PanDepth, an ultrafast and efficient genomic tool for coverage calculation.

Coverage quantification is required in many sequencing datasets within the field of genomics research. However, most existing tools fail to provide comprehensive statistical results and exhibit limited performance gains from multithreading. Here, we present PanDepth, an ultra-fast and efficient tool for calculating coverage and depth from sequencing alignments. PanDepth outperforms other tools in computation time and memory efficiency for both BAM and CRAM-format alignment files from sequencing data, regardless of read length. It employs chromosome parallel computation and optimized data structures, resulting in ultrafast computation speeds and memory efficiency. It accepts sorted or unsorted BAM and CRAM-format alignment files as well as GTF, GFF and BED-formatted interval files or a specific window size. When provided with a reference genome sequence and the option to enable GC content calculation, PanDepth includes GC content statistics, enhancing the accuracy and reliability of copy number variation analysis. Overall, PanDepth is a powerful tool that accelerates scientific discovery in genomics research.

Microtubule-associated protein SlMAP70 interacts with IQ67-domain protein SlIQD21a to regulate fruit shape in tomato.

Tomato (Solanum lycopersicum) fruit shape is related to microtubule organization and the activity of microtubule-associated proteins (MAPs). However, insights into the mechanism of fruit shape formation from a cell biology perspective remain limited. Analysis of the tissue expression profiles of different microtubule regulators revealed that functionally distinct classes of MAPs, including members of the plant-specific MICROTUBULE-ASSOCIATED PROTEIN 70 (MAP70) and IQ67 DOMAIN (IQD, also named SUN in tomato) families, are differentially expressed during fruit development. SlMAP70-1-3 and SlIQD21a are highly expressed during fruit initiation, which relates to the dramatic microtubule pattern rearrangements throughout this developmental stage of tomato fruits. Transgenic tomato lines overexpressing SlMAP70-1 or SlIQD21a produced elongated fruits with reduced cell circularity and microtubule anisotropy, while their loss-of-function mutants showed the opposite phenotype, harboring flatter fruits. Fruits were further elongated in plants coexpressing both SlMAP70-1 and SlIQD21a. We demonstrated that SlMAP70s and SlIQD21a physically interact and that the elongated fruit phenotype is likely due to microtubule stabilization induced by the SlMAP70-SlIQD21a interaction. Together, our results identify SlMAP70 proteins and SlIQD21a as important regulators of fruit elongation and demonstrate that manipulating microtubule function during early fruit development provides an effective approach to alter fruit shape.

Plant lysin motif extracellular proteins are required for arbuscular mycorrhizal symbiosis.

Arbuscular mycorrhizal fungi (AMF) can form a mutually beneficial symbiotic relationship with most land plants. They are known to secrete lysin motif (LysM) effectors into host root cells for successful colonization. Intriguingly, plants secrete similar types of LysM proteins; however, their role in plant-microbe interactions is unknown. Here, we show that Medicago truncatula deploys LysM extracellular (LysMe) proteins to facilitate symbiosis with AMF. Promoter analyses demonstrated that three M. truncatula LysMe genes MtLysMe1/2/3, are expressed in arbuscule-containing cells and those adjacent to intercellular hyphae. Localization studies showed that these proteins are targeted to the periarbuscular space between the periarbuscular membrane and the fungal cell wall of the branched arbuscule. M. truncatula mutants in which MtLysMe2 was knocked out via CRISPR/Cas9-targeted mutagenesis exhibited a significant reduction in AMF colonization and arbuscule formation, whereas genetically complemented transgenic plants restored wild-type level AMF colonization. In addition, knocking out the ortholog of MtLysMe2 in tomato resulted in a similar defect in AMF colonization. In vitro binding affinity precipitation assays suggested binding of MtLysMe1/2/3 with chitin and chitosan, while microscale thermophoresis (MST) assays revealed weak binding of these proteins with chitooligosaccharides. Moreover, application of purified MtLysMe proteins to root segments could suppress chitooctaose (CO8)-induced reactive oxygen species production and expression of reporter genes of the immune response without impairing chitotetraose (CO4)-triggered symbiotic responses. Taken together, our results reveal that plants, like their fungal partners, also secrete LysM proteins to facilitate symbiosis establishment.

