes. Detailed analysis of the promoter region of the two copies among various plant species showed insertion of several transposable elements harboring heat responsive elements in the heat inducible copy of the gene. The conserved RCA copy of wheat didn't have any transposable insertions whereas in that of maize has one heat shock element and sorghum had two. It would be interesting to study if the higher level of heat stress tolerance observed in sorghum and maize is associated with the differences observed for RCA. Key message This manuscript is reporting a grass family-specific tandem duplication event in RCA genes of cereals. The duplicated copies underwent neo-functionalization to evolve novel function to deal with heat stress. One copy of the tandem duplication maintained a high level of conservation whereas the second copy showed tremendous divergence to evolve species specific function of the gene. Specific function to respond to heat stress likely evolved via the insertion of various heat responsive elements carried by transposable elements.

A transposon DNA/hAT-Ac insertion promotes the formation of yellow tepals in lotus (Nelumbo)

Yellow tepal is a unique trait of the American lotus (Nelumbo lutea), and all yellow lotus cultivars in the market possess genetic material from the American lotus. However, the formation of yellow tepals in lotus and the genetic mechanism of their formation remain unclear. In this study, we identified a transposon DNA/hAT-Ac, located within the promoter region of an R2R3-MYB transcription factor, MYB12, by comparing the insertion patterns of transposons in the genomes of American and Asian lotus (Nelumbo nucifera). The transposon was found exclusively in yellow lotus cultivars and not in red or white lotus. The insertion of DNA/hAT-Ac facilitated the specific expression of MYB12 in the yellow lotus tepals. Transient expression in lotus tepals, dual-luciferase, and yeast one-hybrid assays demonstrated that MYB12 promotes the accumulation of carotenoids and flavonols by activating the expression of genes involved in carotenoid and flavonols biosynthesis, and it directly binds to the promoters of PSY and FLS. Our results indicated that the transposon DNA/hAT-Ac-mediated specific expression of MYB12 is crucial for the formation of yellow tepals in lotus, and the findings provide a theoretical basis for the breeding of yellow lotus cultivars.

Transposable Elements Contribute to the Regulation of Long Noncoding RNAs in Drosophila melanogaster

Background: Transposable elements (TEs) and noncoding sequences are major components of the genome, yet their functional contributions to long noncoding RNAs (lncRNAs) are not well understood. Although many lncRNAs originating from TEs (TE-lncRNAs) have been identified across various organisms, their characteristics and regulatory roles, particularly in insects, remain largely unexplored. This study integrated multi-omics data to investigate TE-lncRNAs in D. melanogaster, focusing on the influence of transposons across different omics levels. Results: We identified 16,118 transposons overlapping with lncRNA sequences that constitute 2119 TE-lncRNAs (40.4% of all lncRNAs) using 256 public RNA-seq samples and 15 lncRNA-seq samples of Drosophila S2 cells treated with heavy metals. Of these, 67.2% of TE-lncRNAs contain more than one TE. The LTR/Gypsy family was the most common transposon insertion. Transposons preferred to insert into promoters, transcription starting sites, and intronic regions, especially in chromosome ends. Compared with lncRNAs, TE-lncRNAs showed longer lengths, a lower conservation, and lower levels but a higher specificity of expression. Multi-omics data analysis revealed positive correlations between transposon insertions and chromatin openness at the pre-transcriptional level. Notably, a total of 516 TE-lncRNAs provided transcriptional factor binding sites through transposon insertions. The regulatory network of a key transcription factor was rewired by transposons, potentially recruiting other transcription factors to exert regulatory functions under heavy metal stress. Additionally, 99 TE-lncRNAs were associated with m6A methylation modification sites, and 115 TE-lncRNAs potentially provided candidate small open reading frames through transposon insertions. Conclusions: Our data analysis demonstrated that TEs contribute to the regulation of lncRNAs. TEs not only promote the transcriptional regulation of lncRNAs, but also facilitate their post-transcriptional and epigenetic regulation.

