A near-complete assembly of an Arabidopsis thaliana genome

Analysis of the root mRNA interactome from canola and rice: Crop species that span the eudicot-monocot boundary

The advent of RNA interactome capture (RIC) has been important in characterizing the mRNA-binding proteomes (mRBPomes) of several eukaryotic taxa. To date, published plant poly(A)+ RIC studies have been restricted to Arabidopsis thaliana and specific to seedlings, suspension cell cultures, mesophyll protoplasts, leaves and embryos. The focus of this study was to expand RIC to root tissue in two crop species, the oilseed eudicot Brassica napus (canola) and the cereal monocot Oryza sativa (rice). The optimization and application of root RIC in these species resulted in the identification of 499 proteins and 334 proteins comprising the root mRBPomes of canola and rice, respectively, with 182 shared orthologous proteins between these two species. In both mRBPomes, approximately 80 % of captured proteins were linked to RNA biology, with RRM-containing proteins and ribosomal proteins among the most overrepresented protein groups. Consistent with trends observed in other RIC studies, novel RNA-binding proteins were captured that lacked known RNA-binding domains and included numerous metabolic enzymes. The root mRBPomes from canola and rice shared a high degree of similarity at the compositional level, as shown by a comparative analysis of orthologs predicted for captured proteins to the published Arabidopsis RIC-derived mRBPomes, as well as our Arabidopsis root mRBPome data presented here. This analysis also revealed that 46 proteins in the canola and rice root mRBPomes were unique when orthologs were compared to the published Arabidopsis RBPomes, including those identified recently using phase separation approach that identified proteins bound to all RNA types. The results from this research expands the plant mRBPome into root tissue using two crop species that span the eudicot-monocot clade boundary, and provides fundamental knowledge on RNA-binding protein function in post-transcriptional control of gene expression in crop species for possible future development of beneficial traits.

Mapping-based genome size estimation

While the size of chromosomes can be measured under a microscope, obtaining the exact size of a genome remains a challenge. Biochemical methods and k-mer distribution-based approaches allow only estimations. An alternative approach to estimate the genome size based on high contiguity assemblies and read mappings is presented here. Analyses of Arabidopsis thaliana and Beta vulgaris data sets are presented to show the impact of different parameters. Oryza sativa, Brachypodium distachyon, Solanum lycopersicum, Vitis vinifera, and Zea mays were also analyzed to demonstrate the broad applicability of this approach. Further, MGSE was also used to analyze Escherichia coli, Saccharomyces cerevisiae, and Caenorhabditis elegans datasets to show its utility beyond plants. Mapping-based Genome Size Estimation (MGSE) and additional scripts are available on GitHub: https://github.com/bpucker/MGSE . MGSE predicts genome sizes based on short reads or long reads requiring a minimal coverage of 5-fold.

Near-complete assembly and comprehensive annotation of the wheat Chinese Spring genome

A complete reference genome assembly is crucial for biological research and genetic improvement. Owing to its large size and highly repetitive nature, there are numerous gaps in the globally used wheat Chinese Spring (CS) genome assembly. In this study, we generated a 14.46 Gb near-complete assembly of the CS genome, with a contig N50 of over 266 Mb and an overall base accuracy of 99.9963%. Among the 290 gaps that remained (26, 257, and 7 gaps from the A, B, and D subgenomes, respectively), 278 were extremely high-copy tandem repeats, whereas the remaining 12 were transposable-element-associated gaps. Four chromosome assemblies were completely gap-free, including chr1D, chr3D, chr4D, and chr5D. Extensive annotation of the near-complete genome revealed 151 405 high-confidence genes, of which 59 180 were newly annotated, including 7602 newly assembled genes. Except for the centromere of chr1B, which has a gap associated with superlong GAA repeat arrays, the centromeric sequences of all of the remaining 20 chromosomes were completely assembled. Our near-complete assembly revealed that the extent of tandem repeats, such as simple-sequence repeats, was highly uneven among different subgenomes. Similarly, the repeat compositions of the centromeres also varied among the three subgenomes. With the genome sequences of all six types of seed storage proteins (SSPs) fully assembled, the expression of ω-gliadin was found to be contributed entirely by the B subgenome, whereas the expression of the other five types of SSPs was most abundant from the D subgenome. The near-complete CS genome will serve as a valuable resource for genomic and functional genomic research and breeding of wheat as well as its related species.

Assessment of bisulfite sequencing alignment tools for whole genome analysis in plants

DNA methylation, a key component of epigenetic regulation, is essential for preserving normal cellular functions, supporting plant growth, and facilitating development and responses to stress. Whole genome bisulfite sequencing (WGBS) is the definitive method for studying DNA methylation and is extensively used in functional genomics research across both animal and plant species. While various analysis tools have been created for WGBS, a thorough evaluation of their performance in analyzing plant data remains lacking. This study provides a comprehensive assessment of six widely used alignment methods (Abismal, Bismark-his2, BSSeeker2-bwt2-local, BSSeeker2-bwt2-e2e, Bismark-bwt2-e2e, and BSMAP) across four DNA methylation analysis tools. The evaluation encompassed aspects such as runtime efficiency, memory resource utilization, alignment quality, and identification of methylation sites by analyzing DNA methylation data from three major crops: Arabidopsis thaliana, Oryza sativa, and Glycine max. The results indicated that although BSMAP required larger memory requirements, it exhibited higher efficiency in terms of running speed, particularly when dealing with large-scale genomic data. Furthermore, BSMAP showed excellent performance in alignment quality and identification of methylated sites, ensuring the reliability and precision of the results. The study highlights the importance of researchers carefully selecting alignment tools and considering factors like available computational resources, specific research needs, and the balance between processing speed and memory usage. This work offers valuable analytical guidance for scientists engaged in DNA methylation studies plants, contributing to improved research efficiency and result reliability. 1 t holds significant scientific importance for a deeper analysis of DNA methylation in plant biology.

Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet

The Short Internodes-Related Sequence (SRS) family, a class of plant-specific transcription factors crucial for diverse biological processes, was systematically investigated in foxtail millet using pan-genome data from 110 core germplasm resources as well as two high-quality genomes (xm and Yu1). We identified SRS members and analyzed their intra-species distribution patterns, including copy number variation (CNV) and interchromosomal translocations. A novel standardized nomenclature (Accession_SiSRSN[.n]_xDy or xTy) was proposed to unify gene family nomenclature, enabling the direct visualization of member number variation across germplasms and the identification of core/variable members while highlighting chromosomal translocations. Focusing on the two high-quality genomes, both harboring six core SRS members, we performed whole-genome collinearity analysis with Arabidopsis, rice, maize, soybean, and green foxtail. Ka/Ks analysis of collinear gene pairs revealed purifying selection acting on SiSRS genes. Promoter analysis identified abundant stress-responsive cis-elements. Among core members, the xm_SiSRS5 gene exhibited the highest expression during vegetative growth but showed significant downregulation under drought and salt stress, suggesting its role as a key negative regulator in abiotic stress responses. This study demonstrates the utility of pan-genomics in resolving gene family dynamics and establishes SiSRS5 as a critical target for stress tolerance engineering in foxtail millet.

Telomere-to-telomere gapless genome assembly of Triplophysa yaopeizhii

The genus Triplophysa exhibits remarkable adaptability to the unique environment found at the Qinghai-Tibet Plateau (QTP). Higher quality genomes are helpful to the study of the adaptability to the extreme environment in the plateau. This study utilized PacBio HiFi, Ultra-long ONT, and Hi-C sequencing of Triplophysa yaopeizhii to construct the first telomere-to-telomere (T2T) gapless genome assembly of the genus Triplophysa. The genome size is 671.58 Mb, with a contig N50 length of 26.04 Mb. The sequences were anchored onto 25 chromosomes with all centromeres and telomeres. Furthermore, 293.98 Mb (43.77%) of repetitive sequences and 26,487 protein-coding genes were identified. Comparative analyses with the genomes of closely related species demonstrated high completeness, continuity, and accuracy of the genome. The genomic quality was further substantiated by the QV of 31.82 with 96.60% of BUSCO. This study provides a valuable genetic resource of the genus Triplophysa and serves as an essential reference for elucidating the adaptive genetic mechanisms of plateau fish to the high altitude.

Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development

The incorporation of histone variants, distinct paralogs of core histones, into chromatin affects all DNA-templated processes in the cell, including the regulation of transcription. In recent years, much research has been focused on H2A.Z, an evolutionarily conserved H2A variant found in all eukaryotes. In order to investigate the functional conservation of H2A.Z histones during eukaryotic evolution we transformed h2a.z deficient Arabidopsis thaliana plants with each of the three human H2A.Z variants to assess their ability to rescue the mutant defects. We discovered that human H2A.Z.1 and H2A.Z.2.1 fully complement the phenotypic abnormalities of h2a.z plants despite significant divergence in the N-terminal tail sequences of Arabidopsis and human H2A.Zs. In contrast, the brain-specific splice variant H2A.Z.2.2 has a dominant-negative effect in wild-type plants, mimicking an H2A.Z deficiency phenotype. Furthermore, human H2A.Z.1 almost completely re-establishes normal H2A.Z chromatin occupancy in h2a.z plants and restores the expression of more than 84% of misexpressed genes. Finally, we used a series of N-terminal tail truncations of Arabidopsis HTA11 to reveal that the N-terminal tail of Arabidopsis H2A.Z is not necessary for normal plant development under optimal growth conditions but does play an important role in mounting proper abiotic stress responses.

Two CENH3 paralogs in the green alga Chlamydomonas reinhardtii have a redundantly essential function and associate with ZeppL-LINE1 elements

Centromeres in eukaryotes are defined by the presence of histone H3 variant CENP-A/CENH3. Chlamydomonas encodes two predicted CENH3 paralogs, CENH3.1 and CENH3.2, that have not been previously characterized. We generated peptide antibodies to unique N-terminal epitopes for each of the two predicted Chlamydomonas CENH3 paralogs as well as an antibody against a shared CENH3 epitope. All three CENH3 antibodies recognized proteins of the expected size on immunoblots and had punctate nuclear immunofluorescence staining patterns. These results are consistent with both paralogs being expressed and localized to centromeres. CRISPR-Cas9-mediated insertional mutagenesis was used to generate predicted null mutations in either CENH3.1 or CENH3.2. Single mutants were viable but cenh3.1 cenh3.2 double mutants were not recovered, confirming that the function of CENH3 is essential. We sequenced and assembled two chromosome-scale Chlamydomonas genomes from strains CC-400 and UL-1690 (a derivative of CC-1690) with complete centromere sequences for 17/17 and 14/17 chromosomes respectively, enabling us to compare centromere evolution across four isolates with near complete assemblies. These data revealed significant changes across isolates between homologous centromeres including mobility and degeneration of ZeppL-LINE1 (ZeppL) transposons that comprise the major centromere repeat sequence in Chlamydomonas. We used cleavage under targets and tagmentation (CUT&Tag) to purify and map CENH3-bound genomic sequences and found enrichment of CENH3-binding almost exclusively at predicted centromere regions. An interesting exception was chromosome 2 in UL-1690, which had enrichment at its genetically mapped centromere repeat region as well as a second, distal location, centered around a single recently acquired ZeppL insertion. The CENH3-bound regions of the 17 Chlamydomonas centromeres ranged from 63.5 kb (average lower estimate) to 175 kb (average upper estimate). The relatively small size of its centromeres suggests that Chlamydomonas may be a useful organism for testing and deploying artificial chromosome technologies.

A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat

The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays and 5,611 rDNA units. Genome-wide rearrangements, centromeric elements, transposable element expansion and segmental duplications were deciphered during tetraploidization and hexaploidization, providing a comprehensive understanding of wheat subgenome evolution. Among them, transposable element insertions during hexaploidization greatly influenced gene expression balances, thus increasing the genome plasticity of transcriptional levels. Additionally, we generated 163,329 full-length cDNA sequences and proteomic data that helped annotate 141,035 high-confidence protein-coding genes. The complete T2T reference genome (CS-IAAS), along with its transcriptome and proteome, represents a significant step in our understanding of wheat genome complexity and provides insights for future wheat research and breeding.

