Biology subjects

Fei, Z.

Publications and source records attributed to Fei, Z..

At least 19 recordsLinked to original sources

bioRxiv2026

Graph-based pangenome of Venturia inaequalis, the apple scab fungus, reveals structural variants associated with population differentiation

Plant pathogen genomes adapt across coding and non-coding regions in response to their hosts, environments, and disease management practices. Venturia inaequalis, the causal agent of apple scab, has evolved alongside its Malus host throughout apple domestication. We generated 17 high-quality genome assemblies, including the first chromosome-scale assembly of V. inaequalis, to define the species' complete gene content and investigate the role of structural variation in genome evolution. Together with a previously published scaffold-level reference, these assemblies were used to construct a gene-based pangenome containing 215,301 predicted protein-coding genes clustered into 13,240 orthogroups, 88.11% of which were core (73.86%) or soft-core (14.25%), 11.88% shell (present in 2-16 isolates), and 0.1% private, indicating a highly conserved gene repertoire. Virulence-associated effectors were significantly enriched in the soft-core and shell components, and accessory apoplastic effectors displayed elevated nucleotide diversity and nonsynonymous-to-synonymous substitution ratios (Ka/Ks) relative to core effectors, consistent with diversification. We further identified a putative accessory chromosome of variable size (23-132.6 kb) in European and U.S. isolates encoding genes with virulence function. A graph-based pangenome identified 38,799 non-redundant structural variants (SVs), largely driven by Gypsy LTR retrotransposons. We used the graph-based pangenome to genotype 136 globally distributed V. inaequalis isolates and identified variants differentiating populations associated with domesticated apple (Malus domestica) from those associated with its Central Asian wild progenitor, M. sieversii. Together, these resources establish a foundation for future studies of diversity, host adaptation, and genome evolution in V. inaequalis.

genomics↗

bioRxiv2026

A chromosome-scale reference genome and single-nucleus root atlas reveal the cellular and molecular basis of coastal adaptation in sand bean (Strophostyles helvola)

Plants adapted to saline coastal habitats provide valuable systems for understanding how natural selection reshapes stress-response programs, yet the cellular and molecular basis of this adaptation remains poorly resolved. Here, we generated a chromosome-scale reference genome and a single-nucleus transcriptomic atlas of roots from sand bean (Strophostyles helvola), a wild legume represented by salt-tolerant Beach and salt-sensitive Inland ecotypes. The atlas comprised 87,901 nuclei assigned to 25 transcriptional clusters representing 16 major root cell types. Salt exposure elicited cell-type-specific transcriptional responses that differed between Beach and Inland roots. Beach roots preferentially maintained respiration-, energy metabolism-, and protein-homeostasis-associated functions, whereas Inland roots showed stronger induction of canonical abiotic-stress, ABA, water-deficit, hypoxia, and oxidative-stress programs. Integrating baseline ecotype differences with salt-responsive expression revealed that many genes induced by salt in Inland roots were already expressed at higher levels in untreated Beach roots. This baseline-enriched configuration comprised a broadly distributed regulatory backbone, including ERF-family transcription factors and RING-type E3 ubiquitin ligases, together with cell-type-associated modules involving ion and water transport at the root-soil interface, redox and dehydration protection in outer-root tissues, endodermal barrier-associated genes, and vascular regulatory candidates. These findings support a model in which Beach salt tolerance is associated not with entirely distinct stress-response pathways, but with the pre-existing and spatially organized deployment of conserved protective programs that remain responsive to salt exposure. Our study establishes genomic and cellular resources for sand beans and provides a framework for investigating how natural variation in the regulation and cellular organization of conserved pathways contributes to environmental stress tolerance.

plant biology↗

bioRxiv2026

Multiple Particle Tracking via Velocity Filtering (MPT-vVF): a velocity filtering framework for robust tracking moving organelles in living cells

