Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species

Genomic insights into the domestication and genetic basis of yield in papaya

Papaya (Carica papaya L.) is an important tropical and subtropical fruit crop, and understanding its genome is essential for breeding. In this study, we assembled a high-quality genome of 344.17 Mb for the newly cultivated papaya 'Zihui', which contains 22 250 protein-coding genes. By integrating 201 resequenced papaya genomes, we identified four distinct papaya groups and a 34 Mb genomic region with strong domestication selection signals. Within these regions, two key genes associated with papaya yield were discovered: Cp_zihui06549, encoding a leucine-rich receptor-like protein kinase, and Cp_zihui06768, encoding the accumulation of photosystem one 1 (APO1) protein. Heterologous expression of Cp_zihui06549 in tomato confirmed that the total number of fruits in transgenic lines more than doubled compared to wild-type plants, resulting in a significant yield increase. Furthermore, we constructed a pan-genome of papaya and obtained a 77.41 Mb nonreference sequence containing 1543 genes. Within this pan-genome, 2483 variable genes, we detected, including four genes annotated as the 'terpene synthase activity' Gene Ontology term, which were lost in cultivars during domestication. Finally, gene retention analyses were performed using gene presence and absence variation data and differentially expressed genes across various tissues and organs. This study provides valuable insights into the genes and loci associated with phenotypes and domestication processes, laying a solid foundation for future papaya breeding efforts.

Graph-based pangenome provides insights into structural variations and genetic basis of metabolic traits in potato

Potato is the world's most important nongrain crop. In this study, to assess genetic diversity within the Petota section, 29 genomes from Petota and Etuberosum sections were newly de novo assembled and 248 accessions of wild potatoes, landraces, and modern cultivars were re-sequenced at >25× depth. Subsequently, a graph-based pangenome was constructed using DM8.1 as the backbone, integrating194,330 nonredundant structural variants. To characterize the metabolome of tubers and illuminate the genomic basis of metabolic traits, LC-MS/MS was employed to obtain the metabolome of 157 accessions, and 9,321 structural variants (SVs) were detected to be significantly associated with 1,258 distinct metabolites via PAV (presence and absence variations)-based metabolomics-GWAS analysis, including metabolites of flavonoids, phenolic acids, and phospholipids. To facilitate the utilization of pangenome resources, a comprehensive platform, the Potato Pangenome Database (PPDB), was developed. Our study provides a comprehensive genomic resource for dissecting the genomic basis of agronomic and metabolic traits in potato, which will accelerate functional genomics studies and genetic improvements in potato.

Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus

KEY MESSAGE

Pangenome graphs enable population-scale genotyping and improve expression analysis, revealing that structural variations (SVs), particularly transposable elements (TEs), significantly contribute to gene expression variation in winter oilseed rape. Structural variations (SVs) impact important traits, from yield to flowering behaviour and stress responses. Pangenome graphs capture population-level diversity, including SVs, within a single data structure and provide a robust framework for downstream applications. They have the potential to serve as unbiased references for SV genotyping, pan-transcriptomic analyses, and association studies, offering significant advantages over single reference genomes. However, their full potential for expression quantitative trait locus (eQTL) analysis is yet to be explored. We combined long and short-read whole genome sequencing data with expression profiling of Brassica napus (oilseed rape) to assess the impact of SVs on gene expression regulation and explored the utility of pangenome graphs for eQTL analysis. Over 90,000 SVs were discovered from 57 long-read datasets. Pangenome graph as reference was evaluated and used for SV genotyping with short reads and transcript expression quantification. Using SVs genotyped from the graph and 100 expression datasets, we identified 267 gene proximal (cis) SV-eQTLs. Over 70% of eQTL-SVs had similarity to transposable elements (TEs), especially Helitrons. The highest proportion of cis-eQTL-SVs were found in promoter regions. About a third of transcripts whose expression was associated with SVs, had no associated SNPs, suggesting that including SVs allows capturing of relationship which would be missed in SNP-only analyses. This study demonstrated that pangenome graphs provide a unifying framework for eQTL analysis by allowing population-scale SV genotyping and gene expression quantification. We also showed that SVs make an appreciable contribution to gene expression variation in winter oilseed rape.

Two telomere-to-telomere pig genome assemblies and pan-genome analyses provide insights into genomic structural landscape and genetic adaptations

This study presented two high-precision telomere-to-telomere genome assemblies for Min and Rongchang pigs, including a detailed exploration of the telomeric and centromeric regions. By integrating pan-genome and multi-omics analyses, structural variations linked to genetic adaptation were identified, providing a valuable resource for advancing pig breeding and genetic improvement.

Deletion of GhSCY2D Causes Impaired Chloroplast Development and Temperature-Dependent Leaf Yellowing in Cotton (Gossypium hirsutum L.)

Leaf colour mutants play an important role in understanding chlorophyll metabolism and photosynthesis. In this study, we characterised a temperature-sensitive yellow leaf cotton mutant. Genome re-sequencing and comparison identified a 10.327 Kb deletion on the D12 chromosome (D12:670726-681053) in the mutant. The deletion region contains two annotated genes, GH_D12G0047 and GH_D12G0048. Investigations integrating gene mapping, comparative transcriptome analysis, gene annotation, virus-induced gene silencing and gene complementation, found deletion of GH_D12G0047 or GhSCY2D, a crucial constituent of the Sec2 complex essential for the function of chloroplasts, being responsible for the yellow leaf phenotype. The yellow leaf mutant had disrupted chloroplast structure and hindered chlorophyll synthesis when temperature was below 28°C but regained normal green leaf colour at 32°C. By analysing the transcriptome data and hormonal level changes of the mutant under conditions of 25°C and 32°C, it was found that the jasmonic acid signalling pathway and GhSCY2 work in concert to maintain the structural integrity of chloroplasts. The outcomes of the study reveal the indispensable role of GhSCY2 and jasmonic acid in sustaining chloroplast homoeostasis, providing new insights into the regulation of cotton leaf colour and paving the way for advancement in high photosynthetic efficiency breeding strategies.

Solanaceae pan-genomes reveal extensive fractionation and functional innovation of duplicated genes

The Solanaceae family contains many agriculturally important crops, including tomato, potato, pepper, and tobacco, as well as other species with potential for agricultural development, such as the orphan crops groundcherry, wolfberry, and pepino. Research progress varies greatly among these species, with model crops like tomato being far ahead. This disparity limits the broader agricultural application of other Solanaceae species. In this study, we constructed an interspecies pan-genome for the Solanaceae family and identified various gene retention patterns. Our findings reveal that the activity of specific transposable elements is closely associated with gene fractionation and transposition. The pan-genome was further resolved at the level of T subgenomes, which were generated by Solanaceae-specific paleo-hexaploidization (T event). We demonstrate substantial gene fractionation (loss) and divergence events following ancient duplications. For example, all class A and E flower model genes in Solanaceae originated from two tandemly duplicated genes, which expanded through the γ and T events before fractionating into 10 genes in tomato, each acquiring distinct functions critical for fruit development. Based on these results, we developed the Solanaceae Pan-Genome Database (SolPGD, http://www.bioinformaticslab.cn/SolPGD), which integrates datasets from both inter- and intra-species pan-genomes of Solanaceae. These findings and resources will facilitate future studies of solanaceous species, including orphan crops.

