Search Results (293)

Cultivated sweetpotato (Ipomoea batatas (L.) Lam.), a hexaploid (2n = 6x = 90) crop, is the most economically important species within the morning glory genus Ipomoea (Convolvulaceae). Fourteen diploid Ipomoea species and several polyploid accessions have been confirmed to be closely related to sweetpotato, often termed its wild relatives. These wild species harbor abundant elite genes beneficial to sweetpotato improvement and thereby serve as indispensable germplasm reservoirs for breeding programs. In addition, several wild taxa are proposed as potential ancestors of domesticated sweetpotato. Nevertheless, the evolutionary origin and genomic architecture of cultivated sweetpotato have not yet been fully resolved. Cytological investigations, particularly chromosome karyotyping and meiotic pairing analyses, have been pivotal in unravelling the genomic architecture and evolutionary trajectories of polyploid taxa. Herein, we systematically summarize advances in chromosome counting, genome size, karyotyping, and meiotic pairing research on sweetpotato and its wild relatives. Full article

Plant evolution started with unicellular algae, gradually evolving multicellularity and terrestrial colonization. These evolutionary events were accompanied by the interplay of chromosome polyploidization, rearrangement, gene loss, and point mutation. We counted the proportion of nucleotide combinations in the genome sequences of 64 sequenced plants, and analyzed the significant difference in these nucleotide combination proportions among algae, monocotyledons and dicotyledons. The correlation of highly significant different and no significant different nucleotide combinations was analyzed respectively. Nucleotide combinations and their reverse complementary sequence proportions were analyzed in different functional regions of the genome. These results reveal that some nucleotide combinations are subject to strict selection, and these combinations have a higher proportion in the CDS regions and lower proportion in the intergenic regions. Meanwhile, there are some nucleotide combinations that are under less selective pressure, and these combinations have a higher proportion in the intergenic regions and lower proportion in the CDS regions. Cluster analysis based on trinucleotide to octanucleotide combination proportions reveals that plant genome evolution is accompanied by clade-wide differentiation of genome-wide nucleotide composition patterns, in addition to well-documented chromosomal polyploidization, structural rearrangement and gene loss events. We analyzed the changes in the proportion of nucleotide combinations at the genome level in 64 sequenced plants, providing a new idea for studying genome evolution in the plant kingdom. Full article

Sugarcane (Saccharum spp.) is a globally vital high-biomass sugar crop with a massive demand for potassium (K). Low-K⁺ stress severely restricts its yield and stress resistance. Plasma membrane intrinsic proteins (PIPs) play pivotal roles in transmembrane water transport and ion homeostasis; however, their evolutionary characteristics and molecular mechanisms underlying nutritional stress responses in the complex polyploid sugarcane remain poorly understood. In this study, genome-wide identification in the sugarcane cultivar XTT22 yielded 149 PIP gene family members (comprising 54 PIP1s and 95 PIP2s). Phylogenetic and chromosomal localization analyses demonstrated that the sugarcane PIP family underwent drastic paralogous expansion during evolution, with tandem duplication acting as the core driving force for the dramatic expansion of the PIP2 subfamily. Spatiotemporal expression profiling unveiled significant modular functional division among PIP genes, identifying a core co-expression group driving rapid early seedling elongation and a PIP2-specific expression cluster dedicated to the physiological homeostasis of mature stems. Notably, the core member ScPIP2-70 exhibited significant early-induced responses at both transcriptional and protein levels in roots under low-K⁺ stress. Functional complementation assays in the K⁺-uptake deficient yeast strain R5421 further confirmed that the heterologous expression of ScPIP2-70 effectively rescued the growth defects of yeast under low-K⁺ conditions, demonstrating its potential transmembrane K⁺ transport activity. This study not only comprehensively elucidates the evolutionary dynamics and spatiotemporal expression profiles of the sugarcane PIP gene family but also uncovers the novel pleiotropic function of ScPIP2-70 in mediating low-K⁺ stress tolerance, providing critical theoretical support and candidate gene resources for breeding “potassium-efficient” sugarcane cultivars via modern biotechnology. Full article