Third generation sequencing transforming plant genome research: Current trends and challenges

In recent years, third-generation sequencing (TGS) technologies have transformed genomics and transcriptomics research, providing novel opportunities for significant discoveries. The long-read sequencing platforms, with their unique advantages over next-generation sequencing (NGS), including a definitive protocol, reduced operational time, and real-time sequencing, possess the potential to transform plant genomics. TGS optimizes and enhances the efficiency of data analysis by removing the necessity for time-consuming assembly tools. The current review examines the development and application of bioinformatics tools for data analysis and annotation, driven by the rapid advancement of TGS platforms like Oxford Nanopore Technologies and Pacific Biosciences. Transcriptome analysis utilizing TGS has been extensively employed to elucidate complex plant transcriptomes and genomes, particularly those characterized by high frequencies of duplicated genomes and repetitive sequences. As a result, current methodologies that allow for generating transcriptomes and comprehensive whole-genome sequences of complex plant genomes employing tailored hybrid sequencing techniques that integrate NGS and TGS technologies have been emphasized herein. This paper, thus, articulates a vision for a future in which TGS effectively addresses the challenges faced in plant research, offering a comprehensive understanding of its advantages, applications, limitations, and promising prospects.

Genome-wide analysis of GRAS gene family and functional identification of a putative development and maintenance of axillary meristematic tissue gene PlGRAS22 in Paeonia ludlowii

The GRAS gene family, is instrumental in a myriad of biological processes, including plant growth and development. Our findings revealed that Paeonia ludlowii (Stern & G.Taylor) D.Y.Hong) harbored 45 PlGRAS genes, which are categorized into eight subfamilies. These genes are distributed across chromosomes 1 through 5, with their encoded proteins exhibiting variation in physicochemical properties. The promoter regions of the Paeonia ludlowii GRAS genes are enriched with cis-acting elements associated with growth and development, hormonal responses, and light signaling, among others. Among these genes, we have pinpointed PlGRAS22, which bears the closest resemblance to the AtLAS gene in Arabidopsis. Notably, this gene exhibits heightened expression levels within the LAS subfamily across a range of tissues, and it demonstrates an exceptionally robust response to treatments with exogenous gibberellins and cytokinins. The subdued expression of TRV2-PlGRAS22 within the flower buds of the Paeonia ludlowii has resulted in a diminished development of axillary bud primordia. Intriguingly, overexpression of PlGRAS22 in Arabidopsis led to an increase in the number of branches, highlighting its potential role in developmental processes. Furthermore, through the use of luciferase and yeast one-hybrid assays, we have demonstrated that PlGRAS22 interacts with the SPL transcription factor PlSPL3. The comprehensive analysis presented in this study lays a solid foundation for future investigations into the functional roles of Paeonia ludlowii GRAS genes and elucidates the underlying mechanisms governing growth and development in this species.

Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4)

BACKGROUND

Common bean is a significant grain legume in human diets. However, the lack of a complete reference genome for common beans has hindered efforts to improve agronomic cultivars.

FINDINGS

Herein, we present the first telomere-to-telomere (T2T) genome assembly of common bean (Phaseolus vulgaris L., YP4) using PacBio High-Fidelity reads, ONT ultra-long sequencing, and Hi-C technologies. The assembly resulted in a genome size of 560.30 Mb with an N50 of 55.11 Mb, exhibiting high completeness and accuracy (BUSCO score: 99.5%, quality value (QV): 54.86). The sequences were anchored into 11 chromosomes, with 20 of 22 telomeres identified, leading to the formation of 9 T2T pseudomolecules. Furthermore, we identified repetitive elements accounting for 61.20% of the genome and predicted 29,925 protein-coding genes. Phylogenetic analysis suggested an estimated divergence time of approximately 11.6 million years ago between P. vulgaris and Vigna angularis. Comparative genome analysis revealed the expanded gene families and variations between YP4 and G19833 associated with defense response.

CONCLUSIONS

The T2T reference genome and genomic insights presented here are crucial for future genetic studies not only in common bean but also in other legumes.

The evolutionarily diverged single-stranded DNA-binding proteins SSB1/SSB2 differentially affect the replication, recombination and mutation of organellar genomes in Arabidopsis thaliana

Single-stranded DNA-binding proteins (SSBs) play essential roles in the replication, recombination and repair processes of organellar DNA molecules. In Arabidopsis thaliana, SSBs are encoded by a small family of two genes (SSB1 and SSB2). However, the functional divergence of these two SSB copies in plants remains largely unknown, and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete. In this study, phylogenetic, gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants. Based on accurate long-read sequencing results, ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA (mtDNA) and plastid DNA (ptDNA), accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes. Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.

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.

Genome-wide identification and characterization of the LRX gene family in grapevine (Vitis vinifera L.) and functional characterization of VvLRX7 in plant salt response

BACKGROUND

Leucine-rich repeat (LRR) extensins (LRXs), which are cell wall-localized chimeric extensin proteins, are essential for the development of plants and their resistance to stress. Despite the significance of these genes, an extensive genome-wide analysis of the LRX gene family in grapevine (Vitis vinifera L.) is lacking.

RESULTS

We here detected 14 grapevine LRX genes and classified them into four groups through phylogenetic analysis. Then, their physiological and biochemical properties and gene/protein structures were analyzed. According to synteny analysis, tandem and segmental duplications have appreciably affected the expansion of the grapevine LRX gene family. On investigating tissue-specific expression profiles and cis-regulatory elements, we observed that VvLRXs likely serve as regulators of both the growth of grapevines and their responses to various environmental stresses. Salt stress treatments induced the expression of several VvLRXs, and VvLRX7 expression was the most significantly upregulated. Furthermore, VvLRX7 expression was positively correlated with the salt tolerance of grape rootstocks. VvLRX7 overexpression in Arabidopsis markedly enhanced its salt tolerance.

