Biology subjects

Xi, X.

Publications and source records attributed to Xi, X..

At least 19 recordsLinked to original sources

bioRxiv2026

Endosperm secretion remodels the maternal seed coat

In flowering plants and mammals, maternal tissues must accommodate the growth of the offspring they enclose. The maternal seed coat expands around the developing embryo and endosperm. Endosperm pressure and hormonal signals coordinate seed-coat development1,2, but whether the endosperm directly promotes maternal cell elongation remains unclear. Here we show that the coenocytic Arabidopsis endosperm directly supplies cell-wall-loosening proteins to maternal seed-coat walls. The seed-size-regulating HAIKU-WRKY10 pathway activates an endosperm secretory programme enriched in cell-wall-associated proteins. These proteins spread through a shared extracellular domain across multiple inner seed-coat layers, revealing an extensive functional maternal-filial interface through which the endosperm reaches maternal cells it does not directly contact. Among these proteins, three expansins are necessary and sufficient for maternal cell elongation and seed growth. The endosperm therefore promotes its own growth by enabling expansion of the maternal tissues that enclose it. Paternal DNA methylation and maternal Polycomb activity jointly regulate this programme, with Polycomb also required for timely shutdown of expansin expression. These findings link parental epigenetic states to maternal tissue expansion through proteins supplied by the offspring. This cross-generational control of growth parallels epigenetically regulated signaling from mammalian extraembryonic tissues3, suggesting a shared strategy for adapting the maternal environment to offspring development.

plant biology↗

bioRxiv2026

Progressive plyometric training improves jumping performance and reduces force-velocity imbalance in collegiate volleyball players

Few studies have focused on plyometric interventions lasting over 24 weeks in team-sport athletes, and little research has validated the practical utility of personalized force-velocity assessment. A total of 36 university volleyball athletes (21.35{+/-}1.87 years) were randomly allocated into either a 32-week plyometric training group (PT, n=18) or a low-intensity active control group (CON, n=18); 34 players completed the trial (17 per group). PT completed three weekly training sessions, while CON maintained routine technical practice and general low-intensity conditioning. CMJ height, RSImod, and force-velocity profiles (F, V, peak power, FV imbalance) were evaluated at baseline and at weeks 8, 16, 24, and 32. PT increased CMJ height from 33.1{+/-}4.8 cm to 38.4{+/-}5.2 cm, a net gain of 5.3 cm (p<0.01, d=0.99, 95% CI [0.57, 1.41]); CON showed negligible change (+0.5 cm, p=0.68). The PT group also improved RSImod by 31.6% (d=0.87, 95% CI [0.45, 1.29], p<0.01) and peak power by 18.4% (d=0.76, 95% CI [0.35, 1.17], p=0.004). Meanwhile, FV imbalance dropped markedly by 31.4%, from 28.3% to 19.4% (d=-0.68, 95% CI [-1.09, -0.27], p=0.024). No significant F-V changes occurred in CON. The reduction in FV imbalance correlated moderately with CMJ gain (r= - 0.53, p=0.024), whereas the change in peak power did not (r=0.21, p=0.39). Overall, 32 weeks of periodized plyometric training enhanced jump performance, reactive strength, and power, and reduced the force-velocity (FV) imbalance by approximately 31%. The magnitude of improvements in jump performance (16%) and FV imbalance reduction (31%) observed in this 32-week periodized program fall within a similar range to previously reported effects of individualized F-V training (14% and 40%, respectively). However, direct numerical comparisons are confounded by differences in study design, population, and methodology; head-to-head trials are needed.

physiology↗

bioRxiv2026

The effects of breeding timing, clutch size, and nesting strategy on reproductive success in the crested ibis (Nipponia nippon)

