Search

Hydrophiine sea snakes represent ecologically significant and species-rich marine predatory reptiles, many of which inhabit marine environments throughout their entire lifecycles. However, due to morphological variability and limited molecular phylogenetic studies, the taxonomic relationships within this group remain unclear. In this study, we present the first complete mitochondrial genome of Aipysurus sea snakes, specifically Aipysurus eydouxii Gray 1849. The mitogenome comprises 17,228 base pairs and contains a total of 37 genes, plus a putative control region. This study provides valuable genetic data that will contribute to the future taxonomic classification and ecological protection of hydrophiine sea snakes.

Abstract Photosystem I (PSI) from Fittonia albivenis, an Acanthaceae ornamental plant, is notable among green plants for its red-shifted emission spectrum. Here, we solved the structure of a PSI–light harvesting complex I (LHCI) supercomplex from F. albivenis at 2.46-Å resolution using cryo-electron microscopy. The supercomplex contains a core complex of 14 subunits and an LHCI belt with four antenna subunits (Lhca1–4) similar to previously reported angiosperm PSI–LHCI structures; however, Lhca3 differs in three regions surrounding a dimer of low-energy chlorophylls (Chls) termed red Chls, which absorb far-red beyond visible light. The unique amino acid sequences within these regions are exclusively shared by plants with strongly red-shifted fluorescence emission, suggesting candidate structural elements for regulating the energy state of red Chls. These results provide a structural basis for unraveling the mechanisms of light harvest and transfer in PSI–LHCI of under canopy plants and for designing Lhc to harness longer-wavelength light in the far-red spectral range.

Abstract Nanopore direct RNA sequencing (DRS) has emerged as a powerful tool for RNA modification identification. However, concurrently detecting multiple types of modifications in a single DRS sample remains a challenge. Here, we develop TandemMod, a transferable deep learning framework capable of detecting multiple types of RNA modifications in single DRS data. To train high-performance TandemMod models, we generate in vitro epitranscriptome datasets from cDNA libraries, containing thousands of transcripts labeled with various types of RNA modifications. We validate the performance of TandemMod on both in vitro transcripts and in vivo human cell lines, confirming its high accuracy for profiling m6A and m5C modification sites. Furthermore, we perform transfer learning for identifying other modifications such as m7G, Ψ, and inosine, significantly reducing training data size and running time without compromising performance. Finally, we apply TandemMod to identify 3 types of RNA modifications in rice grown in different environments, demonstrating its applicability across species and conditions. In summary, we provide a resource with ground-truth labels that can serve as benchmark datasets for nanopore-based modification identification methods, and TandemMod for identifying diverse RNA modifications using a single DRS sample.

Abstract Holothuria scabra, a commercially valuable yet ecologically vulnerable tropical holothuroid, has experienced a severe decline in its wild populations, especially in China. Genomic resources are crucial for the development of effective genomic breeding projects and stock conservation strategies to restore these natural populations. Until now, a high-quality, chromosome-level reference genome for H. scabra has not been available. Here, we employed Oxford Nanopore and Hi-C sequencing technologies to assemble and annotate a high-quality, chromosome-level reference genome of H. scabra. The final genome comprised 31 scaffolds with a total length of 1.19 Gb and a scaffold N50 length of 53.52 Mb. Remarkably, 1,191.67 Mb (99.95%) of the sequences were anchored to 23 pseudo-chromosomes, with the longest one spanning 79.75 Mb. A total of 34,418 protein-coding genes were annotated in the final genome, with BUSCO analysis revealing 98.01% coverage of metazoa_odb10 genes, marking a significant improvement compared to the previous report. These chromosome-level sequences and annotations will provide an essential genomic basis for further investigation into molecular breeding and conservation management of H. scabra.