CONCLUSION

This study provides a general understanding of the characteristics and evolution of the LRX gene family in grapevine. VvLRX7 may function as a positive regulator of plant's response to salt stress. These findings offer a basis for future studies on the function of grapevine LRXs and their role in improving salt stress tolerance in grapevine.

Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits

A complete goat (Capra hircus) reference genome enhances analyses of genetic variation, thus providing insights into domestication and selection in goats and related species. Here, we assemble a telomere-to-telomere (T2T) gap-free genome (2.86 Gb) from a cashmere goat (T2T-goat1.0), including a Y chromosome of 20.96 Mb. With a base accuracy of >99.999%, T2T-goat1.0 corrects numerous genome-wide structural and base errors in previous assemblies and adds 288.5 Mb of previously unresolved regions and 446 newly assembled genes to the reference genome. We sequence the genomes of five representative goat breeds for PacBio reads, and use T2T-goat1.0 as a reference to identify a total of 63,417 structural variations (SVs) with up to 4711 (7.42%) in the previously unresolved regions. T2T-goat1.0 was applied in population analyses of global wild and domestic goats, which revealed 32,419 SVs and 25,397,794 SNPs, including 870 SVs and 545,026 SNPs in the previously unresolved regions. Also, our analyses reveal a set of selective variants and genes associated with domestication (e.g., NKG2D and ABCC4) and cashmere traits (e.g., ABCC4 and ASIP).

Systematic Survey and Analysis Reveal Jasmonate ZIM-Domain Gene Family in Coix lacryma-jobi Under High Temperature

Jasmonate ZIM-domain (JAZ) acts as the repressor of the JA signaling pathway and plays a significant role in stress-inducible defense, hormone crosstalk, and the regulation of the growth-defense tradeoff. The aim of this study is to systematically survey and analyze the JAZ gene family in Coix lacryma-jobi and unveil its expression profiles in diverse organs under high-temperature stress using transcriptome. The results identified a total of 20 JAZ family proteins randomly mapped on four chromosomes and encoding 159-409 amino acids. They were clustered into six groups and were mainly located in the nucleus. The conserved motifs, gene composition, and secondary structure of ClJAZ members within the same subtribes were similar. Multitudinous cis-regulating elements employed in hormone responsiveness and stress responsiveness were displayed before the promoter sequences of ClJAZ1-ClJAZ20. ClJAZ1-ClJAZ20 were differentially distributed across diverse organs (the roots, shoots, leaves, kernels, glumes, and flowers), exposed to high-temperature stresses, and treated using ABA or MeJA. A total of 29115 DEGs were identified under heat stress, which were mainly involved in biological regulation and the metabolic process. Intriguingly, ClJAZ15 was highly expressed in the leaves of C. lacryma-jobi, down-regulated by MeJA, but up-regulated by heat stress and ABA, inferring that ClJAZ15 might be associated with ABA-inducible heat stress. The results laid a foundation for in-depth study of the role of ClJAZ family genes in C. lacryma-jobi.

Nanopore ultra-long sequencing and adaptive sampling spur plant complete telomere-to-telomere genome assembly

The pursuit of complete telomere-to-telomere (T2T) genome assembly in plants, challenged by genomic complexity, has been advanced by Oxford Nanopore Technologies (ONT), which offers ultra-long, real-time sequencing. Despite its promise, sequencing length and gap filling remain significant challenges. This study optimized DNA extraction and library preparation, achieving DNA lengths exceeding 485 kb; average N50 read lengths of 80.57 kb, reaching up to 440 kb; and maximum reads of 5.83 Mb. Importantly, we demonstrated that combining ultra-long sequencing and adaptive sampling can effectively fill gaps during assembly, evidenced by successfully filling the remaining gaps of a near-complete Arabidopsis genome assembly and resolving the sequence of an unknown telomeric region in watermelon genome. Collectively, our strategies improve the feasibility of complete T2T genomic assemblies across various plant species, enhancing genome-based research in diverse fields.

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.

Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits

Hybrid crops often exhibit increased yield and greater resilience, yet the genomic mechanism(s) underlying hybrid vigor or heterosis remain unclear, hindering our ability to predict the expression of phenotypic traits in hybrid breeding. Here, we generated haplotype-resolved T2T genome assemblies of two pear hybrid varieties, 'Yuluxiang' (YLX) and 'Hongxiangsu' (HXS), which share the same maternal parent but differ in their paternal parents. We then used these assemblies to explore the genome-scale landscape of allele-specific expression (ASE) and create a pangenome graph for pear. ASE was observed for close to 6000 genes in both hybrid cultivars. A subset of ASE genes related to aspects of fruit quality such as sugars, organic acids, and cuticular wax were identified, suggesting their important contributions to heterosis. Specifically, Ma1, a gene regulating fruit acidity, is absent in the paternal haplotypes of HXS and YLX. A pangenome graph was built based on our assemblies and seven published pear genomes. Resequencing data for 139 cultivated pear genotypes (including 97 genotypes sequenced here) were subsequently aligned to the pangenome graph, revealing numerous structural variant hotspots and selective sweeps during pear diversification. As predicted, the Ma1 allele was found to be absent in varieties with low organic acid content, and this association was functionally validated by Ma1 overexpression in pear fruit and calli. Overall, these results reveal the contributions of ASE to fruit-quality heterosis and provide a robust pangenome reference for high-resolution allele discovery and association mapping.

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.