Molecular breeding of tomato: Advances and challenges

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a "two-step domestication" process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

Super pangenome of Vitis empowers identification of downy mildew resistance genes for grapevine improvement

Grapevine (Vitis) is one of the oldest domesticated fruit crops with great cultural and economic importance. Here we assembled and annotated haplotype-resolved genomes of 72 global Vitis accessions including 25 wild and 47 cultivated grapevines, among which genomes for 60 grapevines are newly released. Haplotype-aware phylogenomics disentangled the mysterious hybridization history of grapevines, revealing the enormous genetic diversity of the Vitis genus. Pangenomic analysis reveals that European cultivars, more susceptible to the destructive disease downy mildew (DM), have a smaller repertoire of resistance genes in the NLR family encoding the TIR-NBARC-LRR domain. Through extensive structural variation (SV) characterization, phenotyping, DM-infection transcriptome profiling of 113 Vitis accessions, and SV-expression quantitative trait loci analysis, we have identified over 63 SVs and their relevant genes significantly associated with DM resistance, exemplified by a lysine histidine transporter, VvLHT8. This haplotype-resolved super pangenome of the Vitis genus will accelerate breeding and enrich our understanding of the evolution and biology of grapevines.

The DnaJ1 heat shock protein interacts with the flavanone 3-hydroxylase-like protein F3HL to synergistically enhance drought tolerance by scavenging reactive oxygen species in tomato

The widely distributed heat shock protein DnaJ is renowned for its pivotal role in enhancing thermal tolerance in plants; however, its involvement in drought tolerance remains elusive. In this study, genes encoding DnaJ1 were cloned from drought-resistant wild tomato (Solanum pennellii) and drought-sensitive cultivated tomato (Solanum lycopersicum). SpDnaJ1 and SlDnaJ1 from both tomato species were localized in the chloroplast, and their gene expression was induced by various abiotic stresses. SpDnaJ1 was found to be a more potent regulator than SlDnaJ1 in oxidative stress tolerance when expressed in yeast cells. Overexpression of SpDnaJ1 was demonstrated to confer drought tolerance in transgenic plants of cultivated tomato. These transgenic plants exhibited reduced relative conductivity, leaf water loss rate, and malondialdehyde content as compared to the wild-type plants following drought treatment. RNA-seq analysis revealed that overexpression of SpDnaJ1 primarily affects the expression of genes associated with antioxidants, protease inhibitors, and MAPK signaling in response to drought stress. Screening of a tomato cDNA library in the yeast two-hybrid system identified a flavanone 3-hydroxylase-like protein (F3HL) as an interacting protein of DnaJ1. Subsequent findings revealed that F3HL enhances drought tolerance in tomato by increasing the activity of antioxidant enzymes and scavenging reactive oxygen species. These findings demonstrate a pivotal role of DnaJ1-F3HL interaction in enhancing drought tolerance, unveiling a novel molecular mechanism in drought tolerance in plants.

Functional dissection of three pollen-side quantitative trait loci against multiple stylar unilateral incompatibility mechanisms in Solanum pennellii LA0716

In Solanum pennellii LA0716, three stylar UI (sui) factors and one pollen UI (pui) factor were shown to be involved in S-RNase-independent unilateral incompatibility (UI). However, additional pui factor(s) and the antagonistic relationships among pui and sui factors remain to be investigated. Quantitative trait loci (QTL) mapping, functional and genetic analysis of LA0716-based crosses, and integrated multi-omics data are used to identify pui QTLs and functionally dissect pui QTLs from various types of stylar UI. In addition to the reported pui10.1 (SpFPS2), two pui QTLs (pui6.2 and pui12.1) were identified. In LA0716 styles, the three pui loci additively attenuate stylar UI, among which pui6.2 and pui12.1 appear to antagonize the sui factor, SpHT, via independent mechanisms. Furthermore, pui12.1's function was found to be conserved in the SC styles of Solanum habrochaites LA0407 and Solanum chmielewskii LA1028. Candidate genes linked to pui6.2 and pui12.1 are identified for further analysis. This study reveals several mechanisms for three newly described types of stylar UI and the corresponding pui QTLs in LA0716, which advance our understanding of the complex genetic mechanisms underlying UI in the tomato clade.

The developments and prospects of plant super-pangenomes: Demands, approaches, and applications

By integrating genomes from different accessions, pangenomes provide a more comprehensive and reference-bias-free representation of genetic information within a population compared to a single reference genome. With the rapid accumulation of genomic sequencing data and the expanding scope of plant research, plant pangenomics has gradually evolved from single-species to multi-species studies. This shift has given rise to the concept of a super-pangenome that covers all genomic sequences within a genus-level taxonomic group. By incorporating both cultivated and wild species, the super-pangenome has greatly enhanced the resolution of research in various areas such as plant genetic diversity, evolution, domestication, and molecular breeding. In this review, we present a comprehensive overview of the plant super-pangenome, emphasizing its development requirements, construction strategies, potential applications, and notable achievements. We also highlight the distinctive advantages and promising prospects of super-pangenomes while addressing current challenges and future directions.

Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline

Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specific aligners or optimized for specific organisms, narrowing their applicability, particularly for large and repetitive plant genomes. Here, we introduce SVGAP, a pipeline for structural variant (SV) discovery, genotyping, and annotation from high-quality genome assemblies at the population level. Through extensive benchmarks using simulated SV datasets at individual, population, and phylogenetic contexts, we demonstrate that SVGAP performs favorably relative to existing tools in SV discovery. Additionally, SVGAP is one of the few tools to address the challenge of genotyping SVs within large assembled genome samples, and it generates fully genotyped VCF files. Applying SVGAP to 26 maize genomes revealed hidden genomic diversity in centromeres, driven by abundant insertions of centromere-specific LTR-retrotransposons. The output of SVGAP is well-suited for pan-genome construction and facilitates the interpretation of previously unexplored genomic regions.

Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus

BACKGROUND

India harbors the world's largest cattle population, encompassing over 50 distinct Bos indicus breeds. This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle. To comprehensively characterize the genomic variation within Bos indicus and, specifically, dairy breeds, we aim to identify non-reference sequences and construct a comprehensive pangenome.

