MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome.

Alternative splicing (AS) is an essential post-transcriptional mechanism that regulates many biological processes. However, identifying comprehensive types of AS events without guidance from a reference genome is still a challenge. Here, we proposed a novel method, MkcDBGAS, to identify all seven types of AS events using transcriptome alone, without a reference genome. MkcDBGAS, modeled by full-length transcripts of human and Arabidopsis thaliana, consists of three modules. In the first module, MkcDBGAS, for the first time, uses a colored de Bruijn graph with dynamic- and mixed- kmers to identify bubbles generated by AS with precision higher than 98.17% and detect AS types overlooked by other tools. In the second module, to further classify types of AS, MkcDBGAS added the motifs of exons to construct the feature matrix followed by the XGBoost-based classifier with the accuracy of classification greater than 93.40%, which outperformed other widely used machine learning models and the state-of-the-art methods. Highly scalable, MkcDBGAS performed well when applied to Iso-Seq data of Amborella and transcriptome of mouse. In the third module, MkcDBGAS provides the analysis of differential splicing across multiple biological conditions when RNA-sequencing data is available. MkcDBGAS is the first accurate and scalable method for detecting all seven types of AS events using the transcriptome alone, which will greatly empower the studies of AS in a wider field.

Solidification/stabilisation behaviours of Zn2+ in magnesium potassium phosphate cement: Experiments and density functional theory study.

The solidification/stabilisation behaviours of Zn2+ in magnesium potassium phosphate cement (MKPC) have not been thoroughly investigated. Herein, a series of experiments and a detailed density functional theory (DFT) study were conducted to investigate the solidification/stabilisation behaviours of Zn2+ in MKPC. The results showed that the compressive strength of MKPC reduced with the addition of Zn2+ because the formation of MgKPO4·6H2O (the main hydration product in MKPC) was delayed with the addition of Zn2+, as discovered by the crystal characteristics, and because Zn2+ exhibited a lower binding energy in MgKPO4·6H2O compared to Mg2+, as revealed by DFT results. Additonally, Zn2+ had little influence on the structure of MgKPO4·6H2O, and Zn2+ existed in MKPC as the formation of Zn2(OH)PO4, which was decomposed in the range of around 190-350 °C. Moreover, there were a lot of well-crystallised tabular hydration products before the addition of Zn2+, but the matrix was comprised of irregular prism crystals after adding Zn2+. Furthermore, the leaching toxicity of Zn2+ of MKPC was much smaller than the requirements of Chinese and European standards.

Characteristics and potential functional effects of long insertions in Asian butternuts.

BACKGROUND: Structural variants (SVs) play important roles in adaptation evolution and species diversification. Especially, in plants, many phenotypes of response to the environment were found to be associated with SVs. Despite the prevalence and significance of SVs, long insertions remain poorly detected and studied in all but model species. RESULTS: We used whole-genome resequencing of paired reads from 80 Asian butternuts to detect long insertions and further analyse their characteristics and potential functional effects. By combining of mapping-based and de novo assembly-based methods, we obtained a multiple related species pangenome representing higher taxonomic groups. We obtained 89,312 distinct contigs totaling 147,773,999 base pair (bp) of new sequences, of which 347 were putative long insertions placed in the reference genome. Most of the putative long insertions appeared in multiple species; in contrast, only 62 putative long insertions appeared in one species, which may be involved in the response to the environment. 65 putative long insertions fell into 61 distinct protein-coding genes involved in plant development, and 105 putative long insertions fell into upstream of 106 distinct protein-coding genes involved in cellular respiration. 3,367 genes were annotated in 2,606 contigs. We propose PLAINS ( https://github.com/CMB-BNU/PLAINS.git ), a streamlined, comprehensive pipeline for the prediction and analysis of long insertions using whole-genome resequencing. CONCLUSIONS: Our study lays down an important foundation for further whole-genome long insertion studies, allowing the investigation of their effects by experiments.

Exposing Cu(100) Surface via Ion-Implantation-Induced Oxidization and Etching for Promoting Hydrogen Evolution Reaction.