Chromosome-Scale Assembly and Annotation of Eight Arabidopsis thaliana Ecotypes

The plant Arabidopsis thaliana is a model system used by researchers through much of plant research. Recent efforts have focused on discovering the genomic variation found in naturally occurring ecotypes isolated from around the world. These ecotypes have come from diverse climates and therefore have faced and adapted to a variety of abiotic and biotic stressors. The sequencing and comparative analysis of these genomes can offer insight into the adaptive strategies of plants. While there are a large number of ecotype genome sequences available, the majority were created using short-read technology. Mapping of short-reads containing structural variation to a reference genome bereft of that variation leads to incorrect mapping of those reads, resulting in a loss of genetic information and introduction of false heterozygosity. For this reason, long-read de novo sequencing of genomes is required to resolve structural variation events. In this article, we sequenced the genomes of eight natural variants of A. thaliana using nanopore sequencing. This resulted in highly contiguous assemblies with >95% of the genome contained within five contigs. The sequencing results from this study include five ecotypes from relict and African populations, an area of untapped genetic diversity. With this study, we increase the knowledge of diversity we have across A. thaliana ecotypes and contribute to ongoing production of an A. thaliana pan-genome.

Telomere-to-telomere genome assembly of sorghum

"Cuohu Bazi" (CHBZ) is an ancient sorghum variety collected from the fields of China, known for its agronomic traits like dwarf stature, early maturation. In this study, we present the first telomere-to-telomere (T2T) and gap-free genome assembly of CHBZ using PacBio HiFi reads, Oxford Nanopore Technologies, and Hi-C data. The assembled genome comprises 724.85 Mb, effectively resolving all 3,913 gaps that were present in the previous sorghum BTx623 reference genome. Notably, the T2T assembly captures 10 centromeres and all 20 telomeres, providing strong support for their integrity. This assembly is of high quality in terms of contiguity (contig N50: 71.1 Mb), completeness (BUSCO score: 99.01%, k-mer completeness: 98.88%), and correctness (QV: 61.60). Repetitive sequences accounted for 70.41% of the genome and a total of 32,855 protein-coding genes have been annotated. Furthermore, 161 CHBZ-specific presence/absence variants genes have been identified when comparing to BTx623 genome. This study provides valuable insights for future research on sorghum genetics, genomics, and evolutionary history.

Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development

The incorporation of histone variants, distinct paralogs of core histones, into chromatin affects all DNA-templated processes in the cell, including the regulation of transcription. In recent years, much research has been focused on H2A.Z, an evolutionarily conserved H2A variant found in all eukaryotes. In order to investigate the functional conservation of H2A.Z histones during eukaryotic evolution we transformed h2a.z deficient plants with each of the three human H2A.Z variants to assess their ability to rescue the mutant defects. We discovered that human H2A.Z.1 and H2A.Z.2.1 fully complement the phenotypic abnormalities of h2a.z plants despite significant divergence in the N-terminal tail sequences of Arabidopsis and human H2A.Zs. In contrast, the brain-specific splice variant H2A.Z.2.2 has a dominant-negative effect in wild-type plants, mimicking an H2A.Z deficiency phenotype. Furthermore, H2A.Z.1 almost completely re-establishes normal H2A.Z chromatin occupancy in h2a.z plants and restores the expression of more than 84% of misexpressed genes. Finally, we used a series of N-terminal tail truncations of Arabidopsis HTA11 to reveal that the N-terminal tail of Arabidopsis H2A.Z is not necessary for normal plant development but does play an important role in mounting proper environmental stress responses.

Intraspecific diploidization of a halophyte root fungus drives heterosis

How organisms respond to environmental stress is a key topic in evolutionary biology. This study focused on the genomic evolution of Laburnicola rhizohalophila, a dark-septate endophytic fungus from roots of a halophyte. Chromosome-level assemblies were generated from five representative isolates from structured subpopulations. The data revealed significant genomic plasticity resulting from chromosomal polymorphisms created by fusion and fission events, known as dysploidy. Analyses of genomic features, phylogenomics, and macrosynteny have provided clear evidence for the origin of intraspecific diploid-like hybrids. Notably, one diploid phenotype stood out as an outlier and exhibited a conditional fitness advantage when exposed to a range of abiotic stresses compared with its parents. By comparing the gene expression patterns in each hybrid parent triad under the four growth conditions, the mechanisms underlying growth vigor were corroborated through an analysis of transgressively upregulated genes enriched in membrane glycerolipid biosynthesis and transmembrane transporter activity. In vitro assays suggested increased membrane integrity and lipid accumulation, as well as decreased malondialdehyde production under optimal salt conditions (0.3 M NaCl) in the hybrid. These attributes have been implicated in salinity tolerance. This study supports the notion that hybridization-induced genome doubling leads to the emergence of phenotypic innovations in an extremophilic endophyte.

A telomere-to-telomere gap-free reference genome assembly of avocado provides useful resources for identifying genes related to fatty acid biosynthesis and disease resistance

Avocado (Persea americana Mill.) is an economically valuable plant because of the high fatty acid content and unique flavor of its fruits. Its fatty acid content, especially the relatively high unsaturated fatty acid content, provides significant health benefits. We herein present a telomere-to-telomere gapless genome assembly (841.6 Mb) of West Indian avocado. The genome contains 40 629 predicted protein-coding genes. Repeat sequences account for 57.9% of the genome. Notably, all telomeres, centromeres, and a nucleolar organizing region are included in this genome. Fragments from these three regions were observed via fluorescence in situ hybridization. We identified 376 potential disease resistance-related nucleotide-binding leucine-rich repeat genes. These genes, which are typically clustered on chromosomes, may be derived from gene duplication events. Five NLR genes (Pa11g0262, Pa02g4855, Pa07g3139, Pa07g0383, and Pa02g3196) were highly expressed in leaves, stems, and fruits, indicating they may be involved in avocado disease responses in multiple tissues. We also identified 128 genes associated with fatty acid biosynthesis and analyzed their expression patterns in leaves, stems, and fruits. Pa02g0113, which encodes one of 11 stearoyl-acyl carrier protein desaturases mediating C18 unsaturated fatty acid synthesis, was more highly expressed in the leaves than in the stems and fruits. These findings provide valuable insights that enhance our understanding of fatty acid biosynthesis in avocado.