Living cells are highly dynamic and densely crowded environments in which organelles such as vesicles undergo continuous motion that is essential for cellular processes. Therefore, accurate tracking of individual organelles is crucial for understanding intercellular dynamics and functions. However, precise tracking of individual organelles in living cells remains challenging due to high organelle densities, frequent particle overlap, and the coexistence of stationary and motile organelles. In particular, stationary organelles can obscure the trajectories of moving organelles, leading to tracking errors and fragmented tracks. To overcome these challenges, we developed Multiple Particle Tracking via Velocity Filtering (MPT-vVF), an unbiased, semi-automated tracking framework that incorporates a mathematically derived velocity-filtering algorithm to selectively identify and track moving organelles with high accuracy in crowded intracellular environments. MPT-vVF integrates denoising, background subtraction, and a velocity-matching detection step that discriminates true particle motion from noise based on spatiotemporal continuity, followed by robust trajectory linking. We demonstrate that MPT-vVF can accurately resolve nanometer-scale displacements of immobilized beads, highlighting its high tracking precision. We also validate the robustness of MPT-vVF by quantifying the transport of brain-derived neurotrophic factor (BDNF)-mRFP-containing vesicles in living hippocampal neurons. Furthermore, MPT-vVF reveals that exposure to 50-nm nanoplastics impairs vesicular transport, reducing both travel length and speed of BDNF-containing vesicles in living neurons. These findings establish MPT-vVF as a powerful method for quantitative analysis of intracellular organelles in crowded living cells and suggest its broad application to biophysics, cell biology, and soft matter research.

biophysics↗

bioRxiv2026

Allele-specific expression reveals complex cis- and trans-regulatory divergence underlying fruit phenotypic differences between cultivated and wild tomato species

Tomato (Solanum lycopersicum) is one of the most important agricultural crops and serves as a model system for fleshy fruit biology. However, domestication bottlenecks have led to limited genetic diversity for further crop improvement. Wild relatives represent a rich reservoir of phenotypic diversity, yet the molecular basis underlying such phenotypic diversity remains largely unknown. As gene expression variation is a major driver of phenotypic diversity, we performed genome-wide allele-specific expression analyses in F1 hybrids between cultivated tomato and three wild relatives spanning a range of evolutionary distances, across three fruit tissues and multiple developmental stages. Our analysis generated a multi-species map of cis - and trans-regulatory variation, revealing a predominant role of cis-regulatory effects in expression divergence across species, tissues, and stages. The majority of cis effects were tissue- and/or stage-specific, underscoring the importance of tissue context in regulatory variation. Regulatory mechanisms and inheritance patterns shifted with evolutionary distance, with more distantly related species showing increased cis-regulatory contributions. Finally, we identified extensive regulatory divergence in biosynthetic pathways related to fruit nutritional value and flavor quality, including carotenoids, flavonoids, alkaloids, sugars, and volatiles. This study presents a high-resolution map of regulatory variation underlying tomato fruit development and provides evolutionary insights into the regulation of fruit nutrition and flavor traits.

genomics↗

bioRxiv2026

Graph-based pangenome provides insights into the adaptive evolution of Cucurbita pepo

Understanding how crops respond to environmental variation is crucial for biodiversity conservation and food security. Cucurbita pepo (pumpkin, squash, gourd) is one of the first domesticated crop species and exhibits remarkable phenotypic and ecological diversity, making it a powerful system for investigating the genomic basis of adaptation. Here, we constructed a graph-based C. pepo pangenome using nine chromosome-level assemblies and identified 229,431 high-confidence structural variants (SVs) that were genotyped across 206 wild and cultivated accessions. Our results demonstrate that C. pepo underwent parallel domestication, with two deeply diverged gene pools independently giving rise to the pepo and ovifera cultivated lineages, followed by expansion into diverse environments that produced strong signatures of differentiation largely mediated by young adaptive alleles. Single-nucleotide polymorphisms (SNPs) and SVs contribute complementary dimensions of environmental responsiveness. Biogeographical modeling predicts continued range contraction of wild relatives and elevated genetic offset in Eastern North American populations under projected future climates. Populations with higher genetic load harbor fewer adaptive variants and exhibit greater predicted maladaptation, indicating that deleterious mutations constrain adaptive potential. These findings highlight how genomic variants, adaptive diversity, and genetic load together shape environmental adaptation and inform conservation and crop improvement.