Metallic materials with unique surface structure have attracted much attention due to their unique physical and chemical properties. However, it is hard to prepare bulk metallic materials with special crystal faces, especially at the nanoscale. Herein, we report an efficient method to adjust the surface structure of a Cu plate which combines ion implantation technology with the oxidation-etching process. The large number of vacancies generated by ion implantation induced the electrochemical oxidation of several atomic layers in depth; after chemical etching, the Cu(100) planes were exposed on the surface of the Cu plate. As a catalyst for acid hydrogen evolution reaction, the Cu plate with (100) planes merely needs 273 mV to deliver a current density of 10 mA/cm2 because the high-energy (100) surface has moderate hydrogen adsorption and desorption capability. This work provides an appealing strategy to engineer the surface structure of bulk metallic materials and improve their catalytic properties.

Standing genetic variation as the predominant source for adaptation of a songbird.

What kind of genetic variation contributes the most to adaptation is a fundamental question in evolutionary biology. By resequencing genomes of 80 individuals, we inferred the origin of genomic variants associated with a complex adaptive syndrome involving multiple quantitative traits, namely, adaptation between high and low altitudes, in the vinous-throated parrotbill (Sinosuthora webbiana) in Taiwan. By comparing these variants with those in the Asian mainland population, we revealed standing variation in 24 noncoding genomic regions to be the predominant genetic source of adaptation. Parrotbills at both high and low altitudes exhibited signatures of recent selection, suggesting that not only the front but also the trailing edges of postglacial expanding populations could be subjected to environmental stresses. This study verifies and quantifies the importance of standing variation in adaptation in a cohort of genes, illustrating that the evolutionary potential of a population depends significantly on its preexisting genetic diversity. These findings provide important context for understanding adaptation and conservation of species in the Anthropocene.

Gradient Structure Design of a Floatable Host for Preferential Lithium Deposition.

Herein, a novel sandwichlike host with expandable accommodation and gradient characteristics of lithiophilicity and conductivity is prepared by constructing a reduced graphene oxide (rGO)/SiO2/rGO intercalated structure on the basis of electrospraying and coating an additional PVDF-HFP layer on the top surface. This gradient host electrode enables preferential, ordered, and uniform Li deposition in the SiO2-embedded interlayer space. The dendrite growth and isolated Li are suppressed by the combined rGO/PVDF-HFP layer with robust, flexible, and floatable features, which could function as an artificial solid-electrolyte interphase to impede reckless electrolyte infiltration, homogenize the Li ion flux distribution, and build a stable electrochemical interface. The designed electrodes could be stably cycled with a high capacity of 5 mAh cm-2 and give rise to a high average Coulombic efficiency (CE) of 99.14%. Furthermore, the derived full cells can deliver an average CE of 99.87% in 300 cycles with a capacity retention of 90.22% and successfully operate under lean electrolyte conditions.

A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes.

BACKGROUND: With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from which there will be great opportunities for computational pangenomics. Although genome graphs are among the most useful models for pangenome representation, their structural complexity makes it difficult to present genome information intuitively, such as the linear reference genome. Thus, efficiently and accurately analyzing the genome graph spatial structure and coordinating the information remains a substantial challenge. RESULTS: We developed a new method, a colored superbubble (cSupB), that can overcome the complexity of graphs and organize a set of species- or population-specific haplotype sequences of interest. Based on this model, we propose a tri-tuple coordinate system that combines an offset value, topological structure and sample information. Additionally, cSupB provides a novel method that utilizes complete topological information and efficiently detects small indels (< 50 bp) for highly similar samples, which can be validated by simulated datasets. Moreover, we demonstrated that cSupB can adapt to the complex cycle structure. CONCLUSIONS: Although the solution is made suitable for increasingly complex genome graphs by relaxing the constraint, the directed acyclic graph, the motif cSupB and the cSupB method can be extended to any colored directed acyclic graph. We anticipate that our method will facilitate the analysis of individual haplotype variants and population genomic diversity. We have developed a C + + program for implementing our method that is available at https://github.com/eggleader/cSupB .

Alternative splicing during fruit development among fleshy fruits.