Melatonin is an important stress-protective agent in plant growth. Methyltransferase (ASMT) is an important enzyme in the concluding phase of melatonin production in plants. In this study, we performed the genome-wide identification and functional investigation of the ASMT gene family in hexaploid wheat and 14 other plants. ASMT genes in 15 plants were identified by using HMM scanning against the proteomes derived from a single representative reference genome for each species. They were classified into three subfamilies I-III by constructing four types of phylogenetic trees (Neighbour-joining with p-distance model, Neighbour-joining with JTT model, Maximum likelihood, and Bayesian inference). Based on exon–intron structure and domain diagrams, a conserved structural pattern characterized by successive intron phases 1 and 0 (the “1-0” pattern) was found in ASMT genes during evolution. Collinear events analysis indicated that polyploidization and tandem duplication synergistically promote the expansion of T. aestivum ASMT members. Cis-acting element analysis revealed that numerous stress- and hormone-responsive motifs (such as ABRE and LTR) were present in ASMTs of wheat, suggesting a role for ASMTs in adaptive signal transduction. Transcriptome analysis revealed that specific T. aestivum ASMT genes were strongly responsive to stress; for instance, II_TraesCS2B02G041200 and II_TraesCS2B02G606200 were strongly upregulated under drought and salt stress, respectively. To independently confirm the stress responsiveness of these candidates in a different genetic background, we performed quantitative real-time PCR (qRT-PCR) on selected genes under drought and salt treatments. The result showed that the expression trends of transcriptome and qRT-PCR were almost the same, identifying these ASMT genes as strong stress-responsive candidates under drought and salt treatments. In this study, we performed identification, classification, evolution analysis and expression pattern analysis of ASMTs in wheat and 14 other plants. Our study will provide a framework for the targeted genetic improvement of melatonin-mediated stress resistance. Full article

Plant genomes exhibit extensive structural diversity generated by large-scale genomic alterations, collectively known as structural variations (SVs). Unlike single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels), SVs can reshape genome architecture through changes in sequence content, gene dosage, regulatory landscapes, and chromosome organization. Recent advances in long-read sequencing (LRS), pan-genome construction, and multi-omics technologies have greatly expanded our ability to identify and interpret SVs across plant species. In this review, we summarize recent progress in understanding the formation mechanisms, classification, and functional consequences of plant SVs. We discuss major sources of SV generation, including transposable element activity, non-allelic homologous recombination (NAHR), horizontal gene transfer (HGT), and genome restructuring following polyploidization. We further highlight how LRS and graph-based pan-genomes overcome limitations of traditional linear reference genomes and enable more comprehensive characterization of genetic diversity. Beyond variant discovery, we emphasize the importance of integrating genomic, transcriptomic, epigenomic, proteomic, metabolomic, and spatial omics datasets to decipher how SVs influence gene regulation and complex agronomic traits. We also discuss current challenges, including repetitive genomes, polyploidy, computational complexity, and translation of SV knowledge into practical breeding applications. Together, these advances establish SV-centered genomics as a critical framework for understanding plant genome evolution and accelerating precision crop improvement. Full article

Satellite DNA is a dynamic component of plant genomes and a valuable source of cytogenetic markers, but its diversity and chromosomal distribution in polyploid Triticeae remain insufficiently studied. Here, low-coverage whole-genome sequencing, graph-based repeat clustering, quantitative PCR, multivariate statistics and fluorescence in situ hybridization (FISH) were used to identify and characterize satellite repeats in Elymus and related Triticeae species. Sixteen repeat clusters (E1–E16), with monomer lengths of 118–667 bp, showed distinct taxonomic distributions and copy-number profiles across 14 species. Correlation analysis, principal component analysis and hierarchical clustering revealed concerted variation among repeats and separated the perennial taxa Elymus and Pseudoroegneria from Triticum, Secale, Hordeum and Dasypyrum. Spearman correlation analysis identified E7 and E9 as putative candidates associated with St/StY genomic backgrounds, whereas E10 was identified as a putative candidate associated with the H genome. These statistical associations require independent cytogenetic validation. Contrasting copy numbers of E6 and E11 in bread wheat cv. Chinese Spring versus Dasypyrum villosum (L.) Candargy identified them as V-genome candidates. FISH localized E6 to the terminal regions of chromosomes 3VL, 4VS and 7VS, and E11 to 4VL. Karyotyping further revealed that two lines previously considered as wheat-D. villosum addition lines were in fact substitution lines: W3 was identified as a 3V(3D) substitution line and W4 as a 4V(4B) substitution line, whereas W7 retained its 7V addition status. These results expand the set of chromosomal markers for comparative genomics and introgression analysis in wheat. Full article