An amphipathic Bax core dimer forms part of the apoptotic pore wall in the mitochondrial␣membrane.

Bax proteins form pores in the mitochondrial outer membrane to initiate apoptosis. This might involve their embedding in the cytosolic leaflet of the lipid bilayer, thus generating tension to induce a lipid pore with radially arranged lipids forming the wall. Alternatively, Bax proteins might comprise part of the pore wall. However, there is no unambiguous structural evidence for either hypothesis. Using NMR, we determined a high-resolution structure of the Bax core region, revealing a dimer with the nonpolar surface covering the lipid bilayer edge and the polar surface exposed to water. The dimer tilts from the bilayer normal, not only maximizing nonpolar interactions with lipid tails but also creating polar interactions between charged residues and lipid heads. Structure-guided mutations demonstrate the importance of both types of protein-lipid interactions in Bax pore assembly and core dimer configuration. Therefore, the Bax core dimer forms part of the proteolipid pore wall to permeabilize mitochondria.

Transcription factor SlWRKY50 enhances cold tolerance in tomato by activating the jasmonic acid signaling.

Tomato (Solanum lycopersicum) is a cold-sensitive crop but frequently experiences low-temperature stimuli. However, tomato responses to cold stress are still poorly understood. Our previous studies have shown that using wild tomato (Solanum habrochaites) as rootstock can significantly enhance the cold resistance of grafted seedlings, in which a high concentration of jasmonic acids (JAs) in scions exerts an important role, but the mechanism of JA accumulation remains unclear. Herein, we discovered that tomato SlWRKY50, a Group II WRKY transcription factor that is cold inducible, responds to cold stimuli and plays a key role in JA biosynthesis. SlWRKY50 directly bound to the promoter of tomato allene oxide synthase gene (SlAOS), and overexpressing SlWRKY50 improved tomato chilling resistance, which led to higher levels of Fv/Fm, antioxidative enzymes, SlAOS expression, and JA accumulation. SlWRKY50-silenced plants, however, exhibited an opposite trend. Moreover, diethyldithiocarbamate acid (a JA biosynthesis inhibitor) foliar treatment drastically reduced the cold tolerance of SlWRKY50-overexpression plants to wild-type levels. Importantly, SlMYC2, the key regulator of the JA signaling pathway, can control SlWRKY50 expression. Overall, our research indicates that SlWRKY50 promotes cold tolerance by controlling JA biosynthesis and that JA signaling mediates SlWRKY50 expression via transcriptional activation by SlMYC2. Thus, this contributes to the genetic knowledge necessary for developing cold-resistant tomato varieties.

Folate shapes plant root architecture by affecting auxin distribution.

Folate (vitamin B9) is important for plant root development, but the mechanism is largely unknown. Here we characterized a root defective mutant, folb2, in Arabidopsis, which has severe developmental defects in the primary root. The root apical meristem of the folb2 mutant is impaired, and adventitious roots are frequently found at the root-hypocotyl junction. Positional cloning revealed that a 61-bp deletion is present in the predicted junction region of the promoter and the 5' untranslated region of AtFolB2, a gene encoding a dihydroneopterin aldolase that functions in folate biosynthesis. This mutation leads to a significant reduction in the transcript level of AtFolB2. Liquid chromatography-mass spectrometry analysis showed that the contents of the selected folate compounds were decreased in folb2. Arabidopsis AtFolB2 knockdown lines phenocopy the folb2 mutant. On the other hand, the application of exogenous 5-formyltetrahydrofolic acid could rescue the root phenotype of folb2, indicating that the root phenotype is indeed related to the folate level. Further analysis revealed that folate could promote rootward auxin transport through auxin transporters and that folate may affect particular auxin/indole-3-acetic acid proteins and auxin response factors. Our findings provide new insights into the important role of folic acid in shaping root structure.

A mutation in a C2H2-type zinc finger transcription factor contributed to the transition toward self-pollination in cultivated tomato.