RESULTS

Five representative genomes of prominent dairy breeds, including Gir, Kankrej, Tharparkar, Sahiwal, and Red Sindhi, were sequenced using 10X Genomics 'linked-read' technology. Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb, comparable to the Bos indicus Brahman reference genome. A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods, revealing 8 Mb and 17.7 Mb of novel sequence respectively. A confident set of 6,844 Non-reference Unique Insertions (NUIs) spanning 7.57 Mb was identified through both methods, representing the pangenome of Indian Bos indicus breeds. Comparative analysis with previously published pangenomes unveiled 2.8 Mb (37%) commonality with the Chinese indicine pangenome and only 1% commonality with the Bos taurus pangenome. Among these, 2,312 NUIs encompassing ~ 2 Mb, were commonly found in 98 samples of the 5 breeds and designated as Bos indicus Common Insertions (BICIs) in the population. Furthermore, 926 BICIs were identified within 682 protein-coding genes, 54 long non-coding RNAs (lncRNA), and 18 pseudogenes. These protein-coding genes were enriched for functions such as chemical synaptic transmission, cell junction organization, cell-cell adhesion, and cell morphogenesis. The protein-coding genes were found in various prominent quantitative trait locus (QTL) regions, suggesting potential roles of BICIs in traits related to milk production, reproduction, exterior, health, meat, and carcass. Notably, 63.21% of the bases within the BICIs call set contained interspersed repeats, predominantly Long Interspersed Nuclear Elements (LINEs). Additionally, 70.28% of BICIs are shared with other domesticated and wild species, highlighting their evolutionary significance.

CONCLUSIONS

This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India. The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.

Perspectives and opportunities in forensic human, animal, and plant integrative genomics in the Pangenome era

The Human Pangenome Reference Consortium, the Chinese Pangenome Consortium, and other plant and animal pangenome projects have announced the completion of pilot work aimed at constructing high-quality, haplotype-resolved reference graph genomes representative of global ethno-linguistically different populations or different plant and animal species. These graph-based, gapless pangenome references, which are enriched in terms of genomic diversity, completeness, and contiguity, have the potential for enhancing long-read sequencing (LRS)-based genomic research, as well as improving mappability and variant genotyping on traditional short-read sequencing platforms. We comprehensively discuss the advancements in pangenome-based genomic integrative genomic discoveries across forensic-related species (humans, animals, and plants) and summarize their applications in variant identification and forensic genomics, epigenetics, transcriptomics, and microbiome research. Recent developments in multiplexed array sequencing have introduced a highly efficient and programmable technique to overcome the limitations of short forensic marker lengths in LRS platforms. This technique enables the concatenation of short RNA transcripts and DNA fragments into LRS-optimal molecules for sequencing, assembly, and genotyping. The integration of new pangenome reference coordinates and corresponding computational algorithms will benefit forensic integrative genomics by facilitating new marker identification, accurate genotyping, high-resolution panel development, and the updating of statistical algorithms. This review highlights the necessity of integrating LRS-based platforms, pangenome-based study designs, and graph-based pangenome references in short-read mapping and LRS-based innovations to achieve precision forensic science.

Genome-wide association analysis reveals regulatory genes for the metabolite synthesis of 2-acetyl-1-pyrroline in aromatic coconut (Cocos nucifera L.)

Coconut (Cocos nucifera L.) is a key tropical economic tree valued for its fruit flavor, particularly 2-acetyl-1-pyrroline (2AP), a vital aroma metabolite. To enhance high-aromatic coconut breeding efforts, it is essential to deeply understand the hereditary factors governing the production of 2AP. In this study, a genome-wide association analysis identifies 32 loci that exhibit significant associations with 2AP content based on single nucleotide polymorphism (SNP) variations from 168 aromatic coconut germplasm resources. Transcriptome analysis then pinpoints 22 candidate genes near significant loci involved in 2AP metabolism. Proteins encoded by these genes are involved in amino acid metabolism, glycolysis, and secondary metabolism. Among these, Asparagine synthetase coding gene ASN1, Gamma-glutamylcysteine synthetase coding gene GSH1, and UbiA prenyltransferase coding gene UBIA are enriched in the linkage region constructed by significant locus Chr04_61490504. In particular, the SNP mutation of CnASN1 leads to amino acid changes in the functional region of the coding protein, potentially resulting in differences in 2AP content among haplotype populations. Identifying variations in related candidate genes, particularly the gene CnASN1, provides molecular markers closely associated with 2AP synthesis for coconut breeding and offers further insights into the metabolic mechanisms of 2AP.

Application of machine learning and genomics for orphan crop improvement

Orphan crops are important sources of nutrition in developing regions and many are tolerant to biotic and abiotic stressors; however, modern crop improvement technologies have not been widely applied to orphan crops due to the lack of resources available. There are orphan crop representatives across major crop types and the conservation of genes between these related species can be used in crop improvement. Machine learning (ML) has emerged as a promising tool for crop improvement. Transferring knowledge from major crops to orphan crops and using machine learning to improve accuracy and efficiency can be used to improve orphan crops.

Resistify: A Novel NLR Classifier That Reveals Helitron-Associated NLR Expansion in Solanaceae

Nucleotide-binding domain leucine-rich repeat (NLR) proteins are a key component of the plant innate immune system. In plant genomes, NLRs exhibit considerable presence/absence variation and sequence diversity. Recent advances in sequencing technologies have made the generation of high-quality novel plant genome assemblies considerably more straightforward. Accurately identifying NLRs from these genomes is a prerequisite for improving our understanding of NLRs and identifying novel sources of disease resistance. While several tools have been developed to predict NLRs, they are hampered by low accuracy, speed, and availability. Here, the NLR annotation tool Resistify is presented. Resistify is an easy-to-use, rapid, and accurate tool to identify and classify NLRs from protein sequences. Applying Resistify to the RefPlantNLR database demonstrates that it can correctly identify NLRs from a diverse range of species. Applying Resistify in combination with tools to identify transposable elements to a panel of Solanaceae genomes reveals a previously undescribed association between NLRs and Helitron transposable elements.

Allelic variation in an expansin, MdEXP-A1, contributes to flesh firmness at harvest in apples

Flesh firmness is a core quality trait in apple breeding because of its correlation with ripening and storage. Quantitative trait loci (QTLs) were analyzed through bulked segregant analysis sequence (BSA-seq) and comparative transcriptome analysis (RNA-seq) to explore the genetic basis of firmness formation. In this study, phenotypic data were collected at harvest from 251 F1 hybrids derived from 'Ruiyang' and 'Scilate', the phenotype values of flesh firmness at harvest were extensively segregated for two consecutive years. A total of 11 candidate intervals were identified on chromosomes 03, 05, 06, 07, 13, and 16 via BSA-seq analysis. We characterized a major QTL on chromosome 16 and selected a candidate gene encoding expansin MdEXP-A1 by combining RNA-seq analysis. Furthermore, the genotype of Del-1166 (homozygous deletion) in the MdEXP-A1 promoter was closely associated with the super-hard phenotype of F1 hybrids, which could be used as a functional marker for marker-assisted selection (MAS) in apple. Functional identification revealed that MdEXP-A1 positively expedited fruit softening in both apple fruits and tomatoes that overexpressed MdEXP-A1. Moreover, the promoter sequence of TE-1166 was experimentally validated containing two binding motifs of MdNAC1, and the absence of the MdEXP-A1 promoter fragment reduced its transcription activity. MdNAC1 also promotes the expression of MdEXP-A1, indicating its potential modulatory role in quality breeding. These findings provide novel insight into the genetic control of flesh firmness by MdEXP-A1.