Recurrent excision of a hAT-like transposable element in CmAPRR2 leads to the "shooting star" melon phenotype

The external appearance of fruit commodities is an essential trait that has profound effects on consumer preferences. A natural melon variety, characterized by an uneven and patchy arrangement of dark green streaks and spots on the white-skinned rind, resembles shooting stars streaking across the sky; thus, this variety is called "Shooting Star" (SS). To investigate the mechanism underlying the SS melon rind pattern, we initially discovered that the variegated dark green color results from chlorophyll accumulation on the white skin. We then constructed a segregation population by crossing a SS inbred line with a white rind (WR) inbred line and used bulk segregant analysis (BSA) revealed that the SS phenotype is controlled by a single dominant gene, CmAPRR2, which has been previously confirmed to determine dark green coloration. Further genomic analysis revealed a hAT-like transposable element (TE) inserted in CmAPRR2. This TE in CmAPRR2 is recurrently excised from rind tissues, activating the expression of CmAPRR2. This activation promotes the accumulation of chlorophyll, leading to the variegated dark green color on the rind, and ultimately resulting in the SS rind phenotype. Therefore, we propose that the SS phenotype results from the recurrent excision of the hAT-like TE in CmAPRR2.

Natural Diversity of Heat-Induced Transcription of Retrotransposons in Arabidopsis thaliana

Transposable elements (TEs) are major components of plant genomes, profoundly impacting the fitness of their hosts. However, technical bottlenecks have long hindered our mechanistic understanding of TEs. Using RNA-Seq and long-read sequencing with Oxford Nanopore Technologies' (ONT) direct cDNA sequencing, we analyzed the heat-induced transcription of TEs in three natural accessions of Arabidopsis thaliana (Cvi-0, Col-0, and Ler-1). In addition to the well-studied ONSEN retrotransposon family, we confirmed Copia-35 as a second heat-responsive retrotransposon family with particularly high activity in the relict accession Cvi-0. Our analysis revealed distinct expression patterns of individual TE copies and suggest different mechanisms regulating the GAG protein production in the ONSEN versus Copia-35 families. In addition, analogously to ONSEN, Copia-35 activation led to the upregulation of flanking genes such as APUM9 and potentially to the quantitative modulation of flowering time. ONT data allowed us to test the extent to which read-through formation is important in the regulation of adjacent genes. Unexpectedly, our results indicate that for both families, the upregulation of flanking genes is not predominantly directly initiated by transcription from their 3' long terminal repeats. These findings highlight the intraspecific expressional diversity linked to retrotransposon activation under stress.

A unified framework to analyze transposable element insertion polymorphisms using graph genomes

Transposable elements are ubiquitous mobile DNA sequences generating insertion polymorphisms, contributing to genomic diversity. We present GraffiTE, a flexible pipeline to analyze polymorphic mobile elements insertions. By integrating state-of-the-art structural variant detection algorithms and graph genomes, GraffiTE identifies polymorphic mobile elements from genomic assemblies or long-read sequencing data, and genotypes these variants using short or long read sets. Benchmarking on simulated and real datasets reports high precision and recall rates. GraffiTE is designed to allow non-expert users to perform comprehensive analyses, including in models with limited transposable element knowledge and is compatible with various sequencing technologies. Here, we demonstrate the versatility of GraffiTE by analyzing human, Drosophila melanogaster, maize, and Cannabis sativa pangenome data. These analyses reveal the landscapes of polymorphic mobile elements and their frequency variations across individuals, strains, and cultivars.

Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change

Global climate change is leading to rapid and drastic shifts in environmental conditions, posing threats to biodiversity and nearly all life forms worldwide. Forest trees serve as foundational components of terrestrial ecosystems and play a crucial and leading role in combating and mitigating the adverse effects of extreme climate events, despite their own vulnerability to these threats. Therefore, understanding and monitoring how natural forests respond to rapid climate change is a key priority for biodiversity conservation. Recent progress in evolutionary genomics, driven primarily by cutting-edge multi-omics technologies, offers powerful new tools to address several key issues. These include precise delineation of species and evolutionary units, inference of past evolutionary histories and demographic fluctuations, identification of environmentally adaptive variants, and measurement of genetic load levels. As the urgency to deal with more extreme environmental stresses grows, understanding the genomics of evolutionary history, local adaptation, future responses to climate change, and conservation and restoration of natural forest trees will be critical for research at the nexus of global change, population genomics, and conservation biology. In this review, we explore the application of evolutionary genomics to assess the effects of global climate change using multi-omics approaches and discuss the outlook for breeding of climate-adapted trees.