Abstract Ditylenchus destructor is a migratory plant-parasitic nematode that severely harms many agriculturally important crops. The control of this pest is difficult, thus efficient strategies for its management in agricultural production are urgently required. Cathepsin L-like cysteine protease (CPL) is one important protease that has been shown to participate in various physiological and pathological processes. Here we decided to characterize the CPL gene (Dd-cpl-1) from D. destructor. Analysis of Dd-cpl-1 gene showed that Dd-cpl-1 gene contains a signal peptide, an I29 inhibitor domain with ERFNIN and GNFD motifs, and a peptidase C1 domain with four conserved active residues, showing evolutionary conservation with other nematode CPLs. RT-qPCR revealed that Dd-cpl-1 gene displayed high expression in third-stage juveniles (J3s) and female adults. In situ hybridization analysis demonstrated that Dd-cpl-1 was expressed in the digestive system and reproductive organs. Silencing Dd-cpl-1 in 1-cell stage eggs of D. destructor by RNAi resulted in a severely delay in development or even in abortive morphogenesis during embryogenesis. The RNAi-mediated silencing of Dd-cpl-1 in J2s and J3s resulted in a developmental arrest phenotype in J3 stage. In addition, silencing Dd-cpl-1 gene expression in female adults led to a 57.43% decrease in egg production. Finally, Dd-cpl-1 RNAi-treated nematodes showed a significant reduction in host colonization and infection. Overall, our results indicate that Dd-CPL-1 plays multiple roles in D. destructor ontogenesis and could serve as a new potential target for controlling D. destructor.

Helical growth of the root tip (circumnutation) that permits surface exploration facilitates root penetration into soil. Here, we reveal that rice actin-binding protein RMD aids in root circumnutation, manifested by wavy roots as well as compromised ability to efficiently explore and avoid obstacles in rmd mutants. We demonstrate that root circumnutation defects in rmd depend on brassinosteroid (BR) signaling, which is elevated in mutant roots. Suppressing BR signaling via pharmacological (BR inhibitor) or genetic (knockout of BR biosynthetic or signaling components) manipulation rescues root defects in rmd. We further reveal that mutations in MAPK6 suppress BR signaling and restore normal root circumnutation in rmd, which may be mediated by the interaction between MAPK6, MAPKK4 and BR signaling factor BIM2. Our study thus demonstrates that RMD and MAPK6 control root circumnutation by modulating BR signaling to facilitate early root growth.

IntroductionRemorins (REMs) are plant-specific membrane-associated proteins that play important roles in plant–pathogen interactions and environmental adaptations. Group I REMs are extensively involved in virus infection. However, little is known about the REM gene family in sugarcane (Saccharum spp. hyrid), the most important sugar and energy crop around world.MethodsComparative genomics were employed to analyze the REM gene family in Saccharum spontaneum. Transcriptomics or RT-qPCR were used to analyze their expression files in different development stages or tissues under different treatments. Yeast two hybrid, bimolecular fluorescence complementation and co-immunoprecipitation assays were applied to investigate the protein interaction.ResultsIn this study, 65 REMs were identified from Saccharum spontaneum genome and classified into six groups based on phylogenetic tree analysis. These REMs contain multiple cis-elements associated with growth, development, hormone and stress response. Expression profiling revealed that among different SsREMs with variable expression levels in different developmental stages or different tissues. A pair of alleles, ScREM1.5e-1/-2, were isolated from the sugarcane cultivar ROC22. ScREM1.5e-1/-2 were highly expressed in leaves, with the former expressed at significantly higher levels than the latter. Their expression was induced by treatment with H2O2, ABA, ethylene, brassinosteroid, SA or MeJA, and varied upon Sugarcane mosaic virus (SCMV) infection. ScREM1.5e-1 was localized to the plasma membrane (PM), while ScREM1.5e-2 was localized to the cytoplasm or nucleus. ScREM1.5e-1/-2 can self-interact and interact with each other, and interact with VPgs from SCMV, Sorghum mosaic virus, or Sugarcane streak mosaic virus. The interactions with VPgs relocated ScREM1.5e-1 from the PM to the cytoplasm.DiscussionThese results reveal the origin, distribution and evolution of the REM gene family in sugarcane and may shed light on engineering sugarcane resistance against sugarcane mosaic pathogens.