Pan-genome analyses of 11 Fraxinus species provide insights into salt adaptation in ash trees

Ash trees (Fraxinus) exhibit rich genetic diversity and wide adaptation to various ecological environments, and several species are highly salt tolerant. Dissecting the genomic basis of salt adaptation in Fraxinus is vital for its resistance breeding. Here, we present 11 high-quality chromosome-level genome assemblies for Fraxinus species, which reveal two unequal subgenome compositions and two recent whole-genome triplication events in their evolutionary history. A Fraxinus pan-genome was constructed on the basis of structural variations and revealed that presence-absence variations (PAVs) of transmembrane transport genes have likely contributed to salt adaptation in Fraxinus. Through whole-genome resequencing of an F1 population from an interspecies cross of F. velutina 'Lula 3' (salt tolerant) with F. pennsylvanica 'Lula 5' (salt sensitive), we mapped salt-tolerance PAV-based quantitative trait loci (QTLs) and pinpointed two PAV-QTLs and candidate genes associated with Fraxinus salt tolerance. Mechanistically, FvbHLH85 enhances salt tolerance by mediating reactive oxygen species and Na+/K+ homeostasis, whereas FvSWEET5 enhances salt tolerance by mediating osmotic homeostasis. Collectively, these findings provide valuable genomic resources for Fraxinus salt-resistance breeding and the research community.

Allopolyploidy expanded gene content but not pangenomic variation in the hexaploid oilseed Camelina sativa

Ancient whole-genome duplications are believed to facilitate novelty and adaptation by providing the raw fuel for new genes. However, it is unclear how recent whole-genome duplications may contribute to evolvability within recent polyploids. Hybridization accompanying some whole-genome duplications may combine divergent gene content among diploid species. Some theory and evidence suggest that polyploids have a greater accumulation and tolerance of gene presence-absence and genomic structural variation, but it is unclear to what extent either is true. To test how recent polyploidy may influence pangenomic variation, we sequenced, assembled, and annotated 12 complete, chromosome-scale genomes of Camelina sativa, an allohexaploid biofuel crop with 3 distinct subgenomes. Using pangenomic comparative analyses, we characterized gene presence-absence and genomic structural variation both within and between the subgenomes. We found over 75% of ortholog gene clusters are core in C. sativa and <10% of sequence space was affected by genomic structural rearrangements. In contrast, 19% of gene clusters were unique to one subgenome, and the majority of these were Camelina specific (no ortholog in Arabidopsis). We identified an inversion that may contribute to vernalization requirements in winter-type Camelina and an enrichment of Camelina-specific genes with enzymatic processes related to seed oil quality and Camelina's unique glucosinolate profile. Genes related to these traits exhibited little presence-absence variation. Our results reveal minimal pangenomic variation in this species and instead show how hybridization accompanied by whole-genome duplication may benefit polyploids by merging diverged gene content of different species.

Genomic and cell-specific regulation of benzylisoquinoline alkaloid biosynthesis in opium poppy

Opium poppy is a crop of great commercial value as a source of several opium alkaloids for the pharmaceutical industries including morphine, codeine, thebaine, noscapine, and papaverine. Most enzymes involved in benzylisoquinoline alkaloid (BIA) biosynthesis in opium poppy have been functionally characterized, and opium poppy currently serves as a model system to study BIA metabolism in plants. BIA biosynthesis in opium poppy involves two biosynthetic gene clusters associated respectively with the morphine and noscapine branches. Recent reports have shown that genes in the same cluster are co-expressed, suggesting they might also be co-regulated. However, the transcriptional regulation of opium poppy BIA biosynthesis is not well studied. Opium poppy BIA biosynthesis involves three cell types associated with the phloem system: companion cells, sieve elements, and laticifers. The transcripts and enzymes associated with BIA biosynthesis are distributed across cell types, requiring the translocation of key enzymes and pathway intermediates between cell types. Together, these suggest that the regulation of BIA biosynthesis in opium poppy is multilayered and complex, involving biochemical, genomic, and physiological mechanisms. In this review, we highlight recent advances in genome sequencing and single cell and spatial transcriptomics with a focus on how these efforts can improve our understanding of the genomic and cell-specific regulation of BIA biosynthesis. Such knowledge is vital for opium poppy genetic improvement and metabolic engineering efforts targeting the modulation of alkaloid yield and composition.

Pangenome graphs and their applications in biodiversity genomics

Complete datasets of genetic variants are key to biodiversity genomic studies. Long-read sequencing technologies allow the routine assembly of highly contiguous, haplotype-resolved reference genomes. However, even when complete, reference genomes from a single individual may bias downstream analyses and fail to adequately represent genetic diversity within a population or species. Pangenome graphs assembled from aligned collections of high-quality genomes can overcome representation bias by integrating sequence information from multiple genomes from the same population, species or genus into a single reference. Here, we review the available tools and data structures to build, visualize and manipulate pangenome graphs while providing practical examples and discussing their applications in biodiversity and conservation genomics across the tree of life.

CRISPR/cas9 Allows for the Quick Improvement of Tomato Firmness Breeding

Fruit firmness is crucial for storability, making cultivating varieties with higher firmness a key target in tomato breeding. In recent years, tomato varieties primarily rely on hybridizing ripening mutants to produce F1 hybrids to enhance firmness. However, the undesirable traits introduced by these mutants often lead to a decline in the quality of the varieties. CRISPR/Cas9 has emerged as a crucial tool in accelerating plant breeding and improving specific target traits as technology iterates. In this study, we used a CRISPR/Cas9 system to simultaneously knock out two genes, FIS1 and PL, which negatively regulate firmness in tomato. We generated single and double gene knockout mutants utilizing the tomato genetic transformation system. The fruit firmness of all knockout mutants exhibited a significant enhancement, with the most pronounced improvement observed in the double mutant. Furthermore, we assessed other quality-related traits of the mutants; our results indicated that the fruit quality characteristics of the gene-edited lines remained statistically comparable to those of the wild type. This approach enabled us to create transgenic-free mutants with diverse genotypes across fewer generations, facilitating rapid improvements in tomato firmness. This study offers significant insights into molecular design breeding strategies for tomato.

Grapevine pangenome facilitates trait genetics and genomic breeding

Grapevine breeding is hindered by a limited understanding of the genetic basis of complex agronomic traits. This study constructs a graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemblies and 11 published assemblies. Using Grapepan v.1.0, we build a variation map with 9,105,787 short variations and 236,449 structural variations (SVs) from the resequencing data of 466 grapevine cultivars. Integrating SVs into a genome-wide association study, we map 148 quantitative trait loci for 29 agronomic traits (50.7% newly identified), with 12 traits significantly contributed by SVs. The estimated heritability improves by 22.78% on average when including SVs. We discovered quantitative trait locus regions under divergent artificial selection in metabolism and berry development between wine and table grapes, respectively. Moreover, significant genetic correlations were detected among the 29 traits. Under a polygenic model, we conducted genomic predictions for each trait. In general, our study facilitates the breeding of superior cultivars via the genomic selection of multiple traits.