O_LIStudying the reproduction process, which is a key determinant of individual and population fitness in endangered species, is challenging but urgently needed. The crested ibis (Nipponia nippon), a flagship endangered species recovering from an extreme population bottleneck, provides a valuable opportunity to examine how life-history strategies shape reproductive success and inform future conservation practices. C_LIO_LIWe monitored 176 breeding pairs of crested ibis over three consecutive breeding seasons and investigated the effects of three key life-history traits, namely breeding timing, clutch size, and nesting strategy (solitary versus colonial), on reproductive success (hatching and fledging success). C_LIO_LIOur analysis found that both hatching and fledging success declined significantly as breeding initiated later, and a positive association between clutch size and reproductive success in this species. These patterns were robust and repeatable across three years. Unlike other closely related species in this family, sibling competition is generally non-lethal, leading to large clutch sizes fledged in this endangered species. We consider this pattern to be a main reason underlying the rapid population recovery observed in the crested ibis. On the other hand, nesting strategy (colonial vs. solitary breeding) had no detectable effect on reproductive success. This pattern indicates the crested ibis can adopt different breeding strategies across habitats, highlighting its capacity to flexibly adjust breeding behavior in response to local environmental conditions. C_LIO_LIOur results provide an integrative assessment of how key life-history traits shape reproductive outcomes in a wild population of the crested ibis, serving as a foundation for evaluating its current status of population recovery and refining future conservation strategies for endangered avian species sharing similar life-history characteristics. C_LI

zoology↗

bioRxiv2026

Sexual size dimorphism increases with body size at the intraspecific level in Drosophila melanogaster

Sexual size dimorphism (SSD), the difference in body size between males and females, typically conforms to Renschs rule across species: SSD increases with body size when males are larger but decreases when females are larger. Although this macroevolutionary pattern has been extensively documented, intraspecific analyses remain rare, yet they are essential for understanding the proximate mechanisms underlying the origin and maintenance of sexual dimorphism. In particular, it remains unclear whether within-species variation in SSD is driven primarily by sex-specific differences in growth rate or in development time. Here, we addressed this question by examining SSD scaling in inbred lines of Drosophila melanogaster from the well-established Drosophila melanogaster Genetic Reference Panel (DGRP) reared under two thermal environments (25 {degrees}C and 28 {degrees}C). Females were consistently larger than males, resulting in pronounced female-biased SSD across different lines of this model insect. Moreover, SSD increased with overall body size, representing a reversal of Renschs rule at the intraspecific level. This scaling pattern was largely explained by higher female growth rates rather than sexual differences in development time. Elevated temperature reduced SSD by decreasing female growth rate while slightly enhancing that of males. Together, our results demonstrate that Renschs rule does not universally apply at intraspecific level and underscore the critical role of growth rate and environmental sensitivity in shaping SSD at the intraspecific level.

ecology↗

bioRxiv2025

Monitor individual health and improve breeding success in Crested ibis (Nipponia nippon)

Biodiversity loss has become a pressing issue, requiring effective conservation measures. Drawing lessons from successful examples is essential. The Crested ibis (Nipponia nippon), once critically endangered but now recovering through intensive conservation programs, provides an informative model for evaluating and improving conservation practices. Using 17 years of monitoring data from a captive population spanning eight generations, we applied quantitative genetic tools (Animal Model) to characterize individual growth and improve breeding success of this endangered species. We found that body weight from Day 0 to Day 42 exhibited significant heritability (h2 = 0.195, 95% HPD 0.139 [~] 0.250). As for growth curve parameters, growth time-scale parameter a (h2 = 0.33, 95% HPD: 0.14 [~] 0.55) and growth-rate coefficient b (h2 = 0.22, 95% HPD: 0.10 [~] 0.34) were also significantly heritable, while the heritability of potential maximum weight M was relatively low (h2 = 0.023, 95% HPD: 0.00 [~] 0.16). We further estimated the breeding values of these phenotypical traits to inform future breeding and selections. Intergenerational analyses showed the estimated breeding values for body weight exhibited a tendency to increase, accompanied by a slower growth rate, though trends did not differ significantly from expectations under genetic drift. Comparison of parental and offspring growth trajectories revealed that healthy offspring closely follow parental growth trajectories, whereas unhealthy individuals display reduced growth. Given the multiple breeding times of this long-lived species, this approach enables effective monitoring of individual growth and health, allowing timely veterinary interventions so to enhance conservation efficiency.

zoology↗

bioRxiv2025

Evaluate and simulate the reproduction and survival of a reintroduced population in an endangered bird species Crested ibis (Nipponia nippon)