Alpine wetlands are an important source of methane (CH4) and play a key role in the global carbon cycle. Their CH4 emissions largely depend on microbial CH4 production and oxidation processes that involve external electron acceptors. Seasonal precipitation drives redox cycles of humic acids (HAs), iron oxide and sulfur species, which will in turn affect CH4 production and oxidation. To investigate the effects of electron acceptors on CH4 emissions, soil samples from a typical alpine wetland on the Tibetan Plateau were incubated with the addition of ferrihydrite (HFO), HAs, sodium sulfate (SO42-) or combinations (HAs-HFO, HAs-SO42- and HAs-HFO-SO42-). During long-term anaerobic incubation, CH4 concentrations showed similar trends, increasing rapidly from 0 to 60 days, decreasing from 60 to 240 days, and finally slowly increasing again after 240 days, in all treatments except the sterilised control. Thus, the incubation period was divided into the production, consumption and reproduction phases. The addition of HFO, HAs or HAs-containing electron acceptors promoted the rates of both production and consumption of CH4, increasing the production potential of CH4 by 65–100 % and the oxidation potential of CH4 by 58–115 %. On the other hand, SO42- inhibited the production and consumption of CH4, reducing the production potential by 35 % and the oxidation potential by 50 %. Electron acceptors such as HFO, HAs and SO42- play important roles in CH4 emissions. HAs are the dominant factor affecting CH4 emissions in alpine wetlands. From a broader ecological perspective, organic and inorganic electron acceptors play a key role in CH4 production and oxidation under anaerobic conditions, influencing CH4 emissions from alpine wetlands.

During photosynthesis, light energy is harvested by an antenna systems and delivered to the reaction centers (RCs) for charge separation and electron transfer (ET). The authors report cryo-EM structures of two forms of RC from the microaerophilic Chloracidobacterium thermophilum (CabRC), providing a structural basis for ET within the CabRC.

Stichopus ocellatus, known as eye-spotted sea cucumber, is a commercially important Stichopodidae holothuroid in Indo-Pacific region for its valuable nutrition and medicinal ingredients. However, because the taxonomic analyses based on morphological characters and molecular data within Aspidochirotida are limited, the deep-level evolutionary relationships of Aspidochirotida are still poorly understood. Here, for providing better insight of future evolutionary and taxonomic classification of Stichopodidae, we report the first complete mitogenome of S. ocellatus along with 37 annotated and characterized mitochondrial genes, and the phylogenetic analysis based on mitogenome data reveals sister relationship between S. ocellatus and S. monotuberculatus.

Abstract Formins are actin-binding proteins that are key to maintaining the actin cytoskeleton in cells. However, molecular mechanisms controlling the stability of formin proteins in plants remain unknown. Here, we have identified six rice SIAH-type E3 ligases, named RIP1-6 (RMD Interacting Protein 1–6) respectively, with ubiquitination enzyme activity in vitro. All six proteins can form homo- and hetero-dimers with themselves, and hetero-dimers with type II formin RMD/OsFH5. In vivo assays showed that RIP1-6 proteins localize in the cytoplasm with a punctate distribution, and all of them interact with RMD to change its native diffuse cytoplasmic localization to match that of RIP1-6. To our surprise, degradation experiments revealed that RIP1, RIP5, and RIP6 decrease rather than increase the degradation rate of RMD. Genetic analyses revealed redundancy between these six genes; either single or double mutants did not show any obvious phenotypes. However, the sextuple rip1-6 mutant displayed dwarf height, wrinkled seeds and wider leaves that were similar to the previously reported rmd mutant, and defective microfilaments and increased flag leaf angles that were not reported in rmd mutant. Collectively, our study provides insights into the mechanisms determining formin protein stability in plants.

Boron chloride in the chlorosilane is hard to remove and directly impacts the quality of polysilicon produced by improved Siemens method. Silicon dioxide functionalized with mannitol and citric acid successfully removed boron chloride in organic solution. The effects of immersion concentration and drying temperature were studied to attain the best adsorption performance. The sorption phenomenon was described well by pseudo-second-order kinetic model and Langmuir adsorption isotherm; particle diffusion model proved that the adsorption on the active adsorption site was the rate determining step, with the formation of boronic esters. Thermal stability and degradation kinetic of the adsorbents were investigated by thermogravimetric analysis. The characterization results of Fourier transform infrared spectroscopy, thermogravimetric analysis, X-ray energy spectrometry, and BET showed the silicon dioxide was successfully functionalized by oxygen-containing functional groups, leading to be a better and safer substitute to traditional boron-selective chelating resin.