Clonal gamete-mediated polyploid genome design for stacking genomes

Hybrid vigor in plants confers better agronomically significant traits in offspring compared with either parent. Recently, Wang et al. reported a mitosis instead of meiosis (MiMe) system in tomato for clonal gamete production, showing the potential to exploit autopolyploid progressive heterosis by stacking genomes from four grandparents in tetraploid hybrids, developed from crossing MiMe hybrids.

Nanopore sequencing: flourishing in its teenage years

Over the past decade, nanopore sequencing has experienced significant advancements and changes, transitioning from an initially emerging technology to a significant instrument in the field of genomic sequencing. However, as advancements in next-generation sequencing technology persist, nanopore sequencing also improves. This paper reviews the developments, applications, and outlook on nanopore sequencing technology. Currently, nanopore sequencing supports both DNA and RNA sequencing, making it widely applicable in areas such as telomere-to-telomere (T2T) genome assembly, direct RNA sequencing (DRS), and metagenomics. The openness and versatility of nanopore sequencing have established it as a preferred option for an increasing number of research teams, signaling a transformative influence on life science research. As the nanopore sequencing technology advances, it provides a faster, more cost-effective approach with extended read lengths, demonstrating the significant potential for complex genome assembly, pathogen detection, environmental monitoring, and human disease research, offering a fresh perspective in sequencing technologies.

The near-complete genome assembly of hexaploid wild oat reveals its genome evolution and divergence with cultivated oats

Avena sterilis, the ancestral species of cultivated oats, is a valuable genetic resource for oat improvement. Here we generated a near-complete 10.99 Gb A. sterilis genome and a high-quality 10.89 Gb cultivated oat genome. Genome evolution analysis revealed the centromeres dynamic and structural variations landscape associated with domestication between wild and cultivated oats. Population genetic analysis of 117 wild and cultivated oat accessions worldwide detected many candidate genes associated with important agronomic traits for oat domestication and improvement. Remarkably, a large fragment duplication from chromosomes 4A to 4D harbouring many agronomically important genes was detected during oat domestication and was fixed in almost all cultivated oats from around the world. The genes in the duplication region from 4A showed significantly higher expression levels and lower methylation levels than the orthologous genes located on 4D in A. sterilis. This study provides valuable resources for evolutionary and functional genomics and genetic improvement of oat.

Characterisation of a major QTL for sodium accumulation in tomato grown in high salinity

Soil salinity is a serious concern for tomato culture, affecting both yield and quality parameters. Although some genes involved in tomato salt tolerance have been identified, their genetic diversity has been rarely studied. In the present study, we assessed salt tolerance-related traits at juvenile and adult stages in a large core collection and identified salt tolerance quantitative trait loci (QTLs) by genome-wide association study (GWAS). The results suggested that a major QTL is involved in leaf sodium accumulation at both physiological stages. We were able to identify the underlying candidate gene, coding for a well-known sodium transporter, called SlHKT1.2. We showed that an eQTL for the expression of this gene in roots colocalized with the above ground sodium content QTL. A polymorphism putatively responsible for its variation was identified in the gene promoter. Finally, to extend the applicability of these results, we carried out the same analysis on a test-cross panel composed of the core collection crossed with a distant line. The results indicated that the identified QTL retained its functional impact even in a hybrid genetic context: this paves the way for its use in breeding programs aimed at improving salinity tolerance in tomato cultivars.

Genome evolution and diversity of wild and cultivated rice species

Wild species of crops serve as a valuable germplasm resource for breeding of modern cultivars. Rice (Oryza sativa L.) is a vital global staple food. However, research on genome evolution and diversity of wild rice species remains limited. Here, we present nearly complete genomes of 13 representative wild rice species. By integrating with four previously published genomes for pangenome analysis, a total of 101,723 gene families are identified across the genus, including 9834 (9.67%) core gene families. Additionally, 63,881 gene families absent in cultivated rice species but present in wild rice species are discovered. Extensive structural rearrangements, sub-genomes exchanges, widespread allelic variations, and regulatory sequence variations are observed in wild rice species. Interestingly, expanded but less diverse disease resistance genes in the genomes of cultivated rice, likely due to the loss of some resistance genes and the fixing and amplification of genes encoding resistance genes to specific diseases during domestication and artificial selection. This study not only reveals natural variations valuable for gene-level studies and breeding selection but also enhances our understanding on rice evolution and domestication.

A genome-wide association study of the racing performance traits in Yili horses based on Blink and FarmCPU models

Racing performance traits are the main indicators for evaluating the performance and value of sport horses. The aim of this study was to identify the key genes for racing performance traits in Yili horses by performing a genome-wide association study (GWAS). Breeding values for racing performance traits were calculated for Yili horses (n = 827) using an animal model. Genome-wide association analysis of racing performance traits in horses (n = 236) was carried out using the Blink, and FarmCPU models in GAPIT software, and genes within the significant regions were functionally annotated. The results of GWAS showed that a total of 24 significant SNP markers (P < 6.05 × 10- 9) and 22 suggestive SNP markers (P < 1.21 × 10- 7) were identified. Among them, the Blink associated 16 significant SNP loci and FarmCPU associated 12 significant SNP loci. A total of 127 candidate genes (50 significant) were annotated. Among these, CNTN6 (motor coordination), NIPA1 (neuronal development), and DCC (dopamine pathway maturation) may be the main candidate genes affecting speed traits. SHANK2 (neuronal synaptic regulation), ISCA1 (mitochondrial protein assembly), and KCNIP4 (neuronal excitability) may be the main candidate genes affecting ranking score traits. A common locus (ECA1: 22698579) was significantly associated with racing performance traits, and the function of the genes at this locus needs to be studied in depth. These findings will provide new insights into the detection and selection of genetic variants for racing performance and will help to accelerate the genetic improvement of Yili horses.

Employing genome-wide association studies to investigate acid adaptation mechanisms in Listeria monocytogenes

Listeria monocytogenes is a critical foodborne pathogen known to develop adaptation traits in mildly acidic food processing environments. This study analyzed the genomic data of 49 strains derived from clinical and food sources, utilizing genome-wide association studies (GWAS) to explore the correlation between the genotypic and phenotypic traits of L. monocytogenes, thereby identifying the genetic determinants of its acid adaptation capability. The findings revealed no significant association between the collected acid adaptation genes and the bacterial growth parameters. The GWAS results indicated that numerous single nucleotide polymorphism (SNP) sites were significantly correlated with the growth parameters of L. monocytogenes in a pH = 5.0 acidic environment, whereas the associations diminished as the pH approached neutrality at pH = 6.7. Analysis and annotation of synonymous mutation loci revealed that non-synonymous mutations primarily impact function. The phenotypes pH = 5.0, ΔpH (5.0-5.5), SNPλ, and SNPμmax show the strongest associations with non-synonymous mutation loci. The genes lmo0017, lmo1173, lmo0794, and lmo2783 are significant non-synonymous mutation loci influencing acid adaptation. These genes play critical roles in intracellular pH regulation, cell wall synthesis and environmental response control, directly or indirectly affecting bacterial acid tolerance. Future research could leverage existing data combined with machine learning and causal inference methods to further dissect the genotype-phenotype causal relationships, identifying causative genetic factors that govern the acid adaptation in L. monocytogenes, providing insights for risk assessment and management strategies in food safety.