O_LIReintroduction programs are critical for restoring endangered species. However, scientific assessments and management recommendations based on comprehensive vital rates across the entire life cycle remain limited for such programs. The Crested ibis (Nipponia nippon), once nearly extinct, has been the focus of intensive conservation efforts, including reintroduction into its historical range. Here, we systematically evaluate the success of a Crested ibis reintroduction population by integrating long-term field monitoring with population dynamic modeling. C_LIO_LIWe conducted a systematic, multi-year (2023-2025) demographic study of a reintroduced Crested ibis population in Dongzhai National Nature Reserve, China. From 2013 to 2023, a total of 133 captive Crested ibises were released in seven batches within the nature reserve. By 2025, the wild population had exceeded 500. Based on the combination of field monitoring (n = 176 pairs) and GPS telemetry (n = 74 GPS tags, the longest monitoring time lasting 4 years), we quantified reproductive output and mortality rates across six life stages: nest building, incubation, offspring provisioning, fledgling (< 1 year), sub-adult (1-2 years), and adult (> 2 years). C_LIO_LIThe results show that the average clutch size of this population is 3.24 {+/-} 0.08, and each pair of parent birds can rear 1.31 {+/-} 0.12 nestlings to fledging each year. We found that high mortality during the incubation (32.5%, n = 425 eggs), offspring provisioning (34.1%, n = 287 chicks), and fledgling stages (38.6%, n = 63 birds). Key causes included unfertilized eggs, predation, starvation, and human disturbance. On the other hand, the mortalities in the nest building (9.1%, n = 176 pairs), sub-adult (9.8%, n = 28 birds) and adult stage (21.3%, n = 15 birds) were relatively low. Stage-structured matrix model shows a positive population growth of this reintroduced population (growth rate {lambda} = 1.053), with the population expected to increase 13-fold over 50 years (6,858 individuals). Sensitivity analysis indicates that adult survival had the strongest influence on population growth. Correspondingly, we predict that by 2075, its distribution range will expand 13-fold in tandem with population growth, exceeding 51,000 km{superscript 2} and covering several surrounding cities. C_LIO_LIOur comprehensive monitoring, evaluation, and simulation across the full life-cycle confirm that the reintroduced population is successfully established and self-sustaining. This finding addresses a critical research gap: the lack of a scientific and systematic framework for assessing population reintroductions in endangered species. Furthermore, we identified key conservation practices to enhance population growth and stability, including predator control, supplemental feeding, the rescue of weak chicks, and reducing human disturbance through public engagement. To ensure long-term viability, we also recommend implementing genetic management to avoid inbreeding. The resulting framework provides a practical model for improving reintroduction success and promoting species recovery in other endangered species. C_LI

ecology↗

bioRxiv2025

Candling analysis of egg development in an endangered bird species Crested ibis (Nipponia nippon)

Identifying key factors influencing the survival of animals, particularly rare and endangered species is crucial to biodiversity conservation. In birds, hatching failure is pronounced in endangered species. Accurate assessment of egg development and the ability to distinguish non-viable eggs are essential prerequisites for identifying the causes of hatching failure and applying appropriate conservation practices. The Crested ibis (Nipponia nippon), a flagship endangered species, has a long history of captive breeding, which has contributed to population recovery. However, little is known about the specific process and characteristics of its egg development. In this study, we provided the first comprehensive description of normal egg development in the Crested ibis, including both the changes observed in unfertilized eggs during incubation and embryonic development via candling (n = 106 eggs, with 1,423 candling images), a commonly used non-invasive method for assessing egg fertility and embryonic status, and offered a practical reference for assessing fertilization status and embryo viability. In addition, we estimated the timing of embryo mortality and found that most deaths occurred during mid-incubation (Day 7[~]15) (n = 12, 60.0%) and shortly before hatching (Day 23[~]29) (n = 7, 35.0%), highlighting these critical periods that require particular attention. This species-specific documentation of egg development provides a valuable reference for accurately assessing embryonic progress, evaluating environmental effects on survival, and guiding adaptive management, benefiting both captive breeding programs and field conservation efforts.

zoology↗

bioRxiv2025

RIP2 inhibits DOCK8-mediated platelet dense granule release and alleviates experimental myocardial infarction