The degree of stigma exsertion has a major influence on self-pollination efficiency in tomato, and its improvement is essential for raising productivity and for fixing advantageous traits in cultivated tomato. To study the evolution of stigma exsertion degree in tomato, we searched for genes associated with this trait and other aspects of flower morphology, including the lengths of anthers, styles, and ovaries. We performed a genome-wide association on 277 tomato accessions and discovered a novel stigma exsertion gene (SE3.1). We reannotated the structure of the gene, which encodes a C2H2-type zinc finger transcription factor. A mutation of the lead single nucleotide polymorphism creates a premature termination codon in SE3.1 and an inserted stigma in cultivated tomatoes. SE3.1 is essential for the conversion of flush stigmas to inserted stigmas. This conversion has a major impact on the rate of self-fertilization. Intriguingly, we found that both SE3.1 and Style2.1 contribute to the transition from stigma exsertion to insertion during the domestication and improvement of tomato. Style2.1 controls the first step of exserted stigmas to flush stigmas, and SE3.1 controls the second step of flush stigmas to inserted stigmas. We provide molecular details for the two-step process that controls the transition from stigma exsertion to insertion, which is of great agronomic importance in tomato.

Mechanistic Insights into the Inhibition of a Common CTLA-4 Gene Mutation in the Cytoplasmic Domain.

Cytotoxic T-lymphocyte antigen 4 (CTLA-4) is a pivotal immune checkpoint receptor, playing a crucial role in modulating T-cell activation. In this study, we delved into the underlying mechanism by which a common mutation, G199R, in the cytoplasmic domain of CTLA-4 impacts its inhibitory function. Utilizing nuclear magnetic resonance (NMR) spectroscopy and biochemical techniques, we mapped the conformational changes induced by this mutation and investigated its role in CTLA-4 activity. Our findings reveal that this mutation leads to a distinct conformational alteration, enhancing protein-membrane interactions. Moreover, functional assays demonstrated an improved capacity of the G199R mutant to downregulate T-cell activation, underscoring its potential role in immune-related disorders. These results not only enhance our understanding of CTLA-4 regulatory mechanisms but also provide insights for targeted therapeutic strategies addressing immune dysregulation linked to CTLA-4 mutations.

Ultrathin Rh Nanosheets with Rich Grain Boundaries for Efficient Hydrogen Oxidation Electrocatalysis.

Two-dimensional (2D) Pt-group ultrathin nanosheets (NSs) are promising advanced electrocatalysts for energy-related catalytic reactions. However, improving the electrocatalytic activity of 2D Pt-group NSs through the addition of abundant grain boundaries (GBs) and understanding the underlying formation mechanism remain significant challenges. Herein, we report the controllable synthesis of a series of Rh-based nanocrystals (e.g., Rh nanoparticles, Rh NSs, and Rh NSs with GBs) through a CO-mediated kinetic control synthesis route. In light of the 2D NSs' structural advantages and GB modification, the Rh NSs with rich GBs exhibit an enhanced electrocatalytic activity compared to pure Rh NSs and commercial Pt/C toward the hydrogen oxidation reaction (HOR) in alkaline media. Both experimental results and theoretical computations corroborate that the GBs in the Rh NSs have the capacity to ameliorate the adsorption free energy of reaction intermediates during the HOR, thus resulting in outstanding HOR catalytic performance. Our work offers novel perspectives in the realm of developing sophisticated 2D Pt-group metal electrocatalysts with rich GBs for the energy conversion field.

Critical roles of mitochondrial fatty acid synthesis in tomato development and environmental response.

Plant mitochondrial fatty acid synthesis (mtFAS) appears to be important in photorespiration based on the reverse genetics research from Arabidopsis (Arabidopsis thaliana) in recent years, but its roles in plant development have not been completely explored. Here, we identified a tomato (Solanum lycopersicum) mutant, fern-like, which displays pleiotropic phenotypes including dwarfism, yellowing, curly leaves, and increased axillary buds. Positional cloning and genetic and heterozygous complementation tests revealed that the underlying gene FERN encodes a 3-hydroxyl-ACP dehydratase enzyme involved in mtFAS. FERN was causally involved in tomato morphogenesis by affecting photorespiration, energy supply, and the homeostasis of reactive oxygen species. Based on lipidome data, FERN and the mtFAS pathway may modulate tomato development by influencing mitochondrial membrane lipid composition and other lipid metabolic pathways. These findings provide important insights into the roles and importance of mtFAS in tomato development.

Bimetallic Organic Framework-Decorated Leaf-like 2D Nanosheets as Flexible Air Cathode for Rechargeable Zn-air Batteries.