Characterization of the CsCENH3 protein and centromeric DNA profiles reveal the structures of centromeres in cucumber

Centromeres in eukaryotes mediate the accurate segregation of chromosomes during cell division. They serve as essential functional units of chromosomes and play a core role in the process of genome evolution. Centromeres are composed of satellite repeats and highly repetitive centromeric retrotransposons (CRs), which vary greatly even among closely related species. Cucumber (Cucumis sativus) is a globally cultivated and economically important vegetable and the only species in the Cucumis genus with seven pairs of chromosomes. Therefore, studying the centromeres of the Cucumis subgenus may yield valuable insights into its genome structure and evolution. Using chromatin immunoprecipitation (ChIP) techniques, we isolated centromeric DNA from cucumber reference line 9930. Our investigation into cucumber centromeres uncovered the centromeric satellite sequence, designated as CentCs, and the prevalence of Ty1/Copia long terminal repeat retrotransposons. In addition, active genes were identified in the CsCENH3 nucleosome regions with low transcription levels. To the best of our knowledge, this is the first time that characterization of centromeres has been achieved in cucumber. Meanwhile, our results on the distribution of CentCs and CsCRs in the subgenus Cucumis indicate that the content of centromeric repeats in the wild variants was significantly reduced compared with the cultivated cucumber. The results provide evidence for centromeric DNA amplification that occurred during the domestication process from wild to cultivated cucumber. Furthermore, these findings may offer new information for enhancing our understanding of phylogenetic relationships in the Cucumis genus.

A complete reference genome of broomcorn millet

Broomcorn millet (Panicum miliaceum L.), known for its traits of drought resistance, adaptability to poor soil, short growth period, and high photosynthetic efficiency as a C4 plant, represents one of the earliest domesticated crops globally. This study reports the telomere-to-telomere (T2T) gap-free reference genome for broomcorn millet (AJ8) using PacBio high-fidelity (HiFi) long reads, Oxford Nanopore long-read technologies and high-throughput chromosome conformation capture (Hi-C) sequencing data. The size of AJ8 genome was approximately 834.7 Mb, anchored onto 18 pseudo-chromosomes. Notably, 18 centromeres and 36 telomeres were obtained. The assembled genome showed high quality in terms of completeness (BUSCO score: 99.6%, QV: 61.7, LAI value: 20.4). In addition, 63,678 protein-coding genes and 433.8 Mb (~52.0%) repetitive sequences were identified. The complete reference genome for broomcorn millet provides a valuable resource for genetic studies and breeding of this important cereal crop.

Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis

Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of their tissue specificity remain obscure due to the lack of high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes of C. annuum and its wild nonpungent relative C. rhomboideum to investigate the evolution of fruit pungency in chili peppers. We precisely delineate Capsicum centromeres, which lack high-copy tandem repeats but are extensively invaded by CRM retrotransposons. Through phylogenomic analyses, we estimate the evolutionary timing of capsaicinoid biosynthesis. We reveal disrupted coding and regulatory regions of key biosynthesis genes in nonpungent species. We also find conserved placenta-specific accessible chromatin regions, which likely allow for tissue-specific biosynthetic gene coregulation and capsaicinoid accumulation. These T2T genomic resources will accelerate chili pepper genetic improvement and help to understand Capsicum genome evolution.

NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads

The high-fidelity (HiFi) long-read sequencing technology developed by PacBio has greatly improved the base-level accuracy of genome assemblies. However, these assemblies still contain base-level errors, particularly within the error-prone regions of HiFi long reads. Existing genome polishing tools usually introduce overcorrections and haplotype switch errors when correcting errors in genomes assembled from HiFi long reads. Here, we describe an upgraded genome polishing tool - NextPolish2, which can fix base errors remaining in those "highly accurate" genomes assembled from HiFi long reads without introducing excessive overcorrections and haplotype switch errors. We believe that NextPolish2 has a great significance to further improve the accuracy of telomere-to-telomere (T2T) genomes. NextPolish2 is freely available at https://github.com/Nextomics/NextPolish2.

A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range

Although originally primarily a system for functional biology, Arabidopsis thaliana has, owing to its broad geographical distribution and adaptation to diverse environments, developed into a powerful model in population genomics. Here we present chromosome-level genome assemblies of 69 accessions from a global species range. We found that genomic colinearity is very conserved, even among geographically and genetically distant accessions. Along chromosome arms, megabase-scale rearrangements are rare and typically present only in a single accession. This indicates that the karyotype is quasi-fixed and that rearrangements in chromosome arms are counter-selected. Centromeric regions display higher structural dynamics, and divergences in core centromeres account for most of the genome size variations. Pan-genome analyses uncovered 32,986 distinct gene families, 60% being present in all accessions and 40% appearing to be dispensable, including 18% private to a single accession, indicating unexplored genic diversity. These 69 new Arabidopsis thaliana genome assemblies will empower future genetic research.

Technology-enabled great leap in deciphering plant genomes

Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021-2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.

High-quality Gossypium hirsutum and Gossypium barbadense genome assemblies reveal the landscape and evolution of centromeres

Centromere positioning and organization are crucial for genome evolution; however, research on centromere biology is largely influenced by the quality of available genome assemblies. Here, we combined Oxford Nanopore and Pacific Biosciences technologies to de novo assemble two high-quality reference genomes for Gossypium hirsutum (TM-1) and Gossypium barbadense (3-79). Compared with previously published reference genomes, our assemblies show substantial improvements, with the contig N50 improved by 4.6-fold and 5.6-fold, respectively, and thus represent the most complete cotton genomes to date. These high-quality reference genomes enable us to characterize 14 and 5 complete centromeric regions for G. hirsutum and G. barbadense, respectively. Our data revealed that the centromeres of allotetraploid cotton are occupied by members of the centromeric repeat for maize (CRM) and Tekay long terminal repeat families, and the CRM family reshapes the centromere structure of the At subgenome after polyploidization. These two intertwined families have driven the convergent evolution of centromeres between the two subgenomes, ensuring centromere function and genome stability. In addition, the repositioning and high sequence divergence of centromeres between G. hirsutum and G. barbadense have contributed to speciation and centromere diversity. This study sheds light on centromere evolution in a significant crop and provides an alternative approach for exploring the evolution of polyploid plants.