In the present work, duplex stainless steels (DSSs) SAF2507 were friction stir processed with flowing cryogenic medium mixed with liquid nitrogen and industrial ethanol. Homogeneous ultrafine grained (UFG) dual-phase structure with ferrite (α) and austenite (γ) grains with average size of around 1 μm was obtained due to the significantly lower peak temperature and shorter high-temperature duration. The developed UFG dual-phase structure enabled a dramatic enhancement of yield strength by about 22 %, while maintaining a high elongation of 55 % owing to the excellent strain hardening capacity. The grain refinement and increased number of α/γ interfaces were dominantly responsible for the significantly improved YS, while the massive development of geometrically necessary dislocations around the deformation incompatible α/γ interfaces primarily contributed to improving the strain hardening capacity. As a result, the enhanced strength-ductility synergy was achieved by cryogenic friction stir processing. Also, the obtained UFG dual-phase structure helps with enhancing corrosion resistance. This work provides a new strategy for preparing uniform UFG DSSs with outstanding mechanical properties and anticorrosion.

Single-pixel holography generates holographic images with a single-pixel detector making this relatively inexpensive. Here the authors report a high-throughput single-pixel compressive holography method for imaging biological tissue which can either provide a large field of view or high resolution.

Alumina-forming austenitic (AFA) steel is considered as a promising candidate used for advanced energy systems. Fusion welding of austenitic steels usually requires the introduction of a certain delta (δ) ferrite to avoid thermal cracking, but for the AFA steel, the presence of δ ferrite will greatly accelerate the precipitation of hard and brittle sigma (σ) phase at its target service temperature. In this work, for the AFA steel with a typical composition, we demonstrated a superior capability of friction stir welding (FSW) in avoiding the formation of δ and σ phases, and developing the favorable weld microstructures under various welding conditions. The microstructure evolution of AFA steel during FSW with various rotational speeds (300–700 rpm) was studied in detail. The resulting FSW joints all exhibit higher yield strength (YS) and ultimate tensile strength (UTS) than the base metal, especially at low rotational speed, while retaining reasonable ductility, despite decreasing with reducing rotational speed. The associated relationship between the microstructure and mechanical properties of the resulting FSW joints was well correlated. This work provides an effective method to obtain the fully-austenitic welded joints of AFA steel with excellent strength-ductility synergy.

Diatoms are marine algae with an important role in global photosynthetic carbon fixation. Here, the authors present the 2.38 Å cryo-EM structure of photosystem I (PSI) in complex with its 24 fucoxanthin chlorophyll a/c-binding (FCPI) antenna proteins from the diatom Chaetoceros gracilis, which provides mechanistic insights into light-energy harvesting, transfer and quenching of the PSI-FCPI supercomplex.

Abstract Background APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play essential roles in plant growth, development, metabolism, and responses to biotic and abiotic stresses. However, few studies concerning AP2/ERF genes in sugarcane which are the most critical sugar and energy crops worldwide. Results A total of 218 AP2/ERF genes were identified in the Saccharum spontaneum genome. Phylogenetic analysis showed that these genes could be divided into four groups, including 43 AP2s, 160 ERFs and Dehydration-responsive element-binding (DREB) factors, 11 ABI3/VPs (RAV), and four Soloist genes. These genes were unevenly distributed on 32 chromosomes. The structural analysis of SsAP2/ERF genes showed that 91 SsAP2/ERFs lacked introns. Sugarcane and sorghum had a collinear relationship between 168 SsAP2/ERF genes and sorghum AP2/ERF genes that reflected their similarity. Multiple cis-regulatory elements (CREs) present in the SsAP2/ERF promoter were related to abiotic stresses, suggesting that SsAP2/ERF activity could contribute to sugarcane adaptation to environmental changes. The tissue-specific analysis showed spatiotemporal expression of SsAP2/ERF in the stems and leaves of sugarcane at different development stages. In ten sugarcane samples, 39 SsAP2/ERFs were not expressed, whereas 58 SsAP2/ERFs were expressed in all samples. Quantitative PCR experiments showed that SsERF52 expression was up-regulated under salt stress, but suppressed under dehydration stress. SsSoloist4 had the most considerable upregulation in response to treatment with the exogenous hormones ABA and GA. Within 3 h of ABA or PEG6000 treatment, SsSoloist4 expression was up-regulated, indicating that this gene could play a role in the responses to ABA and GA-associated dehydration stress. Analysis of AP2/ERF gene expression patterns under different treatments indicated that SsAP2/ERF genes played an essential role in dehydration and salt stress responses of S. spontaneum. Conclusions In this study, a total of 218 members of the AP2 / ERF superfamily were identified in sugarcane, and their genetic structure, evolution characteristics, and expression patterns were studied and analyzed. The results of this study provide a foundation for future analyses to elucidate the importance of AP2/ERF transcription factors in the function and molecular breeding of sugarcane.