Repeatome evolution across space and time: Unravelling repeats dynamics in the plant genus Erythrostemon Klotzsch (Leguminosae Juss)

Fluctuations in genomic repetitive fractions (repeatome) are known to impact several facets of evolution, such as ecological adaptation and speciation processes. Therefore, investigating the divergence of repetitive elements can provide insights into an important evolutionary force. However, it is not clear how the different repetitive element clades are impacted by the different factors such as ecological changes and/or phylogeny. To discuss this, we used the Neotropical legume genus Erythrostemon (Caesalpinioideae) as a model, given its ancient origin (~33 Mya), lineage-specific niche conservatism, macroecological heterogeneity, and disjunct distribution in Meso- and South American (MA and SA respectively) lineages. We performed a comparative repeatomic analysis of 18 Erythrostemon species to test the impact of environmental variables over repeats diversification. Overall, repeatome composition was diverse, with high abundances of satDNAs and Ty3/gypsy-Tekay transposable elements, predominantly in the MA and SA lineages respectively. However, unexpected repeatome profiles unrelated to the phylogeny/biogeography were found in a few MA (E. coccineus, E. pannosus and E. placidus) and SA (E. calycinus) species, related to reticulate evolution and incongruence between nuclear and plastid topology, suggesting ancient hybridizations. The plesiomorphic Tekay and satDNA pattern was altered in the MA-sensu stricto subclade with a striking genomic differentiation (expansion of satDNA and retraction of Tekay) associated with the colonization of a new environment in Central America around 20 Mya. Our data reveal that the current species-specific Tekay pool was the result of two bursts of amplification probably in the Miocene, with distinct patterns for the MA and SA repeatomes. This suggests a strong role of the Tekay elements as modulators of the genome-environment interaction in Erythrostemon, providing macroevolutionary insights about mechanisms of repeatome differentiation and plant diversification across space and time.

Repetitive element expansions contribute to genome size gigantism in Pamphagidae: A comparative study (Orthoptera, Acridoidea)

Pamphagidae is a family of Acridoidea that inhabits the desert steppes of Eurasia and Africa. This study employed flow cytometry to estimate the genome size of eight species in the Pamphagidae. The results indicate that the genome size of the eight species ranged from 13.88 pg to 14.66 pg, with an average of 14.26 pg. This is the largest average genome size recorded for the Orthoptera families, as well as for the entire Insecta. Furthermore, the study explored the role of repetitive sequences in the genome, including their evolutionary dynamics and activity, using low-coverage next-generation sequencing data. The genome is composed of 14 different types of repetitive sequences, which collectively make up between 59.9% and 68.17% of the total genome. The Pamphagidae family displays high levels of transposable element (TE) activity, with the number of TEs increasing and accumulating since the family's emergence. The study found that the types of repetitive sequences contributing to the TE outburst events are similar across species. Additionally, the study identified unique repetitive elements for each species. The differences in repetitive sequences among the eight Pamphagidae species correspond to their phylogenetic relationships. The study sheds new light on genome gigantism in the Pamphagidae and provides insight into the correlation between genome size and repetitive sequences within the family.

Assembly and comparative analysis of the complete mitochondrial genome of Vaccinium carlesii Dunn

Vaccinium L. is an important fruit tree with nutritional, medicinal, and ornamental values. However, the mitochondrial (mt) genome of Vaccinium L. remains largely unexplored. Vaccinium carlesii Dunn is an endemic wild resource in China, which is crucial for blueberry breeding. The V. carlesii mt genomes were sequenced using Illumina and Nanopore, which total length was 636,904 bp with 37 protein coding genes, 20 tRNA genes, and three rRNA genes. We found four pairs of long repeat fragments homologous recombination mediated the generation of substructures in the V. carlesii mt genome. We predicted 383 RNA editing sites, all converting cytosine (C) to uracil (U). According to the phylogenetic analysis, V. carlesii and V. macrocarpon of the Ericaceae exhibited the closest genetic relationship. This study provides a theoretical basis for understanding the evolution of higher plants, species classification and identification, and will also be useful for further utilization of Vaccinium germplasm resources.

Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis

Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals-tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs-both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, revealing that chemically-induced epigenome changes can have long-term consequences on imprinted gene expression.