Exploring highly active and robust self-supporting air electrodes is the key for flexible Zn-air batteries (FZABs). Therefore, we report a novel 3D structural bimetal-based self-supporting electrode consisting of hybrid Cu, Co nanoparticles co-modified nitrogen-doped carbon nanosheets on carbon cloth (Cu, Co NPs@NCNSs/CC), which displays excellent electrochemical activity and durability of the oxygen reduction/evolution reaction (ORR/OER). The Cu, Co NPs@NCNSs/CC exhibits a half-wave potential of 0.863 V toward ORR and an overpotential of 225 mV at 10 mA cm-2 toward OER, owing to its exposed bimetallic sites accelerating the kinetic reaction. In addition, the density functional theory calculation proves that the synergistic effect of CuCo sites favors ORR and OER. Hence, the FZABs based on Cu, Co NPs@NCNSs/CC achieve a larger open-circuit potential (1.45 V), higher energy density (130.10 mW cm-2 ), and outstanding cycling stability. All remarkable results demonstrate valuable enlightenment for seeking advanced energy materials of portable and wearable electronics.

Densifying Crystalline-Amorphous Ni3S2/NiOOH Interfacial Sites To Boost Electrocatalytic O2 Production.

The development of an efficient and low-cost electrocatalyst for oxygen evolution reaction (OER) is the key to improving the overall efficiency of water electrolysis. Here, we report the design of a three-dimensional (3-D) heterostructured Ni9S8/Ni3S2 precatalyst composed of unstable Ni9S8 and inert Ni3S2 components, which undergoes in situ electrochemical activation to generate an amorphous-NiOOH/Ni3S2 heterostructured catalyst. In situ Raman spectroscopy combined with ex situ characterizations, such as X-ray diffraction, X-ray photoelectron spectroscopy, and transmission electron microscopy, reveals that during the activation, Ni9S8 loses the sulfur element to form nickel oxides and eventually transforms to amorphous NiOOH at O2-evolving potentials, while the Ni3S2 component is rather inert that its majority in the bulk remains, thus forming a 3-D congee-like NiOOH/Ni3S2 heterostructure with the Ni3S2 crystalline particles randomly dispersed among amorphous NiOOH species. Unlike the sparse heterostructure that consists of a layer of NiOOH on top of Ni3S2, our unique congee-like NiOOH/Ni3S2 heterostructure provides plentiful reactive amorphous-crystalline interfacial sites. Moreover, the partial electron transfer between the NiOOH and remaining Ni3S2, benefiting from their dense interfacial sites, contributes to a higher valence state of the Ni3+ active centers in NiOOH, hence optimizing the adsorption of OER intermediates. Density functional theory calculations further disclose that the electronic structure regulation not only optimizes the Gibbs free energy of intermediate adsorption but also tunes the OH* absorption behavior to be exothermic, elucidating the spontaneous occurrence of OH* absorption and hence improves the OER. Therefore, a low overpotential of only 197 mV at an O2-evolving current density of 10 mA/cm2, a small Tafel slope of 38.8 mV/dec, and good stability are achieved on the amorphous-NiOOH/crystalline-Ni3S2 heterostructured catalyst.

Unveiling the Structural Self-Reconstruction and Identifying the Reactive Center of a V, Fe Co-Doped Cobalt Precatalyst toward Enhanced Overall Water Splitting by Operando Raman Spectroscopy.