Pan-genomic characterization and structural variant analysis reveal insights into spore development and species diversity in Ganoderma

Understanding the genomic diversity and functional implications of Ganoderma species is crucial for elucidating their evolutionary history and biotechnological potential. Here, we present the first pan-genomic analysis of Ganoderma spp., combining five newly sequenced genomes with ten publicly available genomes. Our comprehensive comparative study unveiled a rich genomic landscape, identifying core genes shared among all Ganoderma strains and species-specific gene sets. Additionally, we identified structural variants impacting the expression of key genes, including insights into the MSH4 gene involved in DNA repair and recombination processes, which exhibits a 440 bp insertion in the promoter region and a leucine-to-serine mutation in the gene body, potentially increasing spore production in the S3 strain. Overall, our study provides valuable insights into the genomic architecture and functional diversity of Ganoderma, paving the way for further research on its evolutionary dynamics, biotechnological applications and pharmaceutical potential.

Genetic and functional traits limit the success of colonisation by arbuscular mycorrhizal fungi in a tomato wild relative

To understand whether domestication had an impact on susceptibility and responsiveness to arbuscular mycorrhizal fungi (AMF) in tomato (Solanum lycopersicum), we investigated two tomato cultivars ("M82" and "Moneymaker") and a panel of wild relatives including S. neorickii, S. habrochaites and S. pennellii encompassing the whole Lycopersicon clade. Most genotypes revealed good AM colonisation levels when inoculated with the AMF Funneliformis mosseae. By contrast, both S. pennellii accessions analysed showed a very low colonisation, but with normal arbuscule morphology, and a negative response in terms of root and shoot biomass. This behaviour was independent of fungal identity and environmental conditions. Genomic and transcriptomic analyses revealed in S. pennellii the lack of genes identified within QTLs for AM colonisation, a limited transcriptional reprogramming upon mycorrhization and a differential regulation of strigolactones and AM-related genes compared to tomato. Donor plants experiments indicated that the AMF could represent a cost for S. pennellii: F. mosseae could extensively colonise the root only when it was part of a mycorrhizal network, but a higher mycorrhization led to a higher inhibition of plant growth. These results suggest that genetics and functional traits of S. pennellii are responsible for the limited extent of AMF colonisation.

Pan-genome analysis of 13 Spinacia accessions reveals structural variations associated with sex chromosome evolution and domestication traits in spinach

Structural variations (SVs) are major genetic variants that can be involved in the origin, adaptation and domestication of species. However, the identification and characterization of SVs in Spinacia species are rare due to the lack of a pan-genome. Here, we report eight chromosome-scale assemblies of cultivated spinach and its two wild species. After integration with five existing assemblies, we constructed a comprehensive Spinacia pan-genome and identified 193 661 pan-SVs, which were genotyped in 452 Spinacia accessions. Our pan-SVs enabled genome-wide association study identified signals associated with sex and clarified the evolutionary direction of spinach. Most sex-linked SVs (86%) were biased to occur on the Y chromosome during the evolution of the sex-linked region, resulting in reduced Y-linked gene expression. The frequency of pan-SVs among Spinacia accessions further illustrated the contribution of these SVs to domestication, such as bolting time and seed dormancy. Furthermore, compared with SNPs, pan-SVs act as efficient variants in genomic selection (GS) because of their ability to capture missing heritability information and higher prediction accuracy. Overall, this study provides a valuable resource for spinach genomics and highlights the potential utility of pan-SV in crop improvement and breeding programmes.

Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions

Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent and scale of SV impact across a species remain unknown. In the present study, we constructed a reference library of 334,461 SVs from genome assemblies of 16 representative morphotypes of neopolyploid Brassica napus accessions and detected 258,865 SVs in 2,105 resequenced genomes. Coupling with 5 tissue population transcriptomes, we uncovered 285,976 SV-expression quantitative trait loci (eQTLs) that associate with altered expression of 73,580 genes. We developed a pipeline for the high-throughput joint analyses of SV-genome-wide association studies (SV-GWASs) and transcriptome-wide association studies of phenomic data, eQTLs and eQTL-GWAS colocalization, and identified 726 SV-gene expression-trait variation associations, some of which were verified by transgenics. The pervasive SV impact on how SV reshapes trait variation was demonstrated with the glucosinolate biosynthesis and transport pathway. The study highlighting the impact of genome-wide and species-scale SVs provides a powerful methodological strategy and valuable resources for studying evolution, gene discovery and breeding.

Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora

Haplotype-level allelic characterization facilitates research on the functional, evolutionary and breeding-related features of extremely large and complex plant genomes. We report a 21.7-Gb chromosome-level haplotype-resolved assembly in Pinus densiflora. We found genome rearrangements involving translocations and inversions between chromosomes 1 and 3 of Pinus species and a proliferation of specific long terminal repeat (LTR) retrotransposons (LTR-RTs) in P. densiflora. Evolutionary analyses illustrated that tandem and LTR-RT-mediated duplications led to an increment of transcription factor (TF) genes in P. densiflora. The haplotype sequence comparison showed allelic imbalances, including presence-absence variations of genes (PAV genes) and their functional contributions to flowering and abiotic stress-related traits in P. densiflora. Allele-aware resequencing analysis revealed PAV gene diversity across P. densiflora accessions. Our study provides insights into key mechanisms underlying the evolution of genome structure, LTR-RTs and TFs within the Pinus lineage as well as allelic imbalances and diversity across P. densiflora.

Analyzes of pan-genome and resequencing atlas unveil the genetic basis of jujube domestication

Jujube (Ziziphus jujuba Mill.), belonging to the Rhamnaceae family, is gaining increasing prominence as a perennial fruit crop with significant economic and medicinal values. Here, we conduct de novo assembly of four reference-grade genomes, encompassing one wild and three cultivated jujube accessions. We present insights into the population structure, genetic diversity, and genomic variations within a diverse collection of 1059 jujube accessions. Analyzes of the jujube pan-genome, based on our four assemblies and four previously released genomes, reveal extensive genomic variations within domestication-associated regions, potentially leading to the discovery of a candidate gene that regulates flowering and fruit ripening. By leveraging the pan-genome and a large-scale resequencing population, we identify two candidate genes involved in domestication traits, including the seed-setting rate, the bearing-shoot length and the leaf size in jujube. These genomic resources will accelerate evolutionary and functional genomics studies of jujube.