Whole-genome sequencing and identification of antimicrobial peptide coding genes in parsley (Petroselinum crispum), an important culinary and medicinal Apiaceae species

Parsley is a commonly cultivated Apiaceae species of culinary and medicinal importance. Parsley has several recognized health benefits and the species has been utilized in traditional medicine since ancient times. Although parsley is among the most commonly cultivated members of Apiaceae, no systematic genomic research has been conducted on parsley. In the present work, parsley genome was sequenced using the long-read HiFi (high fidelity) sequencing technology and a draft contig assembly of 1.57 Gb that represents 80.9% of the estimated genome size was produced. The assembly was highly repeat-rich with a repetitive DNA content of 81%. The assembly was phased into a primary and alternate assembly in order to minimize redundant contigs. Scaffolds were constructed with the primary assembly contigs, which were used for the identification of AMP (antimicrobial peptide) genes. Characteristic AMP domains and 3D structures were used to detect and verify antimicrobial peptides. As a result, 23 genes (PcAMP1-23) representing defensin, snakin, thionin, lipid transfer protein and vicilin-like AMP classes were identified. Bioinformatic analyses for the characterization of peptide physicochemical properties indicated that parsley AMPs are extracellular peptides, therefore, plausibly exert their antimicrobial effects through the most commonly described AMP action mechanism of membrane attack. AMPs are attracting increasing attention since they display their fast antimicrobial effects in small doses on both plant and animal pathogens with a significantly reduced risk of resistance development. Therefore, identification and characterization of AMPs is important for their incorporation into plant disease management protocols as well as medicinal research for the treatment of multi-drug resistant infections.

Genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation

Pollinator-driven evolution of floral traits is thought to be a major driver of angiosperm speciation and diversification. Ophrys orchids mimic female insects to lure male pollinators into pseudocopulation. This strategy, called sexual deception, is species-specific, thereby providing strong premating reproductive isolation. Identifying the genomic architecture underlying pollinator adaptation and speciation may shed light on the mechanisms of angiosperm diversification. Here, we report the 5.2 Gb chromosome-scale genome sequence of Ophrys sphegodes. We find evidence for transposable element expansion that preceded the radiation of the O. sphegodes group, and for gene duplication having contributed to the evolution of chemical mimicry. We report a highly differentiated genomic candidate region for pollinator-mediated evolution on chromosome 2. The Ophrys genome will prove useful for investigations into the repeated evolution of sexual deception, pollinator adaptation and the genomic architectures that facilitate evolutionary radiations.

Variant calling in polyploids for population and quantitative genetics

Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced-representation sequencing approaches, the genome-wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.

Genetic response of a perennial grass to warm and wet environments interacts and is associated with trait means as well as plasticity

The potential for rapid evolution is an important mechanism allowing species to adapt to changing climatic conditions. Although such potential has been largely studied in various short-lived organisms, to what extent we can observe similar patterns in long-lived plant species, which often dominate natural systems, is largely unexplored. We explored the potential for rapid evolution in Festuca rubra, a long-lived grass with extensive clonal growth dominating in alpine grasslands. We used a field sowing experiment simulating expected climate change in our model region. Specifically, we exposed seeds from five independent seed sources to novel climatic conditions by shifting them along a natural climatic grid and explored the genetic profiles of established seedlings after 3 years. Data on genetic profiles of plants selected under different novel conditions indicate that different climate shifts select significantly different pools of genotypes from common seed pools. Increasing soil moisture was more important than increasing temperature or the interaction of the two climatic factors in selecting pressure. This can indicate negative genetic interaction in response to the combined effects or that the effects of different climates are interactive rather than additive. The selected alleles were found in genomic regions, likely affecting the function of specific genes or their expression. Many of these were also linked to morphological traits (mainly to trait plasticity), suggesting these changes may have a consequence on plant performance. Overall, these data indicate that even long-lived plant species may experience strong selection by climate, and their populations thus have the potential to rapidly adapt to these novel conditions.

A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice

Transposable elements (TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing data. Coupling the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms (SNPs), such as OsRbohB, and validated OsRbohB's relative expression activity using a dual-Luciferase (LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.

Evolutionary insights into the organization of chromatin structure and landscape of transcriptional regulation in plants

Development of complex traits necessitates the functioning and coordination of intricate regulatory networks involving multiple genes. Understanding 3D chromatin structure can facilitate insight into the regulation of gene expression by regulatory elements. This potential, of visualizing the role of chromatin organization in the evolution and function of regulatory elements, remains largely unexplored. Here, we describe new perspectives that arise from the dual considerations of sequence variation of regulatory elements and chromatin structure, with a special focus on whole-genome doubling or polyploidy. We underscore the significance of hierarchical chromatin organization in gene regulation during evolution. In addition, we describe strategies for exploring chromatin organization in future investigations of regulatory evolution in plants, enabling insights into the evolutionary influence of regulatory elements on gene expression and, hence, phenotypes.