Plant microbiota are of great importance for host nutrition and health. As a C4 plant species with a high carbon fixation capacity, sugarcane also associates with beneficial microbes, though mechanisms underlying sugarcane root-associated community development remain unclear. Here, we identify microbes that are specifically enriched around sugarcane roots and report results of functional testing of potentially beneficial microbes propagating with sugarcane plants. First, we analyzed recruitment of microbes through analysis of 16S rDNA enrichment in greenhouse cultured sugarcane seedlings growing in field soil. Then, plant-associated microbes were isolated and assayed for beneficial activity, first in greenhouse experiments, followed by field trials for selected microbial strains. The promising beneficial microbe SRB-109, which quickly colonized both roots and shoots of sugarcane plants, significantly promoted sugarcane growth in field trials, nitrogen and potassium acquisition increasing by 35.68 and 28.35%, respectively. Taken together, this report demonstrates successful identification and utilization of beneficial plant-associated microbes in sugarcane production. Further development might facilitate incorporation of such growth-promoting microbial applications in large-scale sugarcane production, which may not only increase yields but also reduce fertilizer costs and runoff.

Recently, 3D packaging has been regarded as an important technical means to continue Moore’s Law. However, excessive stacking will increase the longitudinal dimension, and one chip with high-density bondings packaging is still needed. Thus, it naturally places higher demand on thermal cycling reliability due to the decreased joint size to satisfy high-density packaging. In this work, the nano-Al2O3 (1 wt.%) modified Sn-1 wt.% Ag-0.5 wt.% Cu low-Ag solder was applied as a solder sample to evaluate the associated thermal cycling reliability. The investigated results revealed that the nano-Al2O3 modified solder did present enhanced thermal cycling reliability, as evidenced by the delayed microstructure coarsening and the inhibited atom inter-diffusion at interface caused by the adsorption of nano-Al2O3 on grain surfaces, and the resultant pinning effect. Worthy of note is that the potential of the newly developed nano-Al2O3 modified solder for high-density packaging applications (e.g., BGA, QFN, and CCGA) was evaluated based on the Finite Element Modeling.

Low- and ultra-low-grade thermal energy have significant recycling value for energy saving and carbon footprint reduction. Efficient thermal energy storage technology based on phase change materials (PCMs) will help improve heat recovery. This study aimed to develop a composite eutectic fatty acid of lauric acid (LA) and stearic acid (SA) binary system with expanded graphite (EG). The experimental measured eutectic temperature was 31.2 °C with an LA-to-SA mass ratio of 7:3. Afterwards, 1~15 wt.% EG was composited to the eutectic acid, and the thermophysical properties of the composite PCMs were measured by differential scanning calorimetry (DSC) and transient plane source (TPS) methods. The results demonstrated that the phase transition temperature and latent heat of the composite PCMs were stable when the content of EG was more than 5%, and the thermal conductivity and thermal diffusion coefficient of the composite PCMs (10–15 wt.%) increased by 2.4–2.6 and 3.2–3.7 times compared with the pure eutectic acid, respectively. On this basis, a finned-coil-type reservoir was prepared, and an experimental study of heat storage and heat release performance was carried out. The results showed that the heat storage and heat release effects of the heat reservoir were the best when the EG ratio was 10 wt.%. The heat storage time was reduced by 20.4%, 8.1%, and 6.2% compared with the other three EG ratios, respectively; meanwhile, the heat release time was reduced by 19.3%, 6.7%, and 5.3%, respectively.