ObjectiveReceptor-interacting protein 2 (RIP2) is an essential mediator of inflammation and innate immunity downstream of pattern recognition receptors (PRRs). Platelets express RIP2, while its role in platelet activation, thrombosis, and myocardial infarction (MI) is unknown. Approach and ResultsHere we show that RIP2 deficiency enhances platelet dense granule secretion in response to GPIb and GPVI activation; platelet aggregation in whole blood and adhesion under arterial shear are also increased. Consistently, RIP2 inhibitor WEHI-345 potentiates human platelet dense granule secretion and inhibits RIP2 phosphorylation induced by thrombin and collagen. These phenotypes are translated into shorter bleeding time, accelerated FeCl3-induced arterial thrombosis. Importantly, platelets from patients with coronary artery disease and mice with atherosclerosis express lower RIP2, and RIP2 deficiency deteriorates MI and cardiac function in a mouse ischemia/reperfusion model. Mechanistically, we found that platelets express dedicator of cytogenesis protein 8 (DOCK8), which is sequestered by phosphorylated RIP2 (p-RIP2), causing inhibition of Cdc42 activation and subsequent dense granule release. ConclusionsIn conclusion, RIP2 inhibits platelet activation, thrombosis, and ameliorates MI. Our results also suggest that a novel PRR-independent pathway, p-RIP2-DOCK8-Cdc42, negatively regulates platelet activation downstream of GPIb and GPVI. Platelet RIP2 pathway may be promising for therapeutic intervention of atherothrombotic diseases from early atherosclerosis stage to arterial thrombosis and MI. HighlightsO_LIRIP2 inhibits platelet dense granule release NOD2-independenly via pRIP2-DOCK8-Cdc42. C_LIO_LIThe negative regulation of RIP2 on platelet activation is translated into enhanced thrombosis, exacerbated myocardial infarction (MI). C_LIO_LIRIP2 pathway booster may be an approach for therapeutic intervention of atherothrombotic diseases. C_LI

molecular biology↗

bioRxiv2025

Intraguild parasitism promotes the persistence of facultative hyperparasitoids by extending temporal host availability

Intraguild predation (IGP) is pervasive in natural food webs, although theoretical models predict restricted parameter space for the coexistence of IG-prey and IG-predators. One potential mechanism is that IGP persistence might be increased when IG-prey extend resource availability for IG-predators. Here we test this hypothesis using manipulative experiments in combination with mathematical modeling. Our experiment system includes Drosophila flies (Drosophila melanogaster, basal resources), primary larval parasitoids (Asobara leveri, IG-prey) and facultative pupal hyperparasitoid (Pachycrepoideus vindemiae, IG-predator). We measured the performance of facultative pupal parasitoids with and without the primary larval parasitoid. Our study revealed that larval parasitoids significantly increased the number of pupal parasitoids emerged from limited host resources, due to the extended resource availability to facultative hyperparasitoid. Specifically, immature primary parasitoids within Drosophila pupae can be explored by facultative hyperparasitoids for up to 14 days, while the healthy fly pupae are available to hyperparasitoids for only 5 days. Despite a significant reduction in offspring fitness of the facultative hyperparasitoids when reared on larval parasitoids versus healthy Drosophila pupae, adult female facultative hyperparasitoids showed no significant preference for healthy fly pupae over immature primary parasitoids. Our theoretical models demonstrated that an extended development period of the primary parasitoid can promote the persistence of the facultative hyperparasitoids and allow their coexistence with the primary parasitoid, although too prolonged development could drive the extinction of the primary parasitoid. As IG-prey often take longer time to develop after consuming the shared resources, extension of temporal resource availability could be a general mechanism contribute to the persistence of intraguild predators. Open research statementData are not yet available, but all of the original experimental data has been displayed in figures 2[~]4. The data will be made publicly available upon manuscript acceptance and archived in the Dryad Digital Repository.

ecology↗

bioRxiv2024

Preventive Effects of Pomegranate Seed Oil on Transient Middle Cerebral Artery Occlusion via the Keap1/Nrf2/NQO1 Pathway in the rats Cortex