BACKGROUND: Alternative splicing (AS) is an important mechanism of posttranscriptional modification and dynamically regulates multiple physiological processes in plants, including fruit ripening. However, little is known about alternative splicing during fruit development in fleshy fruits. RESULTS: We studied the alternative splicing at the immature and ripe stages during fruit development in cucumber, melon, papaya and peach. We found that 14.96-17.48% of multiexon genes exhibited alternative splicing. Intron retention was not always the most frequent event, indicating that the alternative splicing pattern during different developmental process differs. Alternative splicing was significantly more prevalent at the ripe stage than at the immature stage in cucumber and melon, while the opposite trend was shown in papaya and peach, implying that developmental stages adopt different alternative splicing strategies for their specific functions. Some genes involved in fruit ripening underwent stage-specific alternative splicing, indicating that alternative splicing regulates fruits ripening. Conserved alternative splicing events did not appear to be stage-specific. Clustering fruit developmental stages across the four species based on alternative splicing profiles resulted in species-specific clustering, suggesting that diversification of alternative splicing contributes to lineage-specific evolution in fleshy fruits. CONCLUSIONS: We obtained high quality transcriptomes and alternative splicing events during fruit development across the four species. Dynamics and nonconserved alternative splicing were discovered. The candidate stage-specific AS genes involved in fruit ripening will provide valuable insight into the roles of alternative splicing during the developmental processes of fleshy fruits.

Constructing a Reinforced and Gradient Solid Electrolyte Interphase on Si Nanoparticles by In-Situ Thiol-Ene Click Reaction for Long Cycling Lithium-Ion Batteries.

Constructing a stable solid electrolyte interphase (SEI) on high-specific-capacity silicon (Si) anode is one of the most effective methods to reduce the crack of SEI and improve the cycling performance of Si anode. Herein, the authors construct a reinforced and gradient SEI on Si nanoparticles by an in-situ thiol-ene click reaction. Mercaptopropyl trimethoxysilane (MPTMS) with thiol functional groups (SH) is first grafted on the Si nanoparticles through condensation reaction, which then in-situ covalently bonds with vinylene carbonate (VC) to form a reinforced and uniform SEI on Si nanoparticles. The modified SEI with sufficient elastic Lix SiOy can homogenize the stress and strain during the lithiation of Si nanoparticles to reduce their expansion and prevent the SEI from cracking. The Si nanoparticles-graphite blending anode with the reinforced SEI exhibits excellent performance with an initial coulombic efficiency of ≈90%, a capacity of 1053.3 mA h g-1 after 500 cycles and a high capacity of 852.8 mA h g-1 even at a high current density of 3 A g-1 . Moreover, the obtained anode shows superior cycling stability under both high loadings and lean electrolyte. The in-situ thiol-ene click reaction is a practical method to construct reinforced SEI on Si nanoparticles for next-generation high-energy-density lithium-ion batteries.

In Situ Constructed Ionic-Electronic Dual-Conducting Scaffold with Reinforced Interface for High-Performance Sodium Metal Anodes.

The formation of severe dendritic sodium (Na) microstructure reduces the reversibility of anode and further hinders its practical implementation. In this work, an ionic-electronic dual-conducting (IEDC) scaffold composed of Na3 P and carbon nanotubes is in situ developed by a scalable strategy with subsequent alloying reaction, for realizing dendrite-free Na deposition under high current density and large areal capacity. The in situ formed Na3 P with high sodiophilicity not only sets up a hierarchically efficient ionic conducting network, but also participates in the construction of reinforced solid electrolyte interphase, while carbon nanotubes can assemble an electronic conducting framework. As a result, the multifunctional IEDC scaffold contributes to smooth Na plating and exceptionally reversible Na stripping. High average Coulombic efficiency of 99.8% after prolonged 1200 cycles at 3 mA cm-2 and small overpotential of 20 mV over 250 h (equals to 530 cycles) at high rate of 5 mA cm-2 are obtained. The high availability of Na in IEDC scaffold enables the impressive performance of full cell with limited Na, using Na3 V2 (PO4 )3 (NVP) cathode at practical level. More importantly, the as-developed anode-free full cell with IEDC||NVP configuration delivers a high capacity retention with long lifetime, indicating its great potential for practical Na metal batteries.

Different rates of pollen and seed gene flow cause branch-length and geographic cytonuclear discordance within Asian butternuts.