The development of efficient and stable bifunctional electrocatalysts based on non-noble metals for water electrolysis is both urgent and challenging. However, unresolved issues remain regarding the challenge of identifying the active phase and gaining a comprehensive understanding of its surface reconstruction and functionality throughout the reaction process. In this study, we have combined doping and heterostructure construction by a one-step electrodeposition and a subsequent activation treatment to synthesize Fe, V co-doped Co3O4/Co(OH)2 and Co/Co(OH)2 heterointerfaces (referred to as A-Co60Fe1.1V). These heterointerfaces, composed of Co/Co(OH)2 and Co3O4/Co(OH)2, are proposed to facilitate charge transfer process during catalysis. X-ray photoelectron spectroscopy (XPS) analysis demonstrates that the introduction of V and Fe dopants increases the valence state of Co centers in Co3O4 and Co(OH)2. Further operando Raman spectroscopy reveals that Co(OH)2 and Co3O4 with the high-valence Co centers remain stable during the hydrogen evolution reaction (HER) process. These high-valence Co centers are believed to promote the crucial water dissociation step and therefore enhance the overall HER catalysis. On the other hand, during the oxygen evolution reaction (OER), Fe, V co-doping leads to an earlier formation of the active CoOOH species, while Fe doping can further help stabilize the more reactive ß-CoOOH species instead of the less reactive γ-CoOOH. As a result, the A-Co60Fe1.1V catalyst exhibits significantly improved catalytic activity for both HER and OER that it requires low overpotentials of 51 and 250 mV, respectively, to attain a current density of 10 mA cm-2. Moreover, when utilized as both the cathode and anode in alkaline water electrolysis, the A-Co60Fe1.1V catalyst can operate at a mere 1.54 V voltage while maintaining 10 mA cm-2, surpassing the majority of non-noble metal catalysts. Remarkably, it also exhibits stability for at least 40 h at ∼100 mA cm-2.

Enhanced electrocatalytic hydrogen evolution from nitrogen plasma-tailored MoS2 nanostructures.

Two-dimensional (2D) layered transition metal dichalcogenides such as MoS2 have been viewed as the most favorable candidates for replacing noble metals in catalyzing the hydrogen evolution reaction in water splitting owing to their earth abundance, superb chemical stability, and appropriate Gibbs free energy. However, due to its low number of catalytic sites and basal catalytic inertia, the pristine MoS2 displayed intrinsically unsatisfactory HER catalytic activity. Here, the hydrogen evolution catalytic activities of nanostructured MoS2 powder before and after plasma modification with nitrogen doping were experimentally compared, and the influence of treatment parameters on the hydrogen evolution catalytic performance of MoS2 has been studied. The feasibility of regulating hydrogen evolution catalytic activity by nitrogen doping of MoS2 was verified based on density functional theory calculations. Our work demonstrates a more convenient and faster way to develop cheap and efficient MoS2-based catalysts for electrochemical hydrogen evolution reactions. Additionally, theoretical studies reveal that N-doped MoS2 exhibits strong hybridization between Mo-d and N-p states, causing magnetism to evolve, as confirmed by experiments.

Ru Colloidosome Catalysts for the Hydrogen Oxidation Reaction in Alkaline Media.

Developing efficient hydrogen oxidation reaction (HOR) electrocatalysts in alkaline media is of great significance for anion exchange membrane fuel cells. Herein, we report the synthesis of hollow colloidosomes composed of Ru nanocrystals based on a novel gas/liquid interface self-assembly strategy. Structural characterizations reveal that much defects are present in the building block (Ru nanocrystals) of Ru colloidosomes. Theoretical calculations suggest that the defects in the Ru structure can optimize the adsorption binding energy of reaction intermediates for the HOR. Benefiting from the assembled colloidosome and optimized electronic structure, the Ru colloidosomes exhibit remarkable HOR catalytic performance in alkaline media with a mass activity higher than that of benchmark Pt/C. Our work may shed new light on the rational design of advanced electrocatalysts with an assembled structure for energy-related applications.

The tomato CONSTANS-LIKE protein SlCOL1 regulates fruit yield by repressing SFT gene expression.

BACKGROUND: CONSTANS (CO) and CONSTANS-LIKE (COL) transcription factors have been known to regulate a series of cellular processes including the transition from the vegetative growth to flower development in plants. However, their role in regulating fruit yield in tomato is poorly understood. RESULT: In this study, the tomato ortholog of Arabidopsis CONSTANS, SlCOL1, was shown to play key roles in the control of flower development and fruit yield. Suppression of SlCOL1 expression in tomato was found to lead to promotion of flower and fruit development, resulting in increased tomato fruit yield. On the contrary, overexpression of SlCOL1 disturbed flower and fruit development, and significantly reduced tomato fruit yield. Genetic and biochemical evidence indicated that SlCOL1 controls inflorescence development by directly binding to the promoter region of tomato inflorescence-associated gene SINGLE-FLOWER TRUSS (SFT) and negatively regulating its expression. Additionally, we found that SlCOL1 can also negatively regulate fruit size in tomato. CONCLUSIONS: Tomato SlCOL1 binds to the promoter of the SFT gene, down-regulates its expression, and plays a key role in reducing the fruit size.

