Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Pan variation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed2026

A chromosome-scale genome of Capsicum pubescens provides insights into candidate terpene-associated gene clusters and pan variation of terpene synthases.

A chromosome-scale genome of Capsicum pubescens and comparative pan-TPS analysis support structural characterization and gene-level prioritization of a chromosome-9 terpene-associated candidate locus in this accession. Capsicum pubescens is one of the five domesticated Capsicum species, mainly cultivated in mid- to high-elevation regions of the Americas. Despite its distinctive morphology and fruit traits, genomic resources for C. pubescens remain less developed than those for the widely cultivated C. annuum. Here, we assembled a chromosome-scale reference genome for accession HNUCP0001, spanning 3.70 Gb with a scaffold N50 of 278.01 Mb. Comparative genomics revealed 679 significantly expanded gene families enriched in sesquiterpenoid and triterpenoid biosynthesis. Genome-wide biosynthetic gene-cluster mining identified multiple terpene-associated candidate loci, which were subsequently prioritized using genome-derived structural criteria and Capsicum pubescens-specific expression evidence. Subsequently, we curated the terpene synthase (TPS) repertoire and, across 16 Capsicum genomes, resolved 36 TPS orthogroups with pronounced presence/absence variation, highlighting dynamic lineage-specific diversification. Together, these analyses establish HNUCP0001 as an accession-specific genomic resource and provide a comparative framework for prioritizing terpene-associated TPS genes and candidate BGCs in Capsicum. These candidate loci, together with accession-level transcriptomic and metabolomic evidence, offer testable hypotheses for future functional studies of specialized terpenoid metabolism in C. pubescens.

Alkyl and Aryl Transferases↗
PubMed2026

The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.

Plant pan-genomics is entering a new phase beyond genome variation discovery, requiring a shift from cataloguing genomic diversity toward understanding how variation generates biological function and breeding value. Here, we propose that the future of plant pan-genomics will be shaped by three conceptual transitions. First, structural variation (SV), presence-absence variation (PAV), and haplotype diversity should be interpreted not merely as genomic differences, but as regulatory components that influence gene networks, chromatin organization, and complex traits. Second, the expansion from species-level pan-genomes to genus-level super pan-genomes provides an evolutionary framework for uncovering adaptive genetic modules preserved in wild relatives and overlooked during domestication. Third, integrating pan-genomes with pan-omics, three-dimensional genome analyses, and artificial intelligence will enable the transformation of genomic variation into predictive models for crop improvement. We further propose that the ultimate value of pan-genomes lies not in generating increasingly complete genome collections, but in establishing a mechanistic bridge between genome diversity, biological function, and breeding decisions. This transition will move crop improvement from empirical selection toward rational genome design, where evolutionary diversity can be systematically interpreted, predicted, and engineered.

Journal Article↗
PubMed1990

Dental variation in the genus Pan.

Dental measurements and 23 anatomical dental features are observed on 151 Pan troglodytes and 69 Pan paniscus of both sexes, preserved in the Museum of Tervuren (Belgium). Odontometric investigations confirm the reality of the two species in the genus Pan, but do not show any difference between subspecies in Pan troglodytes. Correspondence analysis demonstrates that the qualitative anatomical features are differently distributed in the two chimpanzee species.

Animals↗
PubMed1988

Immunological, morphological, and electrophysiological variation among retinal ganglion cells purified by panning.

Two different monoclonal antibodies to the Thy-1 antigen, T11D7 and 2G12, were used to purify and characterize retinal ganglion cells from postnatal rat retina. Although Thy-1 has been reported to be a specific marker for ganglion cells in retina, retinal cell suspensions contained several other types of Thy-1-positive cells as well. Nevertheless, a simple two-step "panning" procedure allowed isolation of ganglion cells to nearly 100% purity. We found that postnatal ganglion cells differed in antigenic, morphological, and intrinsic electrophysiological characteristics, and that these properties were correlated with one another. Minor variations of this panning protocol should allow rapid, high yield purification to homogeneity of many other neuronal and glial cell types.