Lactuca super-pangenome reduces bias towards reference genes in lettuce research

BACKGROUND

Breeding of lettuce (Lactuca sativa L.), the most important leafy vegetable worldwide, for enhanced disease resistance and resilience relies on multiple wild relatives to provide the necessary genetic diversity. In this study, we constructed a super-pangenome based on four Lactuca species (representing the primary, secondary and tertiary gene pools) and comprising 474 accessions. We include 68 newly sequenced accessions to improve cultivar coverage and add important foundational breeding lines.

RESULTS

With the super-pangenome we find substantial presence/absence variation (PAV) and copy-number variation (CNV). Functional enrichment analyses of core and variable genes show that transcriptional regulators are conserved whereas disease resistance genes are variable. PAV-genome-wide association studies (GWAS) and CNV-GWAS are largely congruent with single-nucleotide polymorphism (SNP)-GWAS. Importantly, they also identify several major novel quantitative trait loci (QTL) for resistance against Bremia lactucae in variable regions not present in the reference lettuce genome. The usability of the super-pangenome is demonstrated by identifying the likely origin of non-reference resistance loci from the wild relatives Lactuca serriola, Lactuca saligna and Lactuca virosa.

CONCLUSIONS

The super-pangenome offers a broader view on the gene repertoire of lettuce, revealing relevant loci that are not in the reference genome(s). The provided methodology and data provide a strong basis for research into PAVs, CNVs and other variation underlying important biological traits of lettuce and other crops.

Genomic variation of 363 diverse tea accessions unveils the genetic diversity, domestication, and structural variations associated with tea adaptation

Domestication has shaped the population structure and agronomic traits of tea plants, yet the complexity of tea population structure and genetic variation that determines these traits remains unclear. We here investigated the resequencing data of 363 diverse tea accessions collected extensively from almost all tea distributions and found that the population structure of tea plants was divided into eight subgroups, which were basically consistent with their geographical distributions. The genetic diversity of tea plants in China decreased from southwest to east as latitude increased. Results also indicated that Camellia sinensis var. assamica (CSA) illustrated divergent selection signatures with Camellia sinensis var. sinensis (CSS). The domesticated genes of CSA were mainly involved in leaf development, flavonoid and alkaloid biosynthesis, while the domesticated genes in CSS mainly participated in amino acid metabolism, aroma compounds biosynthesis, and cold stress. Comparative population genomics further identified ~730 Mb novel sequences, generating 6,058 full-length protein-encoding genes, significantly expanding the gene pool of tea plants. We also discovered 217,376 large-scale structural variations and 56,583 presence and absence variations (PAVs) across diverse tea accessions, some of which were associated with tea quality and stress resistance. Functional experiments demonstrated that two PAV genes (CSS0049975 and CSS0006599) were likely to drive trait diversification in cold tolerance between CSA and CSS tea plants. The overall findings not only revealed the genetic diversity and domestication of tea plants, but also underscored the vital role of structural variations in the diversification of tea plant traits.

Genomic selection for agronomical phenotypes using genome-wide SNPs and SVs in pearl millet

Pearl millet is an essential crop worldwide, with noteworthy resilience to abiotic stress, yet the advancement of its breeding remains constrained by the underutilization of molecular-assisted breeding techniques. In this study, we collected 1,455,924 single nucleotide polymorphism (SNP) and 124,532 structural variant (SV) markers primarily from a pearl millet inbred germplasm association panel consisting of 242 accessions including 120 observed phenotypes, mostly related to the yield. Our findings revealed that the SV markers had the capacity to capture genetic diversity not discerned by SNP markers. Furthermore, no correlation in heritability was observed between SNP and SV markers associated with the same phenotype. The assessment of the nine genomic prediction models revealed that SV markers performed better than SNP markers. When using the SV markers as the predictor variable, the genomic BLUP model achieved the best performance, while using the SNP markers, Bayesian methods outperformed the others. The integration of these models enabled the identification of eight candidate accessions with high genomic estimated breeding values (GEBV) across nine phenotypes using SNP markers. Four candidate accessions were identified with high GEBV across 22 phenotypes using SV markers. Notably, accession 'P23' emerged as a consistent candidate predicted based on both SNP and SV markers specifically for panicle number. These findings contribute valuable insights into the potential of utilizing both SNP and SV markers for genomic prediction in pearl millet breeding. Moreover, the identification of promising candidate accessions, such as 'P23', underscores the accelerated prospects of molecular breeding initiatives for enhancing pearl millet varieties.

Structural variation discovery in wheat using PacBio high-fidelity sequencing

Structural variations (SVs) pervade plant genomes and contribute substantially to the phenotypic diversity. However, most SVs were ineffectively assayed due to their complex nature and the limitations of early genomic technologies. By applying the PacBio high-fidelity (HiFi) sequencing for wheat genomes, we performed a comprehensive evaluation of mainstream long-read aligners and SV callers in SV detection. The results indicated that the accuracy of deletion discovery is markedly influenced by callers, accounting for 87.73% of the variance, whereas both aligners (38.25%) and callers (49.32%) contributed substantially to the accuracy variance for insertions. Among the aligners, Winnowmap2 and NGMLR excelled in detecting deletions and insertions, respectively. For SV callers, SVIM achieved the best performance. We demonstrated that combining the aligners and callers mentioned above is optimal for SV detection. Furthermore, we evaluated the effect of sequencing depth on the accuracy of SV detection, revealing that low-coverage HiFi sequencing is sufficiently robust for high-quality SV discovery. This study thoroughly evaluated SV discovery approaches and established optimal workflows for investigating structural variations using low-coverage HiFi sequencing in the wheat genome, which will advance SV discovery and decipher the biological functions of SVs in wheat and many other plants.

De novo domestication in the Solanaceae: advances and challenges

The advent of highly efficient genome editing (GE) tools, coupled with high-throughput genome sequencing, has paved the way for the accelerated domestication of crop wild relatives. New crops could thus be rapidly created that are well adapted to cope with drought, flooding, soil salinity, or insect damage. De novo domestication avoids the complexity of transferring polygenic stress resistance from wild species to crops. Instead, new crops can be created by manipulating major genes in stress-resistant wild species. However, the genetic basis of certain relevant domestication-related traits often involve epistasis and pleiotropy. Furthermore, pan-genome analyses show that structural variation driving gene expression changes has been selected during domestication. A growing body of work suggests that the Solanaceae family, which includes crop species such as tomatoes, potatoes, eggplants, peppers, and tobacco, is a suitable model group to dissect these phenomena and operate changes in wild relatives to improve agronomic traits rapidly with GE. We briefly discuss the prospects of this exciting novel field in the interface between fundamental and applied plant biology and its potential impact in the coming years.