Telomere-to-telomere gapless genome assembly of the Chinese sea bass (Lateolabrax maculatus)

Chinese sea bass (Lateolabrax maculatus) is a highly sought-after commercial seafood species in Asian regions due to its excellent nutritional value. With the rapid advancement of bioinformatics, higher standards for genome analysis compared to previously published reference genomes are now necessary. This study presents a gapless assembly of the Chinese sea bass genome, which has a length of 632.75 Mb. The sequences were assembled onto 24 chromosomes with a coverage of over 99% (626.61 Mb), and telomeres were detected on 34 chromosome ends. Analysis using Merqury indicated a high level of accuracy, with an average consensus quality value of 54.25. The ONT ultralong and PacBio HiFi data were aligned with the assembly using minimap2, resulting in a mapping rate of 99.9%. The study also identified repeating elements in 20.90% (132.25 Mb) of the genome and inferred 22,014 protein-coding genes. These results establish meaningful groundwork for exploring the evolution of the Chinese sea bass genome and advancing molecular breeding techniques.

Genome-wide identification of the GRF family in sweet orange (Citrus sinensis) and functional analysis of the CsGRF04 in response to multiple abiotic stresses

BACKGROUND

Citrus is one of the most valuable fruits worldwide and an economic pillar industry in southern China. Nevertheless, it frequently suffers from undesirable environmental stresses during the growth cycle, which severely restricts the growth, development and yield of citrus. In plants, the growth-regulating factor (GRF) family of transcription factors (TF) is extensively distributed and plays an vital part in plant growth and development, hormone response, as well as stress adaptation. However, the systematic identification and functional analysis of GRF TFs in citrus have not been reported.

RESULTS

Here, a genome-wide identification of GRF TFs was performed in Citrus sinensis, 9 members of CsGRFs were systematically identified and discovered to be scattered throughout 5 chromosomes. Subsequently, physical and chemical properties, phylogenetic relationships, structural characteristics, gene duplication events, collinearity and cis-elements of promoter were elaborately analyzed. In particular, the expression patterns of the CsGRF genes in response to multiple phytohormone and abiotic stress treatments were investigated. Predicated on this result, CsGRF04, which exhibited the most differential expression pattern under multiple phytohormone and abiotic stress treatments was screened out. Virus-induced gene silencing (VIGS) technology was utilized to obtain gene silenced plants for CsGRF04 successfully. After the three stress treatments of high salinity, low temperature and drought, the CsGRF04-VIGS lines showed significantly reduced resistance to high salinity and low temperature stresses, but extremely increased resistance to drought stress.

CONCLUSIONS

Taken together, our findings systematically analyzed the genomic characterization of GRF family in Citrus sinensis, and excavated a CsGRF04 with potential functions under multiple abiotic stresses. Our study lay a foundation for further study on the function of CsGRFs in abiotic stress and hormone signaling response.

Sequence and epigenetic landscapes of active and silent nucleolus organizer regions in Arabidopsis

Arabidopsis thaliana has two ribosomal RNA (rRNA) gene loci, nucleolus organizer regions NOR2 and NOR4, whose complete sequences are missing in current genome assemblies. Ultralong DNA sequences assembled using an unconventional approach yielded ~5.5- and 3.9-Mbp sequences for NOR2 and NOR4 in the reference strain, Col-0. The distinct rRNA gene subtype compositions of the NORs enabled the positional mapping of their active and inactive regions, using RNA sequencing to identify subtype-specific transcripts and DNA sequencing to identify subtypes associated with flow-sorted nucleoli. Comparisons of wild-type and silencing-defective plants revealed that most rRNA gene activity occurs in the central region of NOR4, whereas most, but not all, genes of NOR2 are epigenetically silenced. Intervals of low CG and CHG methylation overlap regions where gene activity and gene subtype homogenization are high. Collectively, the data reveal the genetic and epigenetic landscapes underlying nucleolar dominance (differential NOR activity) and implicate transcription as a driver of rRNA gene concerted evolution.

The telomere-to-telomere gap-free reference genome of wild blueberry (Vaccinium duclouxii) provides its high soluble sugar and anthocyanin accumulation

Vaccinium duclouxii, endemic to southwestern China, is a berry-producing shrub or small tree belonging to the Ericaceae family, with high nutritive, medicinal, and ornamental value, abundant germplasm resources, and good edible properties. In addition, V. duclouxii exhibits strong tolerance to adverse environmental conditions, making it a promising candidate for research and offering wide-ranging possibilities for utilization. However, the lack of V. duclouxii genome sequence has hampered its development and utilization. Here, a high-quality telomere-to-telomere genome sequence of V. duclouxii was de novo assembled and annotated. All of 12 chromosomes were assembled into gap-free single contigs, providing the highest integrity and quality assembly reported so far for blueberry. The V. duclouxii genome is 573.67 Mb, which encodes 41 953 protein-coding genes. Combining transcriptomics and metabolomics analyses, we have uncovered the molecular mechanisms involved in sugar and acid accumulation and anthocyanin biosynthesis in V. duclouxii. This provides essential molecular information for further research on the quality of V. duclouxii. Moreover, the high-quality telomere-to-telomere assembly of the V. duclouxii genome will provide insights into the genomic evolution of Vaccinium and support advancements in blueberry genetics and molecular breeding.

Improving the Completeness of Chromosome-Level Assembly by Recalling Sequences from Lost Contigs

For a long time, the construction of complete reference genomes for complex eukaryotic genomes has been hindered by the limitations of sequencing technologies. Recently, the Pacific Biosciences (PacBio) HiFi data and Oxford Nanopore Technologies (ONT) Ultra-Long data, leveraging their respective advantages in accuracy and length, have provided an opportunity for generating complete chromosome sequences. Nevertheless, for the majority of genomes, the chromosome-level assemblies generated using existing methods still miss a high proportion of sequences due to losing small contigs in the step of assembly and scaffolding. To address this shortcoming, in this paper, we propose a novel method that is able to identify and fill the gaps in the chromosome-level assembly by recalling the sequences in the lost small contigs. Experimental results on both real and simulated datasets demonstrate that this method is able to improve the completeness of the chromosome-level assembly.