Facet Control of Nickel Nitride Nano-Framework for Efficient Hydrogen Evolution Electrocatalysis via Auxiliary Cooling Assisted Plasma Engineering.

The precise facet modulation of transition metal nitrides (TMNs) has been regarded as an essential issue in boosting electrocatalytic H2 production. Compared to thermal nitridation, the plasma technique serves as a favorable alternative to directly achieve TMNs, but the apparent surface heating effect during plasma treatment inevitably causes the thermally stabilized nitride formation, resulting in the deterioration of the highly reactive facet. To optimize the hydrogen evolution reaction (HER) behavior, an auxiliary cooling assisted plasma system to selectively expose Ni3 N (2-10) with favorable activity by controlling surface heating during plasma nitridation is designed. The resultant nickel nitride (cp-Ni3 N) nano-framework delivers exceptional catalytic performance, evidenced by its low overpotential of 58 and 188 mV at the current density of 10 and 100 mA cm-2 for HER, in stark comparison with that of normal plasma and thermally fabricated Ni3 N. Operando plasma diagnostics along with numerical simulation further confirm the effect of surface heating on typical plasma parameters as well as the Ni3 N nanostructure, indicating the key factor responsible for the high-performance nitride electrocatalyst.

Ni2+ Catalyzed Cleavage of TrpLE-Fused Small Transmembrane Peptides.

In addition to a membrane anchor, the transmembrane domain (TMD) of single-pass transmembrane proteins (SPTMPs) recently has shown essential roles in the cross-membrane activity or receptor assembly/clustering. However, these small TMD peptides are generally hydrophobic and dynamic, difficult to be expressed and purified. Here, we have integrated the power of TrpLE fusion protein and a sequence-specific nickel-assisted cleavage (SNAC)-tag to produce small TMD peptides in a highly efficient way under mild conditions, which uses Ni2+ as the cleavage reagent, avoiding the usage of toxic cyanogen bromide (CNBr). Furthermore, this method simplifies the downstream protein purification and reconstitution. Two representative TMDs, including the Spike-TMD from severe acute respiratory syndrome coronavirus 2 (SARS2), were successfully produced with high-quality nuclear magnetic resonance (NMR) spectra. Therefore, our study provides a more efficient and practical approach for general structural characterization of the small TM proteins.

A novel regulatory complex mediated by Lanata (Ln) controls multicellular trichome formation in tomato.

Trichomes that originate from plant aerial epidermis act as mechanical and chemical barriers against herbivores. Although several regulators have recently been identified, the regulatory pathway underlying multicellular trichome formation remains largely unknown in tomato. Here, we report a novel HD-ZIP IV transcription factor, Lanata (Ln), a missense mutation which caused the hairy phenotype. Biochemical analyses demonstrate that Ln separately interacts with two trichome regulators, Woolly (Wo) and Hair (H). Genetic and molecular evidence demonstrates that Ln directly regulates the expression of H. The interaction between Ln and Wo can increase trichome density by enhancing the expression of SlCycB2 and SlCycB3, which we previously showed are involved in tomato trichome formation. Furthermore, SlCycB2 represses the transactivation of the SlCycB3 gene by Ln and vice versa. Our findings provide new insights into the novel regulatory network controlling multicellular trichome formation in tomato.

Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato.

Tomato (Solanum lycopersicum) is a highly valuable fruit crop, and yield is one of the most important agronomic traits. However, the genetic architecture underlying tomato yield-related traits has not been fully addressed. Based on ∼4.4 million single nucleotide polymorphisms obtained from 605 diverse accessions, we performed a comprehensive genome-wide association study for 27 agronomic traits in tomato. A total of 239 significant associations corresponding to 129 loci, harboring many previously reported and additional genes related to vegetative and reproductive development, were identified, and these loci explained an average of ∼8.8% of the phenotypic variance. A total of 51 loci associated with 25 traits have been under selection during tomato domestication and improvement. Furthermore, a candidate gene, Sl-ACTIVATED MALATE TRANSPORTER15, that encodes an aluminum-activated malate transporter was functionally characterized and shown to act as a pivotal regulator of leaf stomata formation, thereby affecting photosynthesis and drought resistance. This study provides valuable information for tomato genetic research and breeding.