Action Potentials↗
PubMed1986

Variations in the serum esterases of chimpanzees.

Seventy chimpanzees, representing Pan paniscus (the pygmy chimp) and all four races of the common chimpanzee (Pan troglodytes), were examined for electrophoretic variation in their serum esterases. Only three variant electromorphs were observed at these six loci. One of these was at the albumin-associated esterase locus, and the other two were at esterase 4. This is the first report of any variation in an esterase or albumin in chimpanzees.

Animals↗
PubMed2026

Pan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut.

The cultivated peanut is a crucial global legume crop that is essential for food security and nutrition, particularly in developing regions. However, its limited genetic variation hampers breeding progress and yield improvement. Here we constructed a graph-based pan-genome for peanut, incorporating 14 genomes that represent all 6 peanut varieties. Using this pan-genome, we genotyped 2,320 accessions, covering 88.03% of ICRISAT and 59.21% of USDA core germplasm, enriching valuable resources for genomic studies and breeding. We cataloged genomic structural variations and investigated the role of homoeologous exchanges in population divergence. Through our pan-genome approach, we overcame the challenges of genotyping posed by homoeologous exchanges and identified key genes associated with flowering and dwarfism in peanut. By integrating superior haplotypes and germplasm resources guided by the pan-genome, we further developed high-yield dwarf lines. This work provides essential genomic resources to accelerate functional gene discovery and modern peanut breeding.

Journal Article↗
PubMed2025

Molecular mechanisms and breeding strategies for heat tolerance in vegetable crops under global warming.

Extreme heat driven by climate change poses a catastrophic threat to global vegetable production, undermining nutritional security because of the heightened physiological sensitivity and succulent tissues of these crops. This review synthesizes the multistage impacts of heat stress across critical developmental phases-from germination to reproduction-emphasizing morphological impairments (such as leaf wilting and floral abortion) and physiological disruptions (including photosynthetic inhibition and oxidative damage). We systematically dissect thermotolerance mechanisms in vegetables, highlighting transcriptional reprogramming by HSFs, WRKY, and NAC transcription factors; chaperone-mediated proteostasis via HSPs; epigenetic remodeling; Ca2+-ROS signaling pathways; and the role of phase separation dynamics. Importantly, we propose six strategic pathways to develop heat-resilient vegetables: harnessing natural variation through pan-genome-driven allele mining; employing biotechnological interventions such as CRISPR-mediated editing and synthetic promoters; engineering multistress tolerance by targeting conserved 'core response' pathways; exploiting epigenetic memory to achieve transgenerational resilience; optimizing source-sink dynamics with ''Climate-Responsive Carbon Optimization; and applying plant growth regulators and nanotechnology to enhance thermotolerance. Together, these strategies chart a clear roadmap for climate-smart vegetable breeding and call for interdisciplinary collaboration to translate molecular discoveries into practical breeding approaches for sustainable food systems under escalating thermal extremes.

Journal Article↗
PubMed2025

PlantPan: A comprehensive multi-species plant pan-genome database.

The pan-genome represents the complete genomic diversity of specific species, serving as a valuable resource for studying species evolution, crop domestication, and guiding crop breeding and improvement. While there are several single-species-specific plant pan-genome databases, the availability of multi-species pan-genome databases is limited. Additionally, variations in methods and data types used for plant pan-genome analysis across different databases hinder the comparison and integration of pan-genome information from various projects at multi-species or single-species levels. To tackle this challenge, we introduce PlantPan, a comprehensive database housing the results of pan-genome analysis for 195 genomes from 11 plant species. PlantPan aims to provide extensive information, including gene-centric and sequence-centric pan-genome information, graph-based pan-genome, pan-genome openness profiles, gene functions and its variation characteristics, homologous genes, and gene clusters across different species. Statistically, PlantPan incorporates 9 163 011 genes, 694 191 gene clusters, 526 973 370 genome variations, and 1 616 089 non-redundant genome variation groups at the species level, 33 455,098 genome synteny, and 177 827 non-redundant genome synteny groups at the species level. Regarding functional genes, PlantPan contains 5 222 720 genes related to transcription factors, 395 247 literature-reported resistance genes, 455 748 predicted microbial/disease resistance genes, and 1 612 112 genes related to molecular pathways. In summary, PlantPan is a vital platform for advancing the application of pan-genomes in molecular breeding for crops and evolutionary research for plants.