Polyploidization can generate morphological and physiological variation in plants, but the molecular basis underlying leaf trait changes after genome doubling in grapevine remains insufficiently understood. This study aimed to characterize phenotypic, physiological, transcriptomic, and metabolomic differences between diploid and induced autotetraploid plants of ‘Thompson Seedless’ and to identify biological processes potentially associated with the observed leaf trait variation. In this study, autotetraploid plants were induced from axillary buds of ‘Thompson Seedless’ using colchicine treatment, and ploidy levels were confirmed by flow cytometry and chromosome counting. Phenotypic, physiological, transcriptomic, and metabolomic analyses were performed to compare diploid and tetraploid plants. Compared with diploids, tetraploids exhibited enlarged leaves, reduced plant stature, larger but less dense stomata, increased chloroplast number in guard cells, and higher total chlorophyll and carotenoid contents. Fv/Fm remained unchanged, whereas increased Vj and decreased ψEo and φEo suggested differences in electron transport-related characteristics beyond QA. Transcriptomic analysis identified 1564 differentially expressed genes, and metabolomic profiling detected 618 differentially accumulated metabolites. Integrated analyses highlighted coordinated molecular differences associated mainly with cell-wall processes, secondary metabolism, redox-related functions, and carbon-related pathways. These findings identify candidate biological processes for future functional validation and provide a basis for evaluating the potential value of autotetraploid germplasm in grapevine breeding. Full article

Cereal crops including wheat, rice, maize, barley, and sorghum collectively supply most global caloric and protein requirements, yet their productivity is increasingly constrained by combined abiotic stresses that co-occur under field conditions. Simultaneous drought, heat, salinity, and cold impose yield losses that consistently exceed those caused by individual stresses and elicit molecular responses that are qualitatively distinct from single-stress reactions and cannot be inferred from them. Despite this agronomic reality, the molecular mechanisms governing combined stress responses in cereals remain poorly resolved, and no integrated framework connecting the transcriptional, epigenetic, and genome-editing dimensions of combined stress tolerance has previously been articulated for this crop group. This review proposes a three-tier integrated framework for understanding and engineering combined abiotic stress tolerance in major cereals. The first tier encompasses transcription factor networks, including bZIP, WRKY, NAC, AP2/ERF, DREB, MYB, and HSF families, that translate combined stress signals into transcriptional reprogramming through ABA-dependent and ABA-independent pathways, hormonal crosstalk, and osmoprotectant and antioxidant defence systems. The second tier addresses the epigenetic regulatory layer, encompassing DNA methylation, histone modifications, and non-coding RNA pathways that gate TF binding site accessibility and encode stress memory in cereals. The third tier examines CRISPR-based tools, including multiplexed Cas9 editing and dCas9-based epigenome editing, that engineer validated targets from both tiers, while confronting polyploid off-target effects, growth penalties, and a laboratory-to-field validation gap. The three tiers are mechanistically coupled, with TF activity shaping epigenetic landscapes, epigenetic states gating TF access, and both providing precision engineering targets. Critical gaps include the absence of combined-stress epigenomic datasets, limited characterisation in barley and sorghum, and early-stage combined-stress-specific strategies. Full article

Single nucleotide polymorphisms (SNPs) are widely used for genetic diversity analysis, linkage mapping, genome-wide association studies (GWAS), and molecular marker development in crop plants. Genotyping-by-sequencing (GBS) enables cost-effective SNP discovery; however, achieving sufficient marker density in polyploid crops remains challenging because of complex genome structures, high sequence similarity among homologous chromosomes, and repetitive genomic regions. In this study, we optimized a GBS-based bioinformatics pipeline for polyploid kiwifruit (Actinidia spp.) by evaluating restriction enzyme combinations through in silico digestion analysis and comparing the SNP detection efficiency of three variant-calling tools, namely freebayes, bcftools, and Genome Analysis Tool Kit (GATK). The methylation-sensitive ApeKI/TfiI combination generated the highest proportion of DNA fragments within the target size range (200–500 bp) in the kiwifruit reference genome cv. Hongyang (A. chinensis). Using GATK, 828,257 SNPs were identified, approximately 22-fold higher than those detected using freebayes and bcftools, with a comparable transition/transversion (Ts/Tv) ratio. GATK also identified substantially higher absolute numbers of SNPs in genic regions, while the proportion of genic-region SNPs was similar across all three tools. Notably, only the GATK-derived SNP dataset exceeded the estimated marker density discussed in this study for high-density genomic coverage of the kiwifruit genome. These results demonstrate that the combination of methylation-sensitive restriction enzymes and GATK-based variant calling generated a high-density SNP dataset for mixed-ploidy kiwifruit germplasm. Because independent validation of SNP accuracy was beyond the scope of this study, the observed differences should be interpreted as differences in SNP discovery rather than comparative variant-calling accuracy. Full article