genomics↗

bioRxiv2026

Epistasis of two classical color genes, B and L-2, synergistically controls carotenoid accumulation in squash

Carotenoid accumulation underlies fruit color and nutritional quality in squash (Cucurbita pepo). One pair of dominant genes, B and L-2, have been long known to interact epistatically, substantially boosting carotenoid accumulation and producing intensely orange-fleshed fruit. However, their molecular identities and regulatory mechanism are unknown. Here, we show that B encodes a truncated H subunit of magnesium chelatase (CpCHLHB) and L-2 encodes a homolog of Arabidopsis Pseudo-Response Regulator 2 (CpAPRR2-A). Significantly, expression of phytoene synthase (CpPSY-A), which encodes the major rate-limiting enzyme in carotenoid biosynthesis, was dramatically upregulated in fruit of B/B L-2/L-2 plants compared with b/b L-2/L-2 or B/B l-2/l-2, showing that the B and L-2 interaction affects CpPSY-A transcription. A similar upregulation was also observed in Arabidopsis gun5 L-2 transgenic plants, where gun5 is a genetic mimic of the C. pepo B gene. The wild-type CpCHLHb physically interacted with CpAPRR2-A, attenuating the CpAPRR2-A-mediated activation of CpPSY-A. In contrast, the truncated CpCHLHB lost its ability to interact with CpAPRR2-A, enabling CpAPRR2-A to activate CpPSY-A and produce intensely orange fruit. These findings uncover the mechanism underlying the epistatic interaction through which B and L-2 act synergistically to boost carotenoid production, offering novel mechanistic insights and key targets for improving crop quality. One-sentence summarySynergistic epistasis between B and L-2 arises from loss of interaction between their encoded proteins, resulting in dramatically upregulating the key rate-limiting enzyme in carotenoid biosynthesis pathway to produce intensely orange-fleshed fruit in squash.

plant biology↗

bioRxiv2025

Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon

Pangenomes are increasingly critical for harnessing crop genetic diversity, yet their resolution and utility are often limited by insufficient sampling of high-quality genome assemblies. Here, we report a population-level watermelon super-pangenome constructed from 138 reference-grade assemblies, including 135 newly generated near-gapless genomes representing all seven watermelon species. The super-pangenome captures approximately one million structural variants (SVs), enabling accurate variant genotyping across ~900 watermelon accessions and substantially expanding variant discovery both across and within species. Broader sampling within the pangenome provides insights into genome evolution among watermelon species and sheds light on the origin of cultivated watermelon. SV-inclusive genome-wide association studies enhance trait mapping resolution and identify a copy number variation upstream of ClFCI1 that regulates flesh color intensity in a dosage-dependent manner. Leveraging this comprehensive variation map, we developed high-accuracy genomic prediction models for 18 agronomic traits. Together, our findings and genomic resources establish a foundational framework for dissecting complex traits and accelerating precision breeding in watermelon, while offering a valuable model for SV-resolved pangenomics in crop species.

plant biology↗

bioRxiv2025

Graph pangenome reveals structural variation dynamics during cucumber breeding

Structural variants (SVs) represent a significant yet underexplored component of plant genome diversity. Analyzing SV dynamics is important for understanding their contributions to phenotypic variation and their influence on genome evolution. Here, we present a graph-based pangenome for cucumber, constructed from 39 reference-level genome assemblies. The pangenome captures 171,892 high-confidence SVs and enables genotyping of these SVs across 443 cucumber accessions, representing diverse geographic origins and spanning wild progenitors, landraces, and modern cultivars. Our analyses reveal that during cucumber domestication, a substantial portion of mildly deleterious SNPs are retained, whereas SVs are consistently purged, highlighting their potentially highly deleterious nature. During the geographic expansion of cucumber, a reduction in SV burden and a younger age of SVs than SNPs were observed, suggesting stronger purifying selection acting on SVs. Additionally, notable gene flow from wild population to African and European populations was detected, resulting in an increased SV burden, potentially due to hitchhiking effects. Importantly, incorporating SV burden into genomic prediction models improved the prediction accuracy for several agronomically important traits. This study illuminates the dynamics of SVs during cucumber domestication and improvement, highlights the complex interplay between SVs and selection pressures, and underscores the extensive implications of SVs for future cucumber breeding.