Genome, Plant↗
PubMed2026

Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.

Livestock reference genomes have transformed the discovery of variants associated with production, reproduction, health, and environmental adaptation. Nevertheless, a single linear reference represents only one mosaic haplotype and incompletely captures sequence diversity within a species, particularly structural variants, copy-number changes, repeat-rich regions, and breed-specific sequences. Pangenomes address this limitation by integrating multiple high-quality assemblies or population-scale variants into a unified sequence or graph representation. Concurrently, multi-omics approaches connect genomic variation with transcriptomic, epigenomic, manuscriptproteomic, metabolomic, and microbiome responses, thereby improving biological interpretation of genotype-phenotype relationships. This review synthesizes recent progress in livestock pangenomics and multi-omics, with emphasis on cattle, goats, sheep, water buffalo, and chickens. It describes advances in long-read and haplotype-resolved sequencing, graph construction, structural-variant discovery and genotyping, functional annotation, and integrative analysis. Recent pangenome studies have uncovered substantial non-reference sequence, reduced reference bias, identified breed- and population-specific structural variants, and resolved candidate variants underlying pigmentation, body size, tail morphology, cashmere production, altitude adaptation, and other economically relevant traits. However, translation into routine breeding remains constrained by uneven population representation, inconsistent structural-variant definitions, limited functional annotation, computational demands, and insufficient validation across environments. Future progress will depend on diverse near-complete assemblies, graph-aware imputation and genomic prediction, long-read transcriptomics, single-cell and spatial omics, rigorous causal validation, and open, interoperable resources. Together, these developments can support more accurate, resilient, and biologically informed livestock improvement. Importantly, current dairy-cattle evidence indicates that pangenome-derived structural variants can substantially improve variant discovery and functional interpretation while yielding only marginal average gains in routine genomic prediction, favoring targeted augmentation rather than wholesale replacement of established SNP-based evaluations.

Animals↗
PubMed1990

A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data.

A simple method is proposed for estimating the average number of nucleotide substitutions per site within and between populations for the case where a large number of individuals are examined for many restriction enzymes. This method gives essentially the same results as those obtained by Nei and Li's method but saves a large amount of computer time. The variances of the quantities estimated can be obtained by the jackknife method, and these variances are very similar to those obtained by Nei and Jin's more sophisticated method. A similar method can also be applied to DNA sequence data.

Analysis of Variance↗
PubMed2025

An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience.

Tubers are modified underground stems that enable asexual, clonal reproduction and serve as a mechanism for overwintering and avoidance of herbivory. Tubers are wide-spread across angiosperms with some species such as Solanum tuberosum L. (potato) serving as a vital crop for human consumption. Genes responsible for tuber initiation and disease resistance have been characterized in potato including StSP6A, a homolog of Flowering Time, that functions as tuberigen, the equivalent of florigen. To elucidate additional molecular and genetic mechanisms underlying potato biology including tuber initiation, tuber development, and stress responses, we generated a developmental and abiotic/biotic-stress gene expression atlas from 34 tissues and treatments of Atlantic, a tetraploid cultivar. Using the haplotype-phased tetraploid Atlantic genome assembly and expression abundances of 129,218 genes, we constructed gene coexpression modules that represent networks associated with distinct developmental stages as well as stress responses. Functional annotations were given to modules and used to identify genes involved in tuberization and stress resilience. Structural variation from a pan-genomic analysis across four cultivated potato genome assemblies as well as domestication and wild introgression data allowed for deeper insights into the modules to identify key genes involved in tuberization and stress responses. This study underscores the importance of transcriptional regulation in tuberization and provides a comprehensive framework for future research on potato development and improvement.

Journal Article↗
PubMed2025

An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience.