Ischemic stroke remains a pressing challenge that needs to be solved. Energy metabolic failure is a critical factor contributing to mitochondrial dysfunction and oxidative stress in the pathogenesis of brain ischemia, leading to the generation of excessive reactive oxygen species. Pomegranate seed oil (PSO) exhibits antioxidant properties; however, its protective effects against cerebral ischemia/reperfusion injury and the underlying mechanisms remain unclear. In this study, a transient middle cerebral artery occlusion (tMCAO) rat model was employed to simulate cerebral ischemia/reperfusion injury. We investigated the mechanisms by which different concentrations of PSO modulate oxidative damage caused by cerebral ischemia/reperfusion injury through the Keap1/Nrf2/NQO1 pathway in cortex. SD male rats were randomly divided into four groups: Control, tMCAO+NaCl, tMCAO+LO (low concentration of PSO), tMCAO+MO (medium concentration of PSO), and tMCAO+HO (high concentration of PSO). Our findings suggest that low concentration of PSO exerts neuroprotective effects by activating Nrf2 and NQO1, thereby reducing oxidative stress. Furthermore, LO significantly improved neurological scores and reduced neuronal edema. Additionally, the results demonstrated an increase in superoxide dismutase (SOD) levels and a decrease in malondialdehyde (MDA) levels. In contrast, MO and HO exhibited suboptimal effects. To sum up, these results indicate that PSO activates neuroprotective pathways against oxidative stress following cerebral ischemia/reperfusion injury via the Keap1/Nrf2/NQO1 pathway, providing novel insights into potential preventive therapies for cerebral ischemia/reperfusion.

neuroscience↗

bioRxiv2024

Temporal variability in host availability alters the outcome of competition between two parasitoid species

O_LIVariability in the availability of resources through time is a common attribute in trophic interactions, but its effects on the fitness of different consumer species and on interspecific competition between them are not clearly understood. C_LIO_LITo investigate this, we allowed two parasitoid species, Trichopria drosophilae and Pachycrepoideus vindemiae, to exploit Drosophila host pupae under three temporal variability treatments, either on their own or simultaneously. C_LIO_LIWhen tested individually (in the absence of interspecific competition), both parasitoid species had lower fitness when hosts were exposed for a short duration at high density than when exposed for a long duration at low density. When both parasitoid species exploited hosts simultaneously, interspecific competition significantly decreased the number of offspring for both parasitoid species. The outcome of this interspecific competition depended on host temporal variability, with T. drosophilae or P. vindemiae dominating in short and long host exposure treatments, respectively. C_LIO_LIThese results can be explained by the combination of host availability and egg load of female adult parasitoids. When abundant hosts are provided for a short period, the ample mature eggs of the proovigenic T. drosophilae enable them to exploit hosts more efficiently than P. vindemiae, which is synovigenic. However, P. vindemiae is an intrinsically superior competitor and dominates when multiparasitism occurs. Multiparasitism is more frequent when hosts are at low levels relative to the egg load of the parasitoids. C_LIO_LIOur results clearly demonstrate that resource temporal availability can alter the outcome of competition between consumers with different reproductive traits. C_LI

ecology↗

bioRxiv2024

SRP19 and the protein secretion machinery is a targetable vulnerability in cancers with APC loss

Adenomatous Polyposis Coli (APC) is a tumour suppressor that is frequently lost in colorectal and other cancers. A common mechanism for APC loss includes heterozygous APC deletion. Here, we show that SRP19, is located near APC and is often co-deleted in these tumours. Heterozygous APC/SRP19 loss leads to lower levels of SRP19 mRNA and protein. Consequently, cells with APC/SRP19 loss are vulnerable to partial suppression of SRP19. We show that SRP19 loss is a unique vulnerability since SRP19 is rate limiting for the formation of the Signal Recognition Particle (SRP), a complex that mediates translocation of proteins to the ER. Consistent with these observations, partial SRP19 knock-down or low dose Arsenic Trioxide treatment induces ER stress and inhibits proliferation in APC/SRP19 loss cancers. Our work identifies a new strategy to treat cancers with APC/SRP19 heterozygous deletions and provides a framework for identifying vulnerabilities associated with loss of a tumour suppressor.