plant biology↗

bioRxiv2024

Phased chromosome-level genome assembly provides insight into the origin of hexaploid sweetpotato

The hexaploid sweetpotato (Ipomoea batatas [L.] Lam.) is a globally important stable crop and plays a significant role in biofortification. The high resilience and adaptability of sweetpotato provide it with advantages in addressing food security and climate change issues. Here we report a haplotype-resolved chromosome-level genome assembly of an African cultivar, Tanzania, which enables ancestry inference along the haplotype-phased chromosomes. Our analyses reveal that the wild tetraploid I. aequatoriensis, currently found in coastal Ecuador, is the closest known relative of sweetpotato and likely a direct descendant of one of the sweetpotato progenitors. The other unknown progenitor(s) of sweetpotato have a closer genetic relationship to the wild tetraploid I. batatas 4x, distributed in Central America, than to I. aequatoriensis. The different ancestral sequences are not distributed in typical subgenomes but are intertwined on the same chromosomes, possibly due to the known non-preferential recombination among haplotypes. Although I. batatas 4x was not involved in the hexaploidization event, introgression from I. batatas 4x to the hexaploid sweetpotato is evident. Our study improves our understanding of sweetpotato origin and provides valuable genomic resources to accelerate sweetpotato breeding.

plant biology↗

bioRxiv2024

Viral and bacterial plant pathogens suppress antiviral defense against flaviviruses in their insect vectors

A positive, single-stranded RNA virus member within the Flavivirus genus was identified and characterized infecting Myzus persicae. This new insect-specific virus (ISV), Myzus persicae flavivirus (MpFV), is 23,236 nucleotides in length and encodes a large polyprotein from a single open reading frame. Analysis of conserved domains showed that helicases, NS3-proteases, Fts-J methyltransferase, and an RNA-dependent RNA polymerase are present in the coded polyprotein. Aphid-infecting ISVs have been reported to interact with plant viruses within the vector, modulating its titer and manipulating aphid behavior and morphology. Small RNA (sRNA) profile analysis of the M. persicae sRNA profile demonstrated that the circulative plant virus, potato leafroll virus (PLRV), modified the aphid antiviral immunity against MpFV. Abundant sRNA reads matching MpFV were detected when aphids were fed on healthy plants, sucrose diet, and potato virus Y-infected plants. In contrast, no MpFV reads were detected in aphids that had acquired PLRV from infected plants or artificial diet sachets containing purified virions. While the titer of M. persicae densovirus (MpDNV) was previously reported to be regulated by expression of the PLRV silencing suppressor protein P0, P0 had no effect on MpFV titer in the aphid. MpFV was transmitted 100% vertically to the offspring, and exhibited tissue tropisms for the body rather than the head. By artificial diet assays, other aphid species, including Aphis gossypii (cotton aphid), Schizaphis graminum (greenbug aphid), Rhopalosiphum padi (bird cherry-oat aphid), and R. maidis (corn leaf aphid), acquired the MpFV. These findings further support the idea that PLRV suppresses aphid immunity against ISVs, suggest the existence of at least two distinct pathways for PLRV-induced aphid immune system modulation. To test whether other circulative plant pathogens suppress insect anti-viral immunity against insect-specific flaviviruses, we quantified the small RNA response of Diaphorina citri, vector of "Candidatus Liberibacter asiaticus" (CLas) associated with citrus greening disease and showed that CLas also suppresses D. citri anti-viral immunity against D. citri-like flavivirus (DcLFV). These data reveal an evolutionary conserved, unexpected role for diverse circulative plant pathogens in modulating anti-viral immunity in hemipteran vectors.