Topological cytonuclear discordance is commonly observed in plant phylogenetic and phylogeographic studies, yet few studies have attempted to detect two other forms of cytonuclear discordance (branch length and geographical) and to uncover the causes of the discordance. We used the whole nuclear and chloroplast genome data from 80 individual Asian butternuts to reveal the pattern and processes of cytonuclear discordance. Our findings indicate that the chloroplast genome had substantially deeper divergence (branch-length discordance) and a steeper cline in the contact zone (geographic discordance) compared with the nuclear genome. After various hypothesis have been tested, the results suggest that incomplete lineage sorting, positive selection and cytonuclear incompatibility are probably insufficient to explain this pattern. However, isolation-by-distance analysis and gene flow estimation point to a much higher level of gene flow by pollen compared with by seeds, which may have slowed down lineage divergence and mediated wider contact for nuclear genome compared with the chloroplast genome. Altogether, this study highlights a critical role of sex-biased dispersal in causing discordance between the nuclear and plastid genome of Asian butternuts. Given its ubiquity among plants, asymmetric gene flow should be given a high priority in future studies of cytonuclear discordance.

The Four Arabidopsis Choline/Ethanolamine Kinase Isozymes Play Distinct Roles in Metabolism and Development.

Phosphatidylcholine and phosphatidylethanolamine are two major phospholipid classes in eukaryotes. Each biosynthesis pathway starts with the phosphorylation of choline (Cho) or ethanolamine (Etn) catalyzed by either choline or ethanolamine kinase (CEK). Arabidopsis contains four CEK isoforms, but their isozyme-specific roles in metabolism and development are poorly described. Here, we showed that these four CEKs have distinct substrate specificities in vitro. While CEK1 and CEK2 showed substrate preference for Cho over Etn, CEK3 and CEK4 had clear substrate specificity for Cho and Etn, respectively. In vivo, CEK1, CEK2, and CEK3 exhibited kinase activity for Cho but not Etn, although the latter two isoforms showed rather minor contributions to total Cho kinase activity in both shoots and roots. The knockout mutants of CEK2 and CEK3 both affected root growth, and these isoforms had nonoverlapping cell-type-specific expression patterns in the root meristematic zone. In-depth phenotype analysis, as well as chemical and genetic complementation, revealed that CEK3, a Cho-specific kinase, is involved in cell elongation during root development. Phylogenetic analysis of CEK orthologs in Brassicaceae species showed evolutionary divergence between Etn kinases and Cho kinases. Collectively, our results demonstrate the distinct roles of the four CEK isoforms in Cho/Etn metabolism and plant development.

Proteasome Activator Blm10 Regulates Transcription Especially During Aging.

Background: Histones are basic elements of the chromatin and are critical to controlling chromatin structure and transcription. The proteasome activator PA200 promotes the acetylation-dependent proteasomal degradation of the core histones during spermatogenesis, DNA repair, transcription, and cellular aging and maintains the stability of histone marks. Objective: The study aimed to explore whether the yeast ortholog of PA200, Blm10, promotes degradation of the core histones during transcription and regulates transcription especially during aging. Methods: Protein degradation assays were performed to detect the role of Blm10 in histone degradation during transcription. mRNA profiles were compared in WT and mutant BY4741 or MDY510 yeast cells by RNA-sequencing. Results: The core histones can be degraded by the Blm10-proteasome in the non-replicating yeast, suggesting that Blm10 promotes the transcription-coupled degradation of the core histones. Blm10 preferentially regulates transcription in aged yeast, especially transcription of genes related to translation, amino acid metabolism, and carbohydrate metabolism. Mutations of Blm10 at F2125/N2126 in its putative acetyl-lysine binding region abolished the Blm10-mediated regulation of gene expression. Conclusion: Blm10 promotes degradation of the core histones during transcription and regulates transcription, especially during cellular aging, further supporting the critical role of PA200 in maintaining the stability of histone marks from the evolutionary view. These results should provide meaningful insights into the mechanisms underlying aging and the related diseases.

Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut.