The glycine-aspartic acid-serine-leucine (GDSL) esterase/lipase family is a functionally diverse group of hydrolytic enzymes involved in multiple plant biological processes, including stress adaptation and development. However, its evolutionary patterns, functional conservation, and stress-responsive mechanisms in grasses remain not fully elucidated. In this study, a comprehensive comparative genomic analysis was performed on the GDSL gene family across nine representative grass species and Arabidopsis thaliana. Genome-wide identification, phylogenetic analysis, duplication pattern detection, synteny analysis, cis-regulatory element prediction, protein–protein interaction (PPI) network construction, and RNA-seq-based expression profiling were employed. A total of 1707 GDSL genes were identified, with substantial expansion in grasses, especially hexaploid wheat. Whole-genome and segmental duplications were the major drivers of family expansion, with most duplicated genes under strong purifying selection. A grass-specific clade (C3-2) was identified, and extensive syntenic conservation was observed among closely related grasses. Promoter analysis revealed enrichment of stress- and hormone-responsive cis-elements, and RNA-seq showed dynamic GDSL expression under low-temperature stress in rice and wheat. These findings demonstrate that the expansion of the GDSL gene family in grasses is driven by polyploidization and lineage-specific duplication, accompanied by the emergence of a grass-specific clade (C3-2) and regulatory diversification, collectively shaping stress-responsive evolutionary innovation in Poaceae. Full article

Polyploidy is increasingly recognized as a mechanism enhancing physiological resilience in woody fruit crops, yet its functional consequences remain poorly understood in mangoes (Mangifera indica L.), a major tropical species expanding into water-limited environments. Because leaf structure underpins plant water relations and gas exchange, this study evaluated how genome duplication alters foliar traits by comparing diploid and autotetraploid individuals of three polyembryonic cultivars (Gomera-1, Gomera-3, and Kensington Pride). Morphological and anatomical analyses revealed consistent ploidy-related modifications. Autotetraploids exhibited enlarged stomatal guard cells, increased leaf thickness, and changes in mesophyll organization, indicating greater structural investment in leaf tissues. These features are commonly associated with structural strategies that may contribute to water retention and hydraulic regulation, although their direct physiological consequences were not evaluated in the present study. Overall, our results indicate that genome duplication substantially modifies leaf structural traits in mangoes, although the magnitude and direction of these responses were cultivar-dependent. This study provides new insights into how polyploidy reshapes leaf morphology and anatomy in mangoes and advances our understanding of polyploid-induced structural variation in perennial fruit crops. Full article

Introduction: Squalius palaciosi (Doadrio, 1980; Leuciscidae) is a highly threatened freshwater fish species with an extremely restricted distribution, currently confined to a few tributaries on the right bank of the Guadalquivir River basin. During the 1980s, its populations were abundant and constituted a dominant component of local fish communities. However, multiple threats led to a drastic population decline, bringing the species to the brink of extinction. From an evolutionary perspective, S. palaciosi is particularly remarkable due to its polyploid condition and its potential involvement in hybridogenetic complexes, a rare phenomenon in the Iberian Peninsula. Hybridogenetic systems are well documented in its congeners Squalius alburnoides, widely distributed across Iberian river basins, and Squalius sp., restricted to the Guadiana basin. In these systems, the maternal lineage is shared (Squalius pyrenaicus), whereas the paternal lineage varies and remains unknown in S. palaciosi. Objective: This study aims to generate the first genomic data for S. palaciosi and to elucidate its evolutionary origin, as well as its mitochondrial and nuclear phylogenetic relationships within hybridogenetic complexes. Methodology: Genomic DNA was extracted from skeletal remains of preserved specimens housed in the fish collection of the National Museum of Natural Sciences (MNCN-CSIC) and subjected to Illumina short-read sequencing. After quality filtering, potential contaminant reads were removed. The complete mitochondrial genome and several nuclear gene fragments were assembled. Mitochondrial phylogenetic analyses were conducted using publicly available whole-genome sequencing data from Iberian freshwater fish species. Nuclear gene fragments were taxonomically assigned using BLAST analyses. Results: Phylogenetic analyses revealed that S. palaciosi is closely related at the mitochondrial level to S. alburnoides and S. tartessicus, with strong statistical support. BLAST-based taxonomic assignments of nuclear markers suggest the involvement of multiple Iberian freshwater fish species in the hybridogenetic origin of S. palaciosi. Conclusions: Our results provide novel insights into the evolutionary history of S. palaciosi and support a complex hybridogenetic origin involving multiple parental lineages. This study contributes to a better understanding of hybridogenetic speciation in freshwater fishes, a rare but evolutionarily significant process. Full article