microbiology↗

bioRxiv2024

Dissecting the genetic regulation of lateral root development in tomato under salt stress

Roots are the primary site for sensing salt, making them critical to understanding how plants adapt to salinity. Unraveling the genetic and molecular mechanisms that maintain root growth under salt stress is essential for developing resilient crops. Tomatoes are vulnerable to salinity, as over 50% of arable land is projected to become saline by 2050. While salt stress effects on tomato seed germination, shoot growth, and fruit yield are well-documented, the genetic basis of root development under salinity remains underexplored. Previous studies focused on physiological responses of roots in a narrow range of cultivated-tomatoes, overlooking the genetic diversity for salt resilience in wild-relatives like Solanum pimpinellifolium. Here, we investigated salt-induced changes in root system architecture (RSA) across a natural diversity panel of 220 wild- and 25 cultivated-tomato varieties. We identified tolerant accessions with different RSA strategies; prioritizing lateral root elongation versus emergence. To identify genes involved in specific aspects of lateral root development, an F1 hybrid was generated that exhibited both parents combined characteristics. An F2-segregating population was then used to identify four distinct subpopulations for Bulk Segregant Analysis (BSA). Simultaneously, we conducted Genome-Wide-Association Studies (GWAS) on root architecture of wild-tomato accessions under salt stress. By integrating the results of BSA and GWAS, we identified 22 candidates involved in the maintenance of root architecture. We utilized RNA-Seq to examine transcriptome reprogramming of the 22 genes in tomato accessions with contrasting lateral root responses. This approach resulted in the identification of 2 genes, AP2-like-ethylene-responsive transcription factor TOE3 and L-ascorbate peroxidase. Using exogenous ethylene, we demonstrated that root architecture exhibits plasticity, which benefits the plant by reducing Na+ accumulation. We profiled H2O2 waves across root systems of tomatoes, emphasizing the role of ROS in maintaining root system architecture under salt stress. These findings provide novel genetic targets for enhancing salt resilience in tomatoes, opening avenues for future research and breeding programs.

plant biology↗

bioRxiv2024

Molecular basis of one-step methyl anthranilate biosynthesis in grapes, sweet orange, and maize

Plants synthesize an array of volatile compounds, many of which serve ecological roles in attracting pollinators, deterring herbivores, and communicating with their surroundings. Methyl anthranilate is an anti-herbivory defensive volatile responsible for grape aroma that is emitted by several agriculturally relevant plants, including citrus, grapes, and maize. Unlike maize, which uses a one-step anthranilate methyltransferase, grapes have been thought to use a two-step pathway for methyl anthranilate biosynthesis. By mining available transcriptomics data, we identified two anthranilate methyltransferases in Vitis vinifera (wine grape), as well as one ortholog in Concord grape. Many angiosperms methylate the plant hormone salicylic acid to produce methyl salicylate, which acts as a plant-to-plant communication molecule. Because the Citrus sinensis (sweet orange) salicylic acid methyltransferase can methylate both anthranilate and salicylic acid, we used this enzyme to examine the molecular basis of anthranilate activity by introducing rational mutations, which identified several active site residues that increase activity with anthranilate. Reversing this approach, we introduced mutations that imparted activity with salicylic acid in the maize anthranilate methyltransferase, which uncovered different active site residues from those in the citrus enzyme. Sequence and phylogenetic analysis revealed that one of the Vitis anthranilate methyltransferases shares an ancestor with jasmonic acid methyltransferases, similar to the anthranilate methyltransferase from strawberry (Frageria sp.). Collectively, these data demonstrate the molecular mechanisms underpinning anthranilate activity across methyltransferases and identified one-step enzymes by which grapes synthesize methyl anthranilate. Significance StatementWhile the two-step pathway responsible for the biosynthesis of the grape aroma molecule, methyl anthranilate, has remained incomplete in Vitis spp., we identified two one-step anthranilate methyltransferases in wine and one in Concord grapes that can methylate the tryptophan pathway intermediate anthranilate. Tracing the molecular basis of anthranilate activity in the maize and sweet orange methyltransferases uncovered distinct active site amino acids that impart substrate specificity.