Persian walnut (Juglans regia) is cultivated worldwide for its high-quality wood and nuts, but its origin has remained mysterious because in phylogenies it occupies an unresolved position between American black walnuts and Asian butternuts. Equally unclear is the origin of the only American butternut, J. cinerea. We resequenced the whole genome of 80 individuals from 19 of the 22 species of Juglans and assembled the genome of its relatives Pterocarya stenoptera and Platycarya strobilacea. Using phylogenetic-network analysis of single-copy nuclear genes, genome-wide site pattern probabilities, and Approximate Bayesian Computation, we discovered that J. regia (and its landrace J. sigillata) arose as a hybrid between the American and the Asian lineages and that J. cinerea resulted from massive introgression from an immigrating Asian butternut into the genome of an American black walnut. Approximate Bayesian Computation modeling placed the hybrid origin in the late Pliocene, ∼3.45 My, with both parental lineages since having gone extinct in Europe.

CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers.

BACKGROUND: Alternative splicing (AS) plays a critical regulatory role in modulating transcriptome and proteome diversity. In particular, it increases the functional diversity of proteins. Recent genome-wide analysis of AS using RNA-Seq has revealed that AS is highly pervasive in plants. Furthermore, it has been suggested that most AS events are subject to tissue-specific regulation. DESCRIPTION: To reveal the functional characteristics induced by AS and tissue-specific splicing events, a database for exploring these characteristics is needed, especially in plants. To address these goals, we constructed a database of annotated transcripts generated by alternative splicing in cucumbers (CuAS: http://cmb.bnu.edu.cn/alt_iso/index.php) that integrates genomic annotations, isoform-level functions, isoform-level features, and tissue-specific AS events among multiple tissues. CuAS supports a retrieval system that identifies unique IDs (gene ID, isoform ID, UniProt ID, and gene name), chromosomal positions, and gene families, and a browser for visualization of each gene. CONCLUSION: We believe that CuAS could be helpful for revealing the novel functional characteristics induced by AS and tissue-specific AS events in cucumbers. CuAS is freely available at http://cmb.bnu.edu.cn/alt_iso/index.php.

Facile Synthesis of Ant-Nest-Like Porous Duplex Copper as Deeply Cycling Host for Lithium Metal Anodes.

Suppressing the dendrite formation and managing the volume change of lithium (Li) metal anode have been global challenges in the lithium batteries community. Herein, a duplex copper (Cu) foil with an ant-nest-like network and a dense substrate is reported for an ultrastable Li metal anode. The duplex Cu is fabricated by sulfurization of thick Cu foil with a subsequent skeleton self-welding procedure. Uniform Li deposition is achieved by the 3D interconnected architecture and lithiophilic surface of self-welded Cu skeleton. The sufficient space in the porous layer enables a large areal capacity for Li and significantly improves the electrode-electrolyte interface. Simulations reveal that the structure allows proper electric field penetration into the connected tunnels. The assembled Li anodes exhibit high coulombic efficiency (97.3% over 300 cycles) and long lifespan (>880 h) at a current density of 1 mA cm-2 with a capacity of 1 mAh cm-2 . Stable and deep cycling can be maintained up to 50 times at a high capacity of 10 mAh cm-2 .

Determining the impacts of climate change and urban expansion on terrestrial net primary production in China.

Climate change and urbanization strongly affect the variations of terrestrial net primary production (NPP), but the relative contributions of these two factors to NPP changes have not been determined yet (especially on a macroscale). In this study, spatial-temporal variations of NPP in China from 2000 to 2010 were estimated using the Carnegie-Ames-Stanford Approach model, and the effects induced by urbanization and climate change were quantified. The obtained results showed that during the study period, the NPP in China exhibited an annual increase of 0.03 Pg C accompanied by large spatial heterogeneities. During the whole study period, the urban area in China increased by 16.44 × 103 km2, and the corresponding NPP losses amounted to 11.60 × 10-3 Pg C. Urban expansion significantly offset the climate change-induced NPP increases and worsened NPP decreases (the offsetting ratio calculated for China was 5.42%, and its exact magnitudes varied by province). The largest NPP variations were observed over the regions with rapid urban expansion, whose contribution ratio was 32.20% for China and exceeded 30% for most provinces. Climate change contributed considerably to the NPP variations in both the newly urbanized (30.45%) and purely vegetated (46.92%) areas, but its contribution ratios were slightly lower than those of residual factors. Moreover, climate change strongly affected the NPP levels over the arid and semi-arid regions as well as over the Tibet Plateau; however, residual factors dominated the NPP variations over the central and southeast China. Our study highlights a significant role of urbanization in driving terrestrial NPP variations on a macroscale and provides a new perspective on disentangling the impacts of external factors on NPP values.