Cyanobacteria are increasingly recognised as photosynthetic chassis for sustainable metabolic engineering because oxygenic photosynthesis generates ATP and NADPH via the photosynthetic electron transport chain, which drive CO₂ fixation through the Calvin–Benson–Bassham cycle into carbon intermediates that can be redirected toward engineered heterologous pathways. Their genetic tractability, CO₂-fixing capacity, ecological adaptability, and relatively simple cellular organisation make them attractive platforms for developing low-carbon biotechnological processes. This review explores recent progress in engineering cyanobacteria for heterologous pathway construction, critically evaluating genetic tools including transformation methods, genome integration strategies, promoter systems, and CRISPR-based editing, with specific emphasis on challenges of direct relevance to phototrophic chassis: host–pathway metabolic compatibility, precursor supply, cofactor balancing between photosynthetic output and heterologous pathway demand, and achieving genetic stability in polyploid cyanobacterial genomes. The review also addresses key limitations with mechanistic context: metabolic burden from multi-gene pathway expression reduces growth rate and selects against producing cells; polyploidy delays complete chromosomal segregation of engineered constructs; slow photoautotrophic growth constrains volumetric productivity; native regulatory networks resist carbon flux redirection; and cultivation constraints—including light attenuation in dense cultures and mismatches between photosynthetic ATP/NADPH supply and heterologous pathway demand—further limit achievable yields. Full article

The improvement of sucrose yield in sugarcane is impeded by the crop’s complex polyploid genome and slow progress in breeding. To clarify how arginine (Arg) regulates sugar metabolism and identify key genes associated with sucrose transport and accumulation in sugarcane, a screening experiment was performed by spraying L-arginine hydrochloride on the leaves and leaf sheaths of three sugarcane varieties (YZ05-51, YZ08-1609, and YT93-159), which differ in growth vigor, leaf morphology and other phenotypic traits. YZ05-51 exhibited the most prominent sugar-increasing effect, and subsequent optimization experiments on its leaf sheaths revealed that 20 g/mu L-arginine hydrochloride at pH 7.0 was optimal, significantly enhancing stem sucrose content. Transcriptomic analysis revealed the upregulation of genes related to sucrose synthesis and transport, with candidate genes enriched in pathways such as starch-sucrose metabolism, glycolysis/gluconeogenesis, and ATP-binding cassette (ABC) transporters. Metabolomic analysis detected 32 sugar metabolites across three categories, of which 24 were differentially abundant (e.g., glucose, galactose, fructose, and mannose). Integrated multi-omics analysis identified key regulatory genes, including SBEs and TPS1 (sucrose synthesis and carbon flux regulation), RBSK, α-amylases, GH28 (starch breakdown, glycolysis, and sugar mobilization), ABC transporters, GTs, and TIM10/TIM12 (sucrose transporter). Collectively, these analyses demonstrate enhanced activity of genes and metabolites involved in sucrose synthesis/transport in leaf sheaths, accompanied by reduced synthesis of other monosaccharides and oligosaccharides. Vigorously metabolizing leaf sheaths is more conducive to sucrose transport. This study provides valuable insights into the molecular mechanisms underlying Arg-mediated sucrose accumulation specifically in the sugarcane YZ05-51 sugarcane, highlighting its critical regulatory roles. Full article

Controlled degradation of genomic DNA is a hallmark of programmed cell death (PCD) in plants and animals. In plants, nucleic acid degradation during PCD enables nutrient redistribution. S1/P1 nucleases are established participants; however, the staphylococcal-like (SNc) nucleases, represented in Arabidopsis thaliana by plasma membrane-localized AtCAN1 and AtCAN2, have not been characterized in this context. Using promoter-driven GUS reporter assays, we show that AtCAN1, and to a lesser extent AtCAN2, are expressed in three tissue categories: (i) tissues described in the scientific literature as classical examples of PCD-associated structures; (ii) cells at the plant–environment interface susceptible to pathogen attack, root hairs, guard cells, and hydathodes; and (iii) endoreduplicated structures: stipules, trichomes, and basal hypocotyl. Expression patterns were independently confirmed using publicly available microarray and RNA-seq datasets. Loss of AtCAN1 function reduces rosette growth. AtCAN1 is highly tissue-specific; AtCAN2 shows a broader, weaker pattern, consistent with subfunctionalization. Overlapping expression with S1/P1 nucleases in PCD tissues suggests complementary nucleolytic roles. Unlike S1/P1 nucleases, which are nuclear, SNc nucleases localize to the plasma membrane, implying distinct yet cooperative pathways. The expression of SNc nucleases in endoreduplicating organs suggests their potential involvement in an unidentified process of polyploid DNA recycling. Full article