Differences in activity and stability drive transposable element variation in tropical and temperate maize

Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore the extent of TE variation within species, we developed an optimized open-source algorithm, panEDTA, to de novo annotate TEs in a pangenome context. We then generated a unified TE annotation for a maize pangenome derived from 26 reference-quality genomes, which reveals an excess of 35.1 Mb of TE sequences per genome in tropical maize relative to temperate maize. A small number (n = 216) of TE families, mainly LTR retrotransposons, drive these differences. Evidence from the methylome, transcriptome, LTR age distribution, and LTR insertional polymorphisms reveals that 64.7% of the variability is contributed by LTR families that are young, less methylated, and more expressed in tropical maize, whereas 18.5% is driven by LTR families with removal or loss in temperate maize. Additionally, we find enrichment for Young LTR families adjacent to nucleotide-binding and leucine-rich repeat (NLR) clusters of varying copy number across lines, suggesting TE activity may be associated with disease resistance in maize.

Impact and characterization of serial structural variations across humans and great apes

Modern sequencing technology enables the systematic detection of complex structural variation (SV) across genomes. However, extensive DNA rearrangements arising through a series of mutations, a phenomenon we refer to as serial SV (sSV), remain underexplored, posing a challenge for SV discovery. Here, we present NAHRwhals ( https://github.com/WHops/NAHRwhals ), a method to infer repeat-mediated series of SVs in long-read genomic assemblies. Applying NAHRwhals to haplotype-resolved human genomes from 28 individuals reveals 37 sSV loci of various length and complexity. These sSVs explain otherwise cryptic variation in medically relevant regions such as the TPSAB1 gene, 8p23.1, 22q11 and Sotos syndrome regions. Comparisons with great ape assemblies indicate that most human sSVs formed recently, after the human-ape split, and involved non-repeat-mediated processes in addition to non-allelic homologous recombination. NAHRwhals reliably discovers and characterizes sSVs at scale and independent of species, uncovering their genomic abundance and suggesting broader implications for disease.

First insight into the genomes of the Pulmonaria officinalis group (Boraginaceae) provided by repeatome analysis and comparative karyotyping

BACKGROUND

The genus Pulmonaria (Boraginaceae) represents a taxonomically complex group of species in which morphological similarity contrasts with striking karyological variation. The presence of different numbers of chromosomes in the diploid state suggests multiple hybridization/polyploidization events followed by chromosome rearrangements (dysploidy). Unfortunately, the phylogenetic relationships and evolution of the genome, have not yet been elucidated. Our study focused on the P. officinalis group, the most widespread species complex, which includes two morphologically similar species that differ in chromosome number, i.e. P. obscura (2n = 14) and P. officinalis (2n = 16). Ornamental cultivars, morphologically similar to P. officinalis (garden escapes), whose origin is unclear, were also studied. Here, we present a pilot study on genome size and repeatome dynamics of these closely related species in order to gain new information on their genome and chromosome structure.

RESULTS

Flow cytometry confirmed a significant difference in genome size between P. obscura and P. officinalis, corresponding to the number of chromosomes. Genome-wide repeatome analysis performed on genome skimming data showed that retrotransposons were the most abundant repeat type, with a higher proportion of Ty3/Gypsy elements, mainly represented by the Tekay lineage. Comparative analysis revealed no species-specific retrotransposons or striking differences in their copy number between the species. A new set of chromosome-specific cytogenetic markers, represented by satellite DNAs, showed that the chromosome structure in P. officinalis was more variable compared to that of P. obscura. Comparative karyotyping supported the hybrid origin of putative hybrids with 2n = 15 collected from a mixed population of both species and outlined the origin of ornamental garden escapes, presumably derived from the P. officinalis complex.

CONCLUSIONS

Large-scale genome size analysis and repeatome characterization of the two morphologically similar species of the P. officinalis group improved our knowledge of the genome dynamics and differences in the karyotype structure. A new set of chromosome-specific cytogenetic landmarks was identified and used to reveal the origin of putative hybrids and ornamental cultivars morphologically similar to P. officinalis.

Hi-C techniques: from genome assemblies to transcription regulation

The invention of chromosome conformation capture (3C) techniques, in particular the key method Hi-C providing genome-wide information about chromatin contacts, revolutionized the way we study the three-dimensional organization of the nuclear genome and how it affects transcription, replication, and DNA repair. Because the frequency of chromatin contacts between pairs of genomic segments predictably relates to the distance in the linear genome, the information obtained by Hi-C has also proved useful for scaffolding genomic sequences. Here, we review recent improvements in experimental procedures of Hi-C and its various derivatives, such as Micro-C, HiChIP, and Capture Hi-C. We assess the advantages and limitations of the techniques, and present examples of their use in recent plant studies. We also report on progress in the development of computational tools used in assembling genome sequences.

The era of panomics-driven gene discovery in plants

Panomics is an approach to integrate multiple 'omics' datasets, generated using different individuals or natural variations. Considering their diverse phenotypic spectrum, the phenome is inherently associated with panomics-based science, which is further combined with genomics, transcriptomics, metabolomics, and other omics techniques, either independently or collectively. Panomics has been accelerated through recent technological advancements in the field of genomics that enable the detection of population-wide structural variations (SVs) and hence offer unprecedented insights into the genetic variations contributing to important agronomic traits. The present review provides the recent trends of panomics-driven gene discovery toward various traits related to plant development, stress tolerance, accumulation of specialized metabolites, and domestication/dedomestication. In addition, the success stories are highlighted in the broader context of enhancing crop productivity.

Unlocking plant genetics with telomere-to-telomere genome assemblies

Contiguous genome sequence assemblies will help us to realize the full potential of crop translational genomics. Recent advances in sequencing technologies, especially long-read sequencing strategies, have made it possible to construct gapless telomere-to-telomere (T2T) assemblies, thus offering novel insights into genome organization and function. Plant genomes pose unique challenges, such as a continuum of ancient to recent polyploidy and abundant highly similar and long repetitive elements. Owing to progress in sequencing approaches, for most crop plants, chromosome-scale reference genome assemblies are available, but T2T assembly construction remains challenging. Here we describe methods for haplotype-resolved, gapless T2T assembly construction in plants, including various crop species. We outline the impact of T2T assemblies in elucidating the roles of repetitive elements in gene regulation, as well as in pangenomics, functional genomics, genome-assisted breeding and targeted genome manipulation. In conjunction with sequence-enriched germplasm repositories, T2T assemblies thus hold great promise for basic and applied plant sciences.

Deploying deep Solanaceae domestication and virus biotechnology knowledge to enhance food system performance and diversity

Our knowledge of crop domestication, genomics, and of the plant virosphere unevenly represents the taxonomic distribution of the global biodiversity, and, as we show here, is significantly enriched for the Solanaceae. Within the family, potato, tomato, eggplant, pepper, and over 100 lesser-known edible species play important nutrition and cultural roles in global and local food systems. Technologies using engineered viruses are transitioning from proof-of-concept applications in model plants to the precise trait breeding of Solanaceae crops. Leveraging this accumulated knowledge, we highlight the potential of virus-based biotechnologies for fast-track improvement of Solanaceae crop production systems, contributing to enhanced global and local human nutrition and food security.

Plant pangenomes for crop improvement, biodiversity and evolution

Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes - complete sequences of multiple individuals of a species or higher taxonomic unit - have now entered the geneticists' toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.