Plant biology: Phylogenomics of mustards and their relatives

A new nuclear phylogeny for the large family Brassicaceae opens the way for advanced comparative studies of adaptation, development, coevolution, hybridization, and diversification in this crucial group, which is the source for many of the genomic resources now used across the flowering plants.

The pan-genome and local adaptation of Arabidopsis thaliana

Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation. We develop a graph-based pan-genome and identify 61,332 SVs that overlap with 18,883 genes, some of which are highly involved in ecological adaptation of this species. For instance, we observe a specific 332 bp insertion in the promoter region of the HPCA1 gene in the Tibet-0 ecotype that enhances gene expression, thereby promotes adaptation to alpine environments. These findings augment our understanding of the molecular mechanisms underlying the local adaptation of A. thaliana across diverse habitats.

Single-molecule targeted accessibility and methylation sequencing of centromeres, telomeres and rDNAs in Arabidopsis

The short read-length of next-generation sequencing makes it challenging to characterize highly repetitive regions (HRRs) such as centromeres, telomeres and ribosomal DNAs. Based on recent strategies that combined long-read sequencing and exogenous enzymatic labelling of open chromatin, we developed single-molecule targeted accessibility and methylation sequencing (STAM-seq) in plants by further integrating nanopore adaptive sampling to investigate the HRRs in wild-type Arabidopsis and DNA methylation mutants that are defective in CG- or non-CG methylation. We found that CEN180 repeats show higher chromatin accessibility and lower DNA methylation on their forward strand, individual rDNA units show a negative correlation between their DNA methylation and accessibility, and both accessibility and CHH methylation levels are lower at telomere compared to adjacent subtelomeric region. Moreover, DNA methylation-deficient mutants showed increased chromatin accessibility at HRRs, consistent with the role of DNA methylation in maintaining heterochromatic status in plants. STAM-seq can be applied to study accessibility and methylation of repetitive sequences across diverse plant species.

The gap-free genome of mulberry elucidates the architecture and evolution of polycentric chromosomes

Mulberry is a fundamental component of the global sericulture industry, and its positive impact on our health and the environment cannot be overstated. However, the mulberry reference genomes reported previously remained unassembled or unplaced sequences. Here, we report the assembly and analysis of the telomere-to-telomere gap-free reference genome of the mulberry species, Morus notabilis, which has emerged as an important reference in mulberry gene function research and genetic improvement. The mulberry gap-free reference genome produced here provides an unprecedented opportunity for us to study the structure and function of centromeres. Our results revealed that all mulberry centromeric regions share conserved centromeric satellite repeats with different copies. Strikingly, we found that M. notabilis is a species with polycentric chromosomes and the only reported polycentric chromosome species up to now. We propose a compelling model that explains the formation mechanism of new centromeres and addresses the unsolved scientific question of the chromosome fusion-fission cycle in mulberry species. Our study sheds light on the functional genomics, chromosome evolution, and genetic improvement of mulberry species.

Gap-free genome assembly of anadromous Coilia nasus

The Chinese tapertail anchovy, Coilia nasus, is a socioeconomically important anadromous fish that migrates from near ocean waters to freshwater to spawn every spring. The analysis of genomic architecture and information of C. nasus were hindered by the previously released versions of reference genomes with gaps. Here, we report the assembly of a chromosome-level gap-free genome of C. nasus by incorporating high-coverage and accurate long-read sequence data with multiple assembly strategies. All 24 chromosomes were assembled without gaps, representing the highest completeness and assembly quality. We assembled the genome with a size of 851.67 Mb and used BUSCO to estimate the completeness of the assembly as 92.5%. Using a combination of de novo prediction, protein homology and RNA-seq annotation, 21,900 genes were functionally annotated, representing 99.68% of the total predicted protein-coding genes. The availability of gap-free reference genomes for C. nasus will provide the opportunity for understanding genome structure and function, and will also lay a solid foundation for further management and conservation of this important species.

Recent Advances in Assembly of Complex Plant Genomes

Over the past 20 years, tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already, ranging from those of nonvascular plants to those of flowering plants. However, complex plant genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity, highly repetitive sequences, or high ploidy characteristics of complex genomes. Herein, we summarize the challenges of and advances in complex plant genome assembly, including feasible experimental strategies, upgrades to sequencing technology, existing assembly methods, and different phasing algorithms. Moreover, we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes. Finally, we expect that the accurate, gapless, telomere-to-telomere, and fully phased assembly of complex plant genomes could soon become routine.

A near-complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres

Brassica rapa comprises many important cultivated vegetables and oil crops. However, Chiifu v3.0, the current B. rapa reference genome, still contains hundreds of gaps. Here, we presented a near-complete genome assembly of B. rapa Chiifu v4.0, which was 424.59 Mb with only two gaps, using Oxford Nanopore Technology (ONT) ultralong-read sequencing and Hi-C technologies. The new assembly contains 12 contigs, with a contig N50 of 38.26 Mb. Eight of the ten chromosomes were entirely reconstructed in a single contig from telomere to telomere. We found that the centromeres were mainly invaded by ALE and CRM long terminal repeats (LTRs). Moreover, there is a high divergence of centromere length and sequence among B. rapa genomes. We further found that centromeres are enriched for Copia invaded at 0.14 MYA on average, while pericentromeres are enriched for Gypsy LTRs invaded at 0.51 MYA on average. These results indicated the different invasion mechanisms of LTRs between the two structures. In addition, a novel repetitive sequence PCR630 was identified in the pericentromeres of B. rapa. Overall, the near-complete genome assembly, B. rapa Chiifu v4.0, offers valuable tools for genomic and genetic studies of Brassica species and provides new insights into the evolution of centromeres.