Echinoderms (Echinodermata) are morphologically diverse and ecologically important groups of marine invertebrate, many of which are key components of local benthic ecosystem. However, due to morphological plasticity and limited molecular phylogenetic studies, the taxonomic histories in echinoderms have not been completely resolved. The phylogenetic relationships of Phyllophoridae genera and species remain controversial and many species are incorrectly assigned within genus Phyrella. In this study, we report the first complete mitochondrial genome of Phyrella from Phyrella fragilis. The mitogenome has 15,910 base pairs (64.32% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), plus a putative control region. This study will provide useful genetic data for future phylogenetic and taxonomic classification of Phyllophoridae.

The white-bottomed sea cucumber, Actinopyga lecanora, is a valuable inshore fisheries resource which is famous for its high nutrition and pharmacological compounds. However, due to morphological plasticity and limited molecular phylogenetic studies, the taxonomic histories in the genus Actinopyga have not been completely resolved yet. Moreover, there remains a complex of cryptic species within Actinopyga, many of which are incorrectly assigned within the family Holothuriidae. In this study, we report the complete mitochondrial genome of A. lecanora. The mitogenome has 15,568 base pairs (63.40% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), plus a putative control region. This study offers useful mitogenome data for future phylogenetic and taxonomic classification of Holothuriidae.

Whether oil emplacement and diagenetic sequences provoke, deteriorate, or have no effect on pore network evolution, as implied by recent tests and theoretical analysis, are critical factors in forecasting hydrocarbon exploration and development potentials. Therefore, a systematic investigation on the effect of oil emplacement of tight sandstones is conducted to study the importance of this behavior on the pore evolution path. This study evaluated the role played by oil emplacement and diagenesis in the pore network evolution of Upper Triassic tight sandstones in the Ordos Basin. To help provide a comprehensive understanding, we have used a multidisciplinary method including physical properties, casting thin section, scanning electron microscope, X-ray diffraction, fluorometric, and inclusion analysis. The results demonstrate that the sandstones could be divided into four groups based on new criteria: calcareous sandstone, high soft component sandstone, low soft component sandstone with continual oil emplacement, and low soft component sandstone with intermittent oil emplacement. The physical properties of those types of sandstones were gradually reduced. Quartz cement captured hydrocarbon, carbonate captured hydrocarbon, free hydrocarbon, and adsorbed hydrocarbon were the four main kinds of hydrocarbons. The maturity of those sandstones was decreased progressively, indicating that the formation time of those hydrocarbons was favorable to maturity. Four stages of oil emplacement happened, and large-scale emplacement mainly occurred in the late Jurassic and early Craterous. The evidence demonstrated that tight sandstones’ high porosity could be attributed to positive diagenetic contributions with a complex interplay of chemical compaction, early formed clays, and large-scale oil emplacement. This work would provide new sights for a better understanding of the tight oil accumulation modes, and the findings could be applied in the hydrocarbon exploration and development field.

The automated measurement of crop phenotypic parameters is of great significance to the quantitative study of crop growth. The segmentation and classification of crop point cloud help to realize the automation of crop phenotypic parameter measurement. At present, crop spike-shaped point cloud segmentation has problems such as fewer samples, uneven distribution of point clouds, occlusion of stem and spike, disorderly arrangement of point clouds, and lack of targeted network models. The traditional clustering method can realize the segmentation of the plant organ point cloud with relatively independent spatial location, but the accuracy is not acceptable. This paper first builds a desktop-level point cloud scanning apparatus based on a structured-light projection module to facilitate the point cloud acquisition process. Then, the rice ear point cloud was collected, and the rice ear point cloud data set was made. In addition, data argumentation is used to improve sample utilization efficiency and training accuracy. Finally, a 3D point cloud convolutional neural network model called Panicle-3D was designed to achieve better segmentation accuracy. Specifically, the design of Panicle-3D is aimed at the multiscale characteristics of plant organs, combined with the structure of PointConv and long and short jumps, which accelerates the convergence speed of the network and reduces the loss of features in the process of point cloud downsampling. After comparison experiments, the segmentation accuracