Sugarcane (Saccharum spp.) is a vital sugar and bioenergy crop with an exceptionally complex polyploid genome (10-12 sets of chromosomes). This complexity resulted from nobilization-a historical breeding process involving interspecific hybridization and repeated backcrossing1. However, the extreme ploidy has long impeded efforts to elucidate the genetic basis of its considerable sucrose-storing capacity. Here we present a fully phased genome assembly of the foundational cultivar POJ2878, achieved using a Pore-C-based assembly algorithm. This assembly resolved 118 chromosomes, revealing extensive subgenome recombination and non-homologous chromosomal rearrangements. Using identity-by-descent and allele-specific expression profiling, we identified breeder-favoured haplotypes, including a SUS2 haplotype with enhanced sucrose content. Resequencing of 981 Saccharum accessions traced POJ2878's pervasive contribution to modern cultivars and identified key domestication and improvement sweeps. Genes under selection include CBL1 for cold tolerance, TIP1 for cell size regulation and TB1 for tillering control. A genome-wide association study tailored for polyploid genomes resolved loci associated with parenchyma cell size and sucrose storage capacity, including the functionally validated sucrose transporter Saccharum hybrid SUT2. These findings clarify the genetic architecture underlying sugarcane's biomass productivity and sugar yield, offering a genomic foundation for accelerating improvement in sugarcane and other polyploid crops critical for global food and bioenergy security.

Papayas possess three sex genotypes: female XX, male XY, and hermaphrodite XYh. Only male plants produce long peduncles with numerous flowers, a trait that improves reproductive success. The gene SHORT VEGETATIVE PHASE (CpSVP) is located on the Y chromosome, absent from the X chromosome, and disrupted in the Yh chromosome, making it a key candidate gene for long peduncles in male plants. An autosomal CpSVP allele (CpSVP-A) was also annotated in a papaya genome. The overexpression of the male allele in Arabidopsis increases pedicel length, which supports its role in pedicel elongation. Unexpectedly, the autosomal allele CpSVP-A produced a similar phenotype as the male one, while the hermaphroditic allele (CpSVP-Yh) did not cause any significant change in pedicel length. Additionally, only the male allele rescued early flowering in an Atsvp mutant, indicating that it regulates both pedicel length and flowering time. In contrast, the autosomal allele only affected pedicel elongation and had no effect on flowering time. Together, these results demonstrate that CpSVP-Y underwent subfunctionalization, retaining both peduncle elongation and flowering time functions, while CpSVP-A likely lost the latter. Thus, CpSVP-Y contributes to male reproductive fitness through enhanced peduncle development without affecting sex determination, potentially regulated by Y chromosome-specific cis-elements. This study provides new insights into the genetic basis of sexually dimorphic traits in papayas.

Papaya (Carica papaya L.) is a tropical trioecious crop with males, hermaphrodites, and females. There is a sequence difference between male and hermaphrodite SHORT VEGETATIVE PHASE (CpSVP), making SVP a strong candidate gene controlling peduncle length in papaya. To study the spatial and temporal expression and function of CpSVP in Arabidopsis, we constructed a translation fusion structure based on the native promoter of SVP in papaya. In the 2kb promoter, strong GUS staining was observed in the floral organs and pedicels. In the 1kb promoter, there is no GUS expression in the floral organs, and it is barely detectable in pedicels. Removal of a GA responsive P-box cis-element in the 1kb promoter enhanced expression in the floral organs and pedicels, and elongated pedicels. In the transgenic Arabidopsis plants expressing the male CpSVP allele, there was an increase in pedicel length, but not in the plants expressing the hermaphrodite CpSVP allele. CpSVP-Y is capable of pedicel elongation, with no defects in reproductive organs. These findings imply that CpSVP-Y and this P-box play a major role in peduncle elongation but not sex determination in papaya.

Accessory chromosomes are non-essential for growth but poorly characterized in basidiomycetes, unlike in Ascomycota. Here, we report whole-genome sequencing of 16 strains of the basidiomycete Tremella fuciformis (silver ear fungus), generating 27 complete haplotypes (5 monokaryons and 11 dikaryons, each contributing two distinct haplotypes). Genome size varied by over one-third, driven by accessory chromosomes and repetitive sequences in core chromosomes (essential for basic biology). Each strain harbored 8-10 core chromosomes (polymorphic via fusion/fission) and 2-10 accessory chromosomes (total 108), whose distribution reflects phylogeny and symbiotic specificity with the ascomycete Annulohypoxylon stygium. Accessory chromosomes are small, transposon-rich, gene-poor, and exhibit higher sequence similarity but more diverse structural variations than core chromosomes, with few shared genes across phylogenetic branches. Both chromosome types show frequent copy number variation during cell type transformation. Most accessory chromosome genes lack homologs in core chromosomes or existing gene databases. Our study reveals basidiomycete accessory chromosome diversity, suggesting an origin from unexplored species pre-dating T. fuciformis speciation.

The papaya aril is a specialized seed appendage that has been reported to contain germination-inhibiting substances and usually requires removal before seed germination, thereby limiting breeding efficiency. However, the cellular origin and candidate molecular regulators of papaya aril development remain poorly understood. To investigate the early developmental process and candidate regulatory genes of the papaya aril, we combined histological analysis, bulk RNA-seq, and single-cell RNA-seq. Histological observations suggested that aril differentiation begins around 10 days after pollination (DAP) in the funiculus region. Based on this initiation stage, bulk RNA-seq profiling of seeds at 5, 10, and 15 DAP identified genes with initiation-stage-specific expression and prioritized candidate genes potentially related to seed appendage development, including CpRING-like, CpMBR2, and CpNDR8. Single-cell RNA-seq of seeds at 10 and 15 DAP annotated a putative aril cell population and reconstructed its developmental trajectory, revealing five trajectory-associated genes: CpATJ3, CpDYL1, CpGRP-like, CpHIRD11, and CpERD15. Integrative analysis of bulk and single-cell transcriptomic datasets further identified three candidate genes potentially involved in aril development: CpFER3, CpUVI4, and CpCEP1. These findings support the funiculus region as the likely anatomical origin of the papaya aril and provide candidate genes for future functional validation.

Papaya is a major tropical fruit crop with notable nutritional and economic value, yet its genetic improvement through modern breeding technologies faces substantial challenges. The traditional tissue culture process is both labor-intensive and time-consuming, causing gene-editing advancements in papaya to lag behind those in other crops. To overcome these obstacles, we developed a tissue culture-independent hairy root system in papaya, which enables efficient gene editing and significantly enhances the application and development of editing tools. This innovative platform allows for the pre-assessment of editing efficiency and supports the establishment of adenine base editor (ABE) and cytosine base editor (CBE) tools in papaya, thereby mitigating the high failure costs associated with the lengthy cycle of conventional genetic transformation. Utilizing this system, we pre-tested sgRNA activity and achieved high editing efficiency of CpWIP3 during stable transformation. Additionally, through promoter screening, we successfully developed ABE and CBE tools, marking the first precise single-nucleotide editing system in papaya. This gene-editing system provides a crucial platform for advancing functional genomics and accelerating precision breeding in papaya.

Abstract Nutmeg ( Myristica fragrans Houtt.) is a dioecious species that produces one of the most valuable spices and has peculiar holocentric chromosomes with diffuse centromere. The impact of holocentricity on the evolution of sex chromosomes is not well understood. Here, we present the first fully annotated haplotype-resolved chromosome-level genome of a male nutmeg plant, identify its sex chromosomes and analyse evolution of the sex-linked region (SLR). We demonstrate that nutmeg has a male heterogametic (XY) system, with a 0.23 Mb X-linked SLR and a 3.1 Mb Y-linked SLR with limited evidence for Y-degeneration. Low X:Y synonymous divergence for X- and Y-linked homologs (K s < 2.5%) indicates recent evolution of sex linkage, likely through loss(es) of homologous X-linked region(s). Leveraging the new genome and SLR sequences, we developed PCR-based molecular marker for reliable sexing of nutmeg seedlings, enabling efficient management of plantations by ensuring the optimal male to female ratio (1:10).

Cupressaceae , a gymnosperm family, draws attention due to its controversial phylogenetic position. Here, we present a comprehensive genome analysis of Chinese fir (Cunninghamia lanceolata), a Cupressaceae species, to enhance our understanding of gymnosperm evolution. The 11.24 Gb assembled genome, shaped by inefficient long terminal repeat removal, offers insights into its phylogenetic position. Phylogenetic analysis refines gymnosperm relationships between Cycads-Ginkgo and their relation to Gnetales-Pinaceae. Whole-genome duplication (WGD) analysis reveals no evidence for an ancient polyploidization event in the lineage of C. lanceolata, and confirms a seed-plant-shared WGD event. We also explore genomic evidence to explain the population history and adaptability of C. lanceolata, including potential glacial refugia, dispersal centers, and unique sterility. Furthermore, the refined (A)B(C) model for reproductive organ development in C. lanceolata has broader applications across gymnosperms. This study provides a valuable genome sequence and contributes to the understanding of gymnosperm evolution.

IntroductionJacaratia spinosa (Aubl.) A. DC. (J. spinosa) is an important member of the Caricaceae family, valued for its edible properties and potential for protease development. However, organelle genome resources for this species have not been publicly available.MethodsTo fill this gap, we applied a hybrid sequencing approach combining Illumina short reads and Nanopore long reads, and assembled the complete mitochondrial and chloroplast genomes of J. spinosa using established assembly pipelines, followed by comprehensive annotation and genomic feature analysis.ResultsThe circular mitochondrial genome spans 461,675 bp, and encodes 40 protein-coding genes (PCGs), 26 tRNA genes, and 3 rRNA genes. The complete chloroplast genome is 160,000 bp in length, comprising 84 PCGs, 37 tRNA genes, and 8 rRNA genes. Both genomes contain numerous repetitive sequences. Codon usage analysis revealed a preference for leucine and codons ending with A or U, and several non-canonical start and stop codons were corrected via RNA editing. We identified 34 homologous sequence fragments, indicating frequent intracellular gene transfer events between the mitochondrion and chloroplast. Phylogenetic analysis confirmed that J. spinosa is most closely related to C. papaya among the species included, forming a sister group. Synteny analysis revealed that while the chloroplast genome of J. spinosa is highly conserved, the mitochondrial genome exhibited high similarity but with notable structural rearrangements. Selection pressure analysis indicated that the mitochondrial genes ccmFN and rps19, as well as the chloroplast genes ycf2 and rps4, are under positive selection.DiscussionThese findings expand the organelle genome resources for Caricaceae and provide valuable molecular evidence for phylogenetic and evolutionary studies within the family.

Papaya is a trioecious species, but a unified framework for comparing floral sex differentiation has been lacking. We combined stereomicroscopy, paraffin sectioning, and scanning electron microscopy to establish a continuous 12-stage developmental system from floral primordium initiation to anthesis. Male, female, and hermaphroditic flowers followed a common developmental trajectory during Stages 1–4 and diverged at Stage 5. Male flowers formed fertile stamens and a reduced pistillode, female flowers developed a complete gynoecium without stamens, and hermaphroditic flowers displayed normal, aborted, or transitional pistils and carpellodic stamens. RNA sequencing and weighted gene co-expression network analysis of morphologically defined tissues identified gene modules associated with normal pistil development, distinct modes of pistil abortion, and stamen carpellody. These modules were enriched in chromatin and RNA regulation, protein homeostasis, floral-organ identity, hormone and receptor-kinase signaling, pollen-wall formation, and stress-responsive pathways, yielding 30 representative candidate genes. This developmental framework integrates developmental morphology with transcriptional programs underlying reproductive-organ fate and plasticity in papaya.

Variations of meiosis, which normally halve genetic complements prior to fertilization, can have profound consequences. For example, whole-genome duplications (polyploidy) have shaped the evolution and diversification of most angiosperm lineages. The century-long success of sugarcane interspecific hybrids has been attributed to unusual female restitution-an unreduced maternal gamete fusing with a normal haploid paternal gamete1,2. Here we generated haplotype-resolved genomes of octoploid Saccharum officinarum LA Purple and decaploid Saccharum spontaneum US56-14-4. Eight F1 hybrids between these species exhibited 2:1 maternal to paternal genomic ratios, with 2 assemblies revealing canonical haploid sets of approximately 40 paternal and approximately 80 maternal chromosomes. The maternal chromosomes comprise 40 pairs of duplicated, partially recombined sister chromatids that retain around 62.5% of maternal genetic diversity, characteristic of second division restitution. Using single-molecule long-read sequencing and a novel algorithm that is broadly applicable to polyploid genomes, we identified two classes of recombination breakpoints, including a previously unrecognized configuration supported by both recombinant and non-recombinant reads, across all hybrids and diagnostic of second division restitution. These findings resolve a century-old cytological debate, add new insights into meiotic variations, and offer a genomic approach to accelerate genetic gain in this globally critical sugar and bioenergy crop.

The sugarcane genus Saccharum is characterized by complex genomes with diverse ploidy levels. We developed a multiscale graph–based pangenome representation, which integrates nine genome assemblies into a unified reference, representing modern cultivars and founding species. Each homo(eo)logous (encompasses both homologous and homeologous relationships) chromosome set retains 47 to 57 haplotypes and ~74,000 to 271,000 gene alleles. This framework enables multiomics exploration, encompassing homo(eo)log systems and epigenomic signatures. The pangenome facilitates population genomics analyses of 417 mixed-ploidy Saccharum accessions, revealing convergent selection and identifying the Andropogoneae TB1 homolog linked to tillering as a promising gene-editing target to boost cane yield. Additionally, the pangenome supports dosage-informed genome-wide association study, improving heritability estimates and identification of sugar or leaf-angle–associated loci, including SaIRX10 and SaBAK5 . Our analytical framework establishes a foundation for graph-based genetic studies in sugarcane and other polyploid genomes.

Papaya (Carica papaya L.) is a widely cultivated tropical and subtropical fruit crop valued for its rich nutritional content, diverse food industry applications, and the medicinal use of papain. However, bitterness in papaya fruit, particularly in fibrous strands, negatively affects fruit quality and consumer acceptance; therefore, the development of papaya cultivars with stable and desirable quality is of great importance. To identify the bitter compounds in papaya fruit fibrous strands and elucidate the molecular mechanisms underlying their biosynthesis, we performed transcriptomic and metabolomic analyses of fibrous strands from two papaya cultivars at three developmental stages. We identified carpaine, dehydrocarpaine II, and their derivative alkaloids. Furthermore, we identified two key regulatory genes, CpNAC82 and CpHD-Zip ANT2, associated with alkaloid biosynthesis. Finally, using single-nucleus RNA sequencing technology, we constructed a comprehensive gene expression atlas of papaya fibrous strands and stems, successfully identifying multiple cell types, including epidermal cells, guard cells, parenchyma cells, and phloem cells. Epidermal and phloem cells serve as the primary sites of alkaloid metabolism in papaya. These findings provide new insights into the molecular mechanisms of bitterness in papaya's fibrous strands and yield genomic resources for improving fruit quality in papaya.

Papaya is a trioecious species with XX females, XY males, and XYh hermaphrodites. Any combination of Y and Yh chromosomes is lethal. The gene underlying YY lethality is pivotal in the transition from stage 2 to stage 3 in sex chromosome evolution. Here, we identify and functionally validate the YY lethality gene in papaya, CpYYL. Loss of CpYYL function accelerates glycolysis and reduces sucrose accumulation in embryo, causing embryo abortion. CpYYL interacts with CpAKRP and overexpression of both genes partially rescues seed abortion in the heterozygous emb506 and akrp mutants, indicating conserved role in plastid differentiation and embryo development. Viable YYh and YhYh plants are generated through genetic engineering and crossing, although both genotypes show high seedling mortality. Crossing YYh male with XX female papaya shows 1:1 ratio of male to hermaphrodite plants without recombination between MSY and HSY. Identification of CpYYL fills a critical gap in papaya sex chromosome evolution, and provides new resources for genomic and epigenetic studies. Papaya is a trioecious species with XX females, XY males, and XYh hermaphrodites, and the combination of Y and Yh chromosomes is lethal. Here, the authors identify the degeneration of the YY lethality gene on the Y chromosome as the causal balancing lethal factor that reenforces dioecy and stabilizes balanced sex ratios.

Due to limited cytogenetic data, the date palm (Phoenix dactylifera L.), a monocotyledonous and dioecious species, previously had uncertain ploidy levels. This study aimed to determine the chromosome number and develop karyotypic profiles for elite commercial date palm cultivars cultivated across four provinces of Pakistan, with additional comparisons to exotic varieties. All analyzed cultivars were confirmed to be diploid, possessing a chromosome number of 2n = 36. Detailed karyotypic analyses were performed, including measurements of total chromosome length (TCL), lengths of short and long arms, relative length (RL), and centromeric index (CI) for each chromosome. The chromosome complements consisted of metacentric (m), submetacentric (sm), subtelocentric (st), and telocentric (t) chromosomes. Average chromosome lengths varied among cultivars, ranging from 0.99 µm to 6.46 µm. The wild genotype Wild03 exhibited a symmetric karyotype, comprising 11 metacentric, 4 submetacentric, and 3 telocentric chromosomes, suggesting a more primitive chromosomal structure. In contrast, the cultivar Asul Khurmo showed a higher number of telocentric chromosomes, indicating a more derived karyotype. These karyological insights advance our understanding of date palm cytogenetics and offer a valuable foundation for future studies on the origin, evolution, and improvement of date palm varieties.