Temperature responses of mutation rate and mutational spectrum in an Escherichia coli strain and the correlation with metabolic rate.

BACKGROUND: Temperature is a major determinant of spontaneous mutation, but the precise mode, and the underlying mechanisms, of the temperature influences remain less clear. Here we used a mutation accumulation approach combined with whole-genome sequencing to investigate the temperature dependence of spontaneous mutation in an Escherichia coli strain. Experiments were performed under aerobic conditions at 25, 28 and 37 °C, three temperatures that were non-stressful for the bacterium but caused significantly different bacterial growth rates. RESULTS: Mutation rate did not differ between 25 and 28 °C, but was higher at 37 °C. Detailed analyses of the molecular spectrum of mutations were performed; and a particularly interesting finding is that higher temperature led to a bias of mutation to coding, relative to noncoding, DNA. Furthermore, the temperature response of mutation rate was extremely similar to that of metabolic rate, consistent with an idea that metabolic rate predicts mutation rate. CONCLUSIONS: Temperature affects mutation rate and the types of mutation supply, both being crucial for the opportunity of natural selection. Our results help understand how temperature drives evolutionary speed of organisms and thus the global patterns of biodiversity. This study also lend support to the metabolic theory of ecology for linking metabolic rate and molecular evolution rate.

The Genomes of Two Bat Species with Long Constant Frequency Echolocation Calls.

Bats can perceive the world by using a wide range of sensory systems, and some of the systems have become highly specialized, such as auditory sensory perception. Among bat species, the Old World leaf-nosed bats and horseshoe bats (rhinolophoid bats) possess the most sophisticated echolocation systems. Here, we reported the whole-genome sequencing and de novo assembles of two rhinolophoid bats-the great leaf-nosed bat (Hipposideros armiger) and the Chinese rufous horseshoe bat (Rhinolophus sinicus). Comparative genomic analyses revealed the adaptation of auditory sensory perception in the rhinolophoid bat lineages, probably resulting from the extreme selectivity used in the auditory processing by these bats. Pseudogenization of some vision-related genes in rhinolophoid bats was observed, suggesting that these genes have undergone relaxed natural selection. An extensive contraction of olfactory receptor gene repertoires was observed in the lineage leading to the common ancestor of bats. Further extensive gene contractions can be observed in the branch leading to the rhinolophoid bats. Such concordance suggested that molecular changes at one sensory gene might have direct consequences for genes controlling for other sensory modalities. To characterize the population genetic structure and patterns of evolution, we re-sequenced the genome of 20 great leaf-nosed bats from four different geographical locations of China. The result showed similar sequence diversity values and little differentiation among populations. Moreover, evidence of genetic adaptations to high altitudes in the great leaf-nosed bats was observed. Taken together, our work provided a useful resource for future research on the evolution of bats.

The comparison of alternative splicing among the multiple tissues in cucumber.

BACKGROUND: Alternative splicing (AS) is an important post-transcriptional process. It has been suggested that most AS events are subject to tissue-specific regulation. However, the global dynamics of AS in different tissues are poorly explored. RESULTS: To analyse global changes in AS in multiple tissues, we identified the AS events and constructed a comprehensive catalogue of AS events within each tissue based on the genome-wide RNA-seq reads from ten tissues in cucumber. First, we found that 58% of the multi-exon genes underwent AS. We further obtained 565 genes with significantly more AS events compared with random genes. These genes were found significant enrichment in biological processes related to the regulation of actin filament length. Second, significantly different AS event profiles among ten tissues were found. The tissues with the same origin of development are more likely to have a relatively similar AS profile. Moreover, 7370 genes showed tissue-specific AS events and were highly enriched in biological processes related to the positive regulation of cellular component organization. Root-specificity AS genes were related to the cellular response to DNA damage stimulus. Third, the genes with different intron retention (IR) patterns among the ten tissues showed significant difference in GC percentages of the retained intron, and the number of exons and FPKM of the major transcripts. CONCLUSIONS: Our study provided a comprehensive view of AS in multiple tissues. We revealed novel insights into the patterns of AS in multiple tissues and the tissue-specific AS in cucumber.