Tubers are modified underground stems that enable asexual, clonal reproduction and serve as a mechanism for overwintering and avoidance of herbivory. Potato (Solanum tuberosum L.) is cultivated for its tubers, which serve as a major crop. Genes responsible for tuber initiation and disease resistance have been characterized in potato including StSP6A, a homolog of flowering time, that functions as a tuberigen, the equivalent of a florigen. To elucidate additional molecular and genetic mechanisms underlying potato biology including tuber initiation, tuber development, and stress responses, we generated a developmental and abiotic/biotic-stress gene expression atlas from 34 tissues and treatments of the tetraploid potato cultivar, Atlantic. Using the haplotype-phased tetraploid Atlantic genome assembly and expression abundances of 129 218 genes, we constructed gene coexpression modules that represent networks associated with distinct developmental stages as well as stress responses. Functional annotations were given to modules and used to identify genes involved in tuberization and stress resilience. Structural variation from a pan-genomic analysis across four cultivated potato genome assemblies as well as domestication and wild introgression data allowed for deeper insights into the modules to identify key genes involved in tuberization and stress responses. This study underscores the importance of transcriptional regulation in tuberization and provides a comprehensive framework for future research on potato development and improvement.

Solanum tuberosum↗
PubMed1977

[Anatomical variations and taxonomic relatedness in Hominoidea].

31 anatomical variations were examined in 125 Pan paniscus and 96 Gorilla gorilla beringei skulls. Comparisons with published data of Hominoidea show that differences in their frequencies are proportional and parallel to taxonomic relationships on the subspecific, specific and generic level.

Animals↗
PubMed1987

Evolution of P3 morphology in Australopithecus afarensis.

The Australopithecus afarensis dental sample exhibits a wide range of variation, which is most notable in the morphology of the lower third premolar (P3). P3 morphology in the A. afarensis sample ranges from the primitive sectorial extreme in AL 128-23 to the derived, bicuspid (molarized) extreme in AL 333w-1. In this paper, the degree and patterning of variation of the 20 known A. afarensis P3s are examined and the evolutionary implications are discussed. Initially, a series of dental and mandibular metric criteria are evaluated to determine whether this sample may be analyzed as a single species. From the metrics, it is clear that the single species hypothesis cannot be rejected. Next, a series of morphological criteria is devised to measure P3 molarization. Taken as a whole, the A. afarensis P3 sample displays more variation than a sample of modern hominoids (Pan troglodytes) and shows a slight trend toward increased molarization through time. When separated by sex, the A. afarensis sample still displays greater variation than the chimpanzee sample; however, only the male A. afarensis specimens show a trend toward increased molarization. Additionally, the male A. afarensis P3s are more molarized than the female, a pattern that is seen as well (though less markedly) in the chimpanzee sample. The trend toward increased molarization over time indicates selection for grinding in A. afarensis. The sexual differences parallel those seen in the postcrania (cf. Stern and Susman: Am. J. Phys. Anthropol. 60:279-318, 1983), as the females tend to retain the primitive condition, while the males display the derived morphology. Consequently, a model of sexual differences in niche exploitation, with the females exploiting a more arboreal environment, would seem to be supported by both the dental and postcranial evidence.

Africa↗
PubMed1988

The degree of genetic variability among adenovirus type 4 strains isolated from man and chimpanzee.

A total of 8 different genome types of adenovirus type 4 (Ad 4), Ad 4p, Ad 4p 1-3, Ad 4a, Ad 4a 1, Ad 4b, and Ad 4ch were identified among 50 selected human adenovirus isolates and 2 chimpanzee adenovirus strains using 16 restriction endonucleases Bam HI, Bcl I, Bgl I, Bgl II, Bst EII, Dra I, Eco RI, Eco RV, Hind III, Hpa I, Sal I, Sma I, Ssp I, Pst I, Xba I, and Xho I. They could be divided into three genomic clusters. Cluster 1 contained Ad 4p and Ad 4p 1-3; cluster 2 contained Ad 4a, ad 4a 1 and Ad 4b; whereas the chimpanzee Ad 4 genome type was the unique member of cluster 3. The degree of genetic variability within each cluster was minor. The genome types within one cluster display 95-99% pairwise comigrating restriction fragments (PCRF). However, the genetic space between the three clusters was large. The genome types between different clusters share only 25-46% PCRF. A comparative PCRF analysis performed with restriction endonucleases Apa I, Nar I, Nae I, Sac II, and Sma I recognizing exclusively G and C sequences and Dra I, Ssp I recognizing exclusively A and T containing sequences revealed that G and C rich regions were significantly more conserved than A and T rich regions.

Adenoviridae↗
PubMed1985

Evolution of Alu family repeats since the divergence of human and chimpanzee.

The DNA sequences of three members of the Alu family of repeated sequences located 5' to the chimpanzee alpha 2 gene have been determined. The base sequences of the three corresponding human Alu family repeats have been previously determined, permitting the comparison of identical Alu family members in human and chimpanzee. Here we compare the sequences of seven pairs of chimpanzee and human Alu repeats. In each case, with the exception of minor sequence differences, the identical Alu repeat is located at identical sites in the human and chimpanzee genomes. The Alu repeats diverge at the rate expected for nonselected sequences. Sequence conversion has not replaced any of these 14 Alu family members since the divergence between chimpanzee and human.

Animals↗
PubMed1992

Comparison of five tandem repeat loci between humans and chimpanzees.

Five tandem repeat loci were studied in humans and chimpanzees using VNTR probes derived from human DNA. Shared alleles were found at three loci and were often the modal allele in one species but never in both. There was no difference in the mean number of alleles per locus. However, these species exhibited substantially different levels of gene diversity, with chimpanzees monomorphic at two loci. Evidence of reduced variability in chimpanzees corroborates earlier comparisons using isozymes and plasma proteins. Molecular mechanisms, population dynamics, or both may be responsible for these differences. Equal numbers of alleles per locus may reflect high mutation rates. By one test, chimpanzees were out of equilibrium at one locus, which may reflect a typing error or population substructure. The long divergence time, and the high probability of backward mutations, precludes accurate estimation of genetic distance between these species.

Alleles↗
PubMed2025

The MTORC1 signaling pathway related gene POLR3G serves as a potential prognostic biomarker in Hepatocellular Carcinoma.

This study aims to investigate the prognostic significance and potential biological functions of the MTORC1 signaling pathway-associated gene POLR3G in Hepatocellular carcinoma (HCC). A prognostic risk model for HCC was developed by integrating HCC-related datasets and associated clinical data obtained from The Cancer Genome Atlas (TCGA) database. The GSVA website was employed to analyze the model genes across pan-cancer datasets, focusing on copy number variations (CNV), single nucleotide variations (SNV), methylation differences, drug sensitivity and immune cell infiltration profiles. Subsequently, we examined the expression levels and prognostic significance of POLR3G in HCC. Utilizing Spearman correlation analysis, we identified genes associated with POLR3G. Furthermore, Gene Set Enrichment Analysis (GSEA) was employed to elucidate the potential signaling pathways in which POLR3G may be involved. The relationship between POLR3G expression and immune cell abundance in HCC samples was assessed using the ssGSEA algorithm. Finally, the impact of POLR3G on HCC cell proliferation was validated through CCK-8 and EDU cell proliferation assays. Through univariate Cox regression analysis and LASSO regression analysis, we established a prognostic risk model for HCC comprising 13 genes. The analysis revealed that individuals categorized in the low-risk group had a markedly improved overall survival probability relative to those in the high-risk group. POLR3G exhibited a markedly elevated expression in HCC tissues when compared to adjacent normal tissues. The expression of POLR3G was correlated with tumor grade, and elevated POLR3G expression was associated with poor prognosis in HCC patients. Furthermore, the expression level of POLR3G was found to be correlated with the level of immune cell infiltration. Knockdown of POLR3G significantly inhibited the proliferative capacity of hepatocellular carcinoma cells. The findings suggest that POLR3G may serve as a potential biomarker influencing the prognosis of hepatocellular carcinoma patients by modulating the tumor immune microenvironment.

Humans↗