BACKGROUND:Lychee (Litchi chinensis Sonn.), longan (Dimocarpus longan Lour.), and rambutan (Nephelium lappaceum L.) are popular tropical fruits in the family Sapindaceae, known for their succulent arils-specialized seed appendage with significant biological and commercial value. Despite their agricultural relevance, the molecular mechanisms underlying aril development in these species remain poorly understood. RESULTS:We conducted RNA-sequencing to profile transcriptomes during aril development, complemented by in-situ hybridization to validate the spatial expression of LcLBD1. OrthoFinder identified species-specific and shared differentially expressed genes (DEGs), while functional enrichment analyses (GO, KEGG) and transcriptional network modeling elucidated regulatory pathways. After detailed analyses of transcriptomes, species-specific and shared DEGs were identified across lychee, longan, and rambutan using OrthoFinder. Members of the bHLH and MYB gene families were implicated in early aril development. Species-specific DEGs were primarily enriched in metabolic pathways. From shared DEGs, we identified ten transcription factors (AGL8, AP3, SHP1, WOX13, LBD1, LBD3, OBP1, SPL2, SPL3, and SPL9) and three genes (IAA8, CSLD5, and CYCD3;2) as key regulators. Interestingly, in-situ hybridization localized LcLBD1 expression to funicle and small aril cells, suggesting roles in cell differentiation and division. CONCLUSION:We have identified ten transcription factors and three genes affecting aril development in lychee, longan, and rambutan, and validated the expression of LcLBD1 in funicle and aril cells. These results offer a new perspective on the molecular mechanism of aril development and lay the groundwork for future research into the functions and regulatory mechanisms of candidate genes.

Sex determination in Phoenix dactylifera L. (Date palm) remains a critical issue for breeders due to the lack of visible sexual dimorphism in early developmental stages. This study integrates cytogenetic and molecular techniques to identify sex-linked DNA markers and their chromosomal localization in three Pakistani date palm cultivars: Medjool, Gulistan, and Dedhi in in six-month-old seedlings. Sixteen DNA markers were screened, three—SCAR, SRY, and the newly developed DP-2—effectively differentiated male and female genotypes. The SCAR marker amplified distinct bands (406 bp in females and 354 bp in males), while the SRY and DP-2 markers showed male- and female-specific sequences, respectively. Fluorescent in situ hybridization (FISH) was used to physically map these sequences on chromosomes, confirming their association with a homomorphic XY sex-determination system. The 45S rDNA marker showed differential signal patterns, supporting chromosomal differences between sexes. These results demonstrate the potential of molecular cytogenetic tools for early sex identification, offering practical benefits for commercial propagation, breeding efficiency, and conservation of date palm genetic resources.

Papaya is a nutritionally valuable fruit crop cultivated globally in tropical and subtropical regions. Conventional breeding efforts have prioritized enhancing traits such as yield and fruit size, with notable success in developing high-yielding cultivars. However, other critical areas in papaya improvement, such as enhancing genetic diversity, improving disease resistance, optimizing post-harvest management, and addressing consumer preferences for fruit quality and flavor, have experienced relatively limited progress. Addressing these gaps is essential for meeting both production challenges and market demands. Achieving substantial genetic gains in these traits in the shortest timeframe will require integrating traditional breeding practices with emerging genomics tools. Over the past two decades, substantial advancements in papaya genomics have been achieved, resulting in resources including high-density genetic maps, high-quality reference genomes, and transcriptomic and resequencing datasets. These resources have been utilized to develop genome-wide markers and identify marker–trait associations, supporting the development of disease-resistant varieties and uncovering the genetics of consumer-preferred traits. By utilizing these resources in combination with innovative approaches such as genomic selection and speed breeding, sequence-based breeding approaches can significantly accelerate genetic gains in papaya. This will enable the rapid development of elite (high-performance) papaya cultivars that meet both agronomic and consumer expectations.