cancer biology↗

bioRxiv2023

Consensus peaks of chromatin accessibility in the human genome

The rapid advancement of transposase-accessible chromatin using sequencing (ATAC-seq) technology, particularly with the emergence of single-cell ATAC-seq (scATAC-seq), has accelerated the studies of gene regulation. However, the absence of a generic feature reference for ATAC-seq data limits single-cell analyses and hinders the development of comprehensive cell atlases. To address this, we constructed a generic chromatin accessibility reference by aggregating peaks from 624 high-quality bulk ATAC-seq datasets, defining more than 1 million consensus peaks (cPeaks). Leveraging a deep neural network model, we expanded cPeaks to include previously unobserved regions, enhancing their coverage across diverse tissues and cell types. cPeaks exhibit consistent shapes across tissue types, sequencing technologies, and peak-calling methods, indicating that they represent inherent genomic features. Compared to existing feature defining methods and references, cPeaks show superior performance in scATAC-seq analyses, improving cell annotation and rare cell type identification. Additionally, cPeaks provide insights into chromatin dynamics during cellular differentiation and tumor progression. cPeaks can serve as a robust reference for chromatin accessibility studies to promote cross-dataset consistency and accelerate biological discoveries.

bioinformatics↗

bioRxiv2023

Discovery of microRNA-derived RNAs and proteins in human cells

MicroRNAs (miRNAs) are short noncoding RNAs that can regulate gene expression through the binding of their 5-ends to mRNAs. However, the biological effects of miRNA binding via their 3-ends remain unclear. Here, we discover that the exact reverse pairing of the 3-ends of miRNAs or miRNA-like RNAs, collectively termed microsized RNAs (msRNAs), with template RNAs can initiate the production of msRNA-derived RNAs (msdRs), which can subsequently be translated into polypeptides (msdPs). Using 2,632 human msRNAs from miRBase, 11,121 msdRs and 1,239 msdPs were predicted based on a 15-nucleotide pairing threshold, and the presence of representative msdRs and msdPs was confirmed in human cells. Of clinical relevance, msdP0188 is highly expressed in human lung and breast cancers, and its corresponding msRNAs and msdRs represent novel anti-cancer targets. Notably, inhibiting telomerase reverse transcriptase, a putative RNA-dependent RNA polymerase identified by bioinformatic screening, led to reduced levels of msdP0188 in human cancer cells. Our findings reveal a novel "msRNA [->] msdR [->] msdP" axis, expanding the classical central dogma and predicting many previously unrecognized RNAs and polypeptides with potential biological functions in human cells and other systems.

cell biology↗

bioRxiv2022

Soil microbe-induced plant resistance alters aphid inter-genotypic competition leading to rapid evolution with consequences for plant growth and aphid abundance

O_LIPlants and insect herbivores are two of the most diverse multicellular groups in the world, and both are strongly influenced by interactions with the belowground soil microbiome. Effects of reciprocal rapid evolution on ecological interactions between herbivores and plants have been repeatedly demonstrated, but it is unknown if (and how) the soil microbiome could mediate these eco-evolutionary processes. C_LIO_LIWe tested the role of a plant-beneficial soil bacterium (Acidovorax radicis) in altering eco-evolutionary interactions between sap-feeding aphid herbivores (Sitobion avenae) feeding on barley (Hordeum vulgare). We reared two aphid genotypes separately or together on three barley varieties that were inoculated with or without A. radicis bacteria. In the first experiment we counted the aphid number and plant biomass after 7, 14 and 21 days of aphid growth, while in a second experiment we counted and removed offspring every 1-2 days to assess aphid longevity and fecundity. C_LIO_LIResults showed that A. radicis increased plant growth and suppressed aphids of both genotypes. The strength of effect was dependent on aphid genotype and barley variety, while the direction of effect was altered by aphid population mixture. Fescue aphids experienced increased growth when they were sharing the plant with Sickte aphids on inoculated plants; this increase was not seen in the control plants without A. radicis and was only apparent after 14 days of aphid population growth. C_LIO_LIPlant inoculation with A. radicis reduced aphid survival (reduced number of reproductive days) and fecundity (reduced daily reproductive output for surviving aphids). In the second experiment, when density was controlled, Fescue aphids did not experience increased reproduction in mixed populations, suggesting this is a density-dependent effect. Using Lotka-Volterra modelling, we demonstrated that A. radicis inoculation decreased aphid population stability as it increased inter-genotype competition but decreased the intra-genotype competition (likely through reduced population density). C_LIO_LIOur work demonstrates the important role that plant-associated microbiomes can have in mediating eco-evolutionary interactions between herbivores and host plants. C_LI

ecology↗

bioRxiv2021

Improved reference genome annotation of Brassica rapa by PacBio RNA sequencing

The species Brassica rapa includes several important vegetable crops. The draft reference genome of B. rapa ssp. pekinensis was completed in 2011, and it has since been updated twice. The pangenome with structural variations of 18 B. rapa accessions was published in 2021. Although extensive genomic analysis has been conducted on B. rapa, a comprehensive genome annotation including gene structure, alternative splicing events, and non-coding genes is still lacking. Therefore, we used the Pacific Biosciences (PacBio) single-molecular long-read technology to improve gene models and produced the annotated genome version 3.5. In total, we obtained 753,041 full-length non-chimeric (FLNC) reads and collapsed these into 92,810 non-redundant consensus isoforms, capturing 48% of the genes annotated in the B. rapa reference genome annotation v3.1. Based on the isoform data, we identified 830 novel protein-coding genes that were missed in previous genome annotations, defined the UTR regions of 20,340 annotated genes and corrected 886 wrongly-spliced genes. We also identified 28,564 alternative splicing (AS) events and 1,480 long non-coding RNAs (lncRNAs). We produced a relatively complete and high-quality reference transcriptome for B. rapa that can facilitate further functional genomic research.

plant biology↗

bioRxiv2021

A human ensemble cell atlas (hECA) enables in data cell sorting

Single-cell omics data can characterize multifaceted features of massive cells and bring significant insights to biomedical researches. The accumulation of single-cell data provides growing resources for constructing atlases for all cells of a human organ or the whole body. The true assembly of a cell atlas should be cell-centric rather than file-centric. We proposed a unified information framework enabling seamless cell-centric data assembly and developed a human Ensemble Cell Atlas (hECA) as an instance. hECA version 1.0 assembled scRNA-seq data across multiple studies into one orchestrated data repository. It contains 1,093,299 labeled cells and metadata from 116 published human single-cell studies, covering 38 human organs and 11 systems. We invented three methods of applications based on the cell-centric assembly: "In data" cell sorting enables targeted data retrieval in the full atlas with customizable logic expressions; The "quantitative portraiture" system provides a multi-view presentation of biological entities (organs, cell types, and genes) of multiple granularities; The customizable reference creation allows users to use the cell-centric assembly to generate references for their own cell type annotations. Case studies on agile construction of user-defined sub-atlases and "in data" investigation of CAR-T off-targets in multiple organs showed the great potential of cell-centric atlas assembly.

bioinformatics↗

bioRxiv2019

CRISPR-GNL: an improved model for predicting CRISPR activity by machine learning and featurization

MotivationThe CRISPR/Cas9 system has been broadly used in genetic engineering. However, risks of potential off-targets and the variability of on-target activity among different targets are two limiting factors. Several bioinformatic tools have been developed for CRISPR on-target activity and off-target prediction. However, the general application of the current prediction models is hampered by the great variation among different algorithms.\n\nResultsIn this study, we thoroughly re-analyzed 13 published datasets with eight regression models. We proved that the current model gave very low cross-dataset and cross-species prediction outcome. To overcome these limitations, we have developed an improved model (a generalization score, GNL) based on normalized gene editing activity from 8,101 gRNAs and 2,488 features using Bayesian Ridge Regression model. Our results demonstrated that the GNL model is a better general algorithm for CRISPR on-target activity prediction\n\nAvailability and implementationThe prediction scorer is available on GitHub (https://github.com/TerminatorJ/GNL_Scorer).\n\nContactJ.W. (wangjun6@genomics.cn) or Y.L. (luoyonglun@genomics.cn)\n\nSupplementary InformationSupplementary data are available at Bioinformatics online.

bioinformatics↗