plant biology↗

bioRxiv2024

Genome sequencing of 'Fuji' apple clonal varieties reveals evolutionary history and genetic mechanism of the spur-type morphology

Somatic variations arising during asexual reproduction can lead to the emergence of bud sports exhibiting advantageous traits, forming the basis for bud sport breeding in perennial plants. Here, we report a near-complete, fully phased genome assembly of Fuji apple, enabling comprehensive identification of somatic variants across 74 clonally propagated Fuji varieties. Phylogenetic analysis of Fuji sport varieties indicates that the emergence of spur-type and early maturation traits results from multiple independent formation events. A number of putative functional somatic variants are identified, including one spur-type specific deletion located in the promoter of the TCP transcription factor gene MdTCP11. DNA methylation level of the deletion-associated miniature inverted-repeat transposable element is lower in the spur-type varieties compared to the standard-type varieties, while the expression of MdTCP11 is significantly higher. Overexpression of MdTCP11 in apple decreases the plant height, highlighting its important role in the development of spur-type apple varieties. This study sheds light on the 80-year cloning history of Fuji and provides valuable candidate causative mutations for apple breeding.

plant biology↗

bioRxiv2024

Advancing apple genetics research: Malus coronaria and Malus ioensis genomes and a gene family-based pangenome of native North American apples

Wild Malus species flourished in North America long before Europeans introduced domesticated apples. Malus coronaria and M. ioensis are native to the mid-western and eastern USA, while M. angustifolia and M. fusca grow in the southeast and west, respectively. They offer disease resistance, climate and soil adaptability, and horticultural traits for apple breeding. However, their utilization remains limited due to insufficient genomic resources and specific genetics. We report high-quality phased chromosome-scale assemblies of M. coronaria and M. ioensis, generated using long-read and conformation capture sequencing. Phylogenetic and synteny analysis indicated high relatedness between these two genomes and previously-published genome of M. angustifolia, and lower relatedness with M. fusca. Gene family-based pangenome of North American Malus identified 60,211 orthogroups containing 340,087 genes. Genes involved in basic cellular and metabolic processes, growth, and development were core to the existence of these species, whereas genes involved in secondary metabolism, stress response, and interactions with other organisms were accessory and are likely associated with adaptation to specific environments. Structural variation hotspots were mostly overlapping with high gene density. This study offers novel native North American Malus genome resources that can be used to identify genes for apple breeding and understand their evolution and adaptation.

genomics↗

bioRxiv2024

Five-layered robot (F-robot) based on functionally graded multilayer foam antiviral low-carbon (F-MAX) system for Pathogenic Microorganism Elimination

In this study, a revolutionary air filtration technology, the F-MAX multilayer composite plate, is introduced, offering high efficiency and environmental sustainability. This innovative system is designed to capture a wide range of pollutants, including harmful viruses and bacteria, enhancing air quality significantly. The F-MAX combines multiple layers, each tailored to target specific particles, with features like an electrostatically charged melt-blown fabric and eco-friendly materials like lithium brine by-product magnesia. Its durability, antiviral, and antibacterial properties make it a sustainable choice for air purification, suitable for both commercial and residential use. This system represents healthier living environments, effectively removing airborne contaminants, and demonstrating a commitment to a sustainable future. Additionally, the study introduces the F-robot specifically designed for laboratory environments to ensure pristine air quality. One-Sentence SummaryT-robot air filter, which use F-MAX, a multilayer composite consisted of self-healing cellular coating, Desert Rose (DR) coating, melt-blown cloth, and BMSC with high-efficiency, environmentally sustainable filtration, and antiviral properties, suitable for diverse environments.

microbiology↗

bioRxiv2024

Related PP2C phosphatases Pic3 and Pic12 negatively regulate immunity in tomato to Pseudomonas syringae

Type 2C protein phosphatases (PP2Cs) constitute a large family in most plant species but relatively few of them have been implicated in immunity. To identify and characterize PP2C phosphatases that affect tomato immunity, we used CRISPR/Cas9 to generate loss-of-function mutations in 11 PP2C-encoding genes whose expression is altered in response to immune elicitors or pathogens. We report that two closely related PP2C phosphatases, Pic3 and Pic12, are involved in regulating resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Loss-of-function mutations in Pic3 lead to enhanced resistance to Pst in older but not younger leaves, whereas such mutations in Pic12 resulted in enhanced resistance in both older and younger leaves. Overexpression of Pic3 and Pic12 proteins in leaves of Nicotiana benthamiana inhibited resistance to Pst and this effect was dependent on Pic3/12 phosphatase activity and an N-terminal palmitoylation motif associated with localization to the cell periphery. Pic3 but not Pic12 had a slight negative effect on flagellin-associated reactive oxygen species generation, although their involvement in the response to Pst appeared independent of flagellin. RNA-sequencing analysis of Rio Grande (RG)-PtoR wild-type plants and two independent RG-pic3 mutants revealed that the enhanced disease resistance in RG-pic3 older leaves is associated with increased transcript abundance of multiple defense related genes. RG-pic3/RG-pic12 double mutant plants exhibited stronger disease resistance than RG-pic3 or RG-pic12 single mutants. Together, our results reveal that Pic3 and Pic12 negatively regulate tomato immunity in an additive manner through flagellin-independent pathways.

plant biology↗

bioRxiv2024

HortGenome Search Engine, a universal genomic search engine for horticultural crops

Horticultural crops comprising fruit, vegetable, ornamental, beverage, medicinal and aromatic plants play essential roles in food security and human health, as well as landscaping. With the advances of sequencing technologies, genomes for hundreds of horticultural crops have been deciphered in recent years, providing a basis for understanding gene functions and regulatory networks and for the improvement of horticultural crops. However, these valuable genomic data are scattered in warehouses with various complex searching and displaying strategies, which increases learning and usage costs and makes comparative and functional genomic analyses across different horticultural crops very challenging. To this end, we have developed a lightweight universal search engine, HortGenome Search Engine (HSE; http://hort.moilab.net), which allows querying genes, functional annotations, protein domains, homologs, and other gene-related functional information of more than 400 horticultural crops. In addition, four commonly used tools, including BLAST, Batch Query, Enrichment analysis, and Synteny Viewer, have been developed for efficient mining and analysis of these genomic data.

bioinformatics↗

bioRxiv2023

Epigenetic predictors of species maximum lifespan and other life history traits in mammals

Maximum lifespan is an intrinsic characteristic of a biological species and is defined as the longest time an individual of a species has been reported to survive. By analyzing 15K samples derived from 348 mammalian species representing 25 taxonomic orders we previously identified CpG methylation sites associated with maximum lifespan. Here we present accurate DNA methylation-based (DNAm) predictors of maximum lifespan (r=0.89), average gestation time (r=0.96), and age at sexual maturity (r=0.85). Our DNAm maximum lifespan predictor indicates a potential innate longevity advantage for females over males in 17 mammalian species such as humans, red deer, and cattle. The DNAm maximum lifespan predictions do not vary significantly by caloric restriction and partial reprogramming. Genetic disruptions in the somatotropic axis, which includes growth hormone, IGF-1, and their related receptors, have an impact on DNAm maximum lifespan only in select mouse tissues. Cancer mortality rates in major mammalian orders show no correlation with our epigenetic estimates of life history traits. The DNAm maximum lifespan predictor does not detect variation in lifespan between individuals of the same species, such as between the breeds of dogs. We also present the first prototypes of accurate pan mammalian DNAm predictors of sex and tissue type. Collectively, our findings indicate that maximum lifespan is determined, at least in part, by an epigenetic signature that is an intrinsic property of each species and is distinct from the signatures that relate to individual lifespan, which is unaffected by interventions influencing the mortality risk of individuals.

evolutionary biology↗