A WOX homolog disrupted by a transposon led to the loss of spines and contributed to the domestication of lettuce

The loss of spines is one of the most important domestication traits for lettuce (Lactuca sativa). However, the genetics and regulation of spine development in lettuce remain unclear. We examined the genetics of spines in lettuce using a segregating population derived from a cross between cultivated and wild lettuce (Lactuca serriola). A gene encoding WUSCHEL-related homeobox transcription factor, named as WOX-SPINE1 (WS1), was identified as the candidate gene controlling the spine development in lettuce, and its function on spines was verified. A CACTA transposon was found to be inserted into the first exon of the ws1 allele, knocking out its function and leading to the lack of spines in cultivated lettuce. All lettuce cultivars investigated have the nonfunctional ws1 gene, and a selection sweep was found at the WS1 locus, suggesting its important role in lettuce domestication. The expression levels of WS1 were associated with the density of spines among different accessions of wild lettuce. At least two independent loss-of-function mutations in the ws1 gene caused the loss of spines in wild lettuce. These findings provide new insights into the development of spines and facilitate the exploitation of wild genetic resources in future lettuce breeding programs.

Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation

Transposable elements (TEs) exert significant influence on plant genomic structure and gene expression. Here, we explored TE-related aspects across 14 Rosaceae genomes, investigating genomic distribution, transposition activity, expression patterns, and nearby differentially expressed genes (DEGs). Analyses unveiled distinct long terminal repeat retrotransposon (LTR-RT) evolutionary patterns, reflecting varied genome size changes among nine species over the past million years. In the past 2.5 million years, Rubus idaeus showed a transposition rate twice as fast as Fragaria vesca, while Pyrus bretschneideri displayed significantly faster transposition compared with Crataegus pinnatifida. Genes adjacent to recent TE insertions were linked to adversity resistance, while those near previous insertions were functionally enriched in morphogenesis, enzyme activity, and metabolic processes. Expression analysis revealed diverse responses of LTR-RTs to internal or external conditions. Furthermore, we identified 3695 pairs of syntenic DEGs proximal to TEs in Malus domestica cv. 'Gala' and M. domestica (GDDH13), suggesting TE insertions may contribute to varietal trait differences in these apple varieties. Our study across representative Rosaceae species underscores the pivotal role of TEs in plant genome evolution within this diverse family. It elucidates how these elements regulate syntenic DEGs on a genome-wide scale, offering insights into Rosaceae-specific genomic evolution.

Population comparative genomics discovers gene gain and loss during grapevine domestication

Plant domestication are evolutionary experiments conducted by early farmers since thousands years ago, during which the crop wild progenitors are artificially selected for desired agronomic traits along with dramatic genomic variation in the course of moderate to severe bottlenecks. However, previous investigations are mainly focused on small-effect variants, while changes in gene contents are rarely investigated due to the lack of population-level assemblies for both the crop and its wild relatives. Here, we applied comparative genomic analyses to discover gene gain and loss during grapevine domestication using long-read assemblies of representative population samples for both domesticated grapevines (V. vinifera ssp. vinifera) and their wild progenitors (V. vinifera ssp. sylvestris). Only ∼7% of gene families were shared by 16 Vitis genomes while ∼8% of gene families were specific to each accession, suggesting dramatic variations of gene contents in grapevine genomes. Compared to wild progenitors, the domesticated accessions exhibited an increased presence of genes associated with asexual reproduction, while the wild progenitors showcased a higher abundance of genes related to pollination, revealing the transition from sexual reproduction to clonal propagation during domestication processes. Moreover, the domesticated accessions harbored fewer disease-resistance genes than wild progenitors. The SVs occurred frequently in aroma and disease-resistance related genes between domesticated grapevines and wild progenitors, indicating the rapid diversification of these genes during domestication. Our study provides insights and resources for biological studies and breeding programs in grapevine.

Plastid DNA is a major source of nuclear genome complexity and of RNA genes in the orphan crop moringa

BACKGROUND

Unlike Transposable Elements (TEs) and gene/genome duplication, the role of the so-called nuclear plastid DNA sequences (NUPTs) in shaping the evolution of genome architecture and function remains poorly studied. We investigate here the functional and evolutionary fate of NUPTs in the orphan crop Moringa oleifera (moringa), featured by the highest fraction of plastid DNA found so far in any plant genome, focusing on (i) any potential biases in their distribution in relation to specific nuclear genomic features, (ii) their contribution to the emergence of new genes and gene regions, and (iii) their impact on the expression of target nuclear genes.

RESULTS

In agreement with their potential mutagenic effect, NUPTs are underrepresented among structural genes, although their overall transcription levels and broadness were only lower when involved exonic regions; the occurrence of plastid DNA generally did not result in a broader expression, except among those affected in introns by older NUPTs. In contrast, we found a strong enrichment of NUPTs among specific superfamilies of retrotransposons and several classes of RNA genes, including those participating in the protein biosynthetic machinery (i.e., rRNA and tRNA genes) and a specific class of regulatory RNAs. A significant fraction of NUPT RNA genes was found to be functionally expressed, thus potentially contributing to the nuclear pool.

CONCLUSIONS

Our results complete our view of the molecular factors driving the evolution of nuclear genome architecture and function, and support plastid DNA in moringa as a major source of (i) genome complexity and (ii) the nuclear pool of RNA genes.

Molecular Mimicry of Transposable Elements in Plants

Transposable elements (TEs) are mobile DNA elements that are particularly abundant in the plant genomes. They have long been considered as junk DNA; however, a growing body of evidence suggests that TE insertions promote genetic diversity that is essential for the adaptive evolution of a species. Thus far, studies have mainly investigated the cis-acting regulatory roles of TEs generated by their insertions nearby or within the host genes. However, the trans-acting effects of TE-derived RNA and DNA remained obscure to date. TEs contain various regulatory elements within their sequences that can accommodate the binding of specific RNAs and proteins. Recently, it was suggested that some of these cellular regulators are shared between TEs and the host genes, and the competition for the common host factors underlies the fine-tuned developmental reprogramming. In this review, we will highlight and discuss the latest discoveries on the biological functions of plant TEs, with a particular focus on their competitive binding with specific developmental regulators.

Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops

As global arid conditions worsen and groundwater resources diminish, drought stress has emerged as a critical impediment to plant growth and development globally, notably causing declines in crop yields and even the extinction of certain cultivated species. Numerous studies on drought resistance have demonstrated that DNA methylation dynamically interacts with plant responses to drought stress by modulating gene expression and developmental processes. However, the precise mechanisms underlying these interactions remain elusive. This article consolidates the latest research on the role of DNA methylation in plant responses to drought stress across various species, focusing on methods of methylation detection, mechanisms of methylation pattern alteration (including DNA de novo methylation, DNA maintenance methylation, and DNA demethylation), and overall responses to drought conditions. While many studies have observed significant shifts in genome-wide or gene promoter methylation levels in drought-stressed plants, the identification of specific genes and pathways involved remains limited. This review aims to furnish a reference for detailed research into plant responses to drought stress through epigenetic approaches, striving to identify drought resistance genes regulated by DNA methylation, specific signaling pathways, and their molecular mechanisms of action.

Transposable elements cause the loss of self-incompatibility in citrus

Self-incompatibility (SI) is a widespread prezygotic mechanism for flowering plants to avoid inbreeding depression and promote genetic diversity. Citrus has an S-RNase-based SI system, which was frequently lost during evolution. We previously identified a single nucleotide mutation in Sm-RNase, which is responsible for the loss of SI in mandarin and its hybrids. However, little is known about other mechanisms responsible for conversion of SI to self-compatibility (SC) and we identify a completely different mechanism widely utilized by citrus. Here, we found a 786-bp miniature inverted-repeat transposable element (MITE) insertion in the promoter region of the FhiS2-RNase in Fortunella hindsii Swingle (a model plant for citrus gene function), which does not contain the Sm-RNase allele but are still SC. We demonstrate that this MITE plays a pivotal role in the loss of SI in citrus, providing evidence that this MITE insertion prevents expression of the S-RNase; moreover, transgenic experiments show that deletion of this 786-bp MITE insertion recovers the expression of FhiS2-RNase and restores SI. This study identifies the first evidence for a role for MITEs at the S-locus affecting the SI phenotype. A family-wide survey of the S-locus revealed that MITE insertions occur frequently adjacent to S-RNase alleles in different citrus genera, but only certain MITEs appear to be responsible for the loss of SI. Our study provides evidence that insertion of MITEs into a promoter region can alter a breeding strategy and suggests that this phenomenon may be broadly responsible for SC in species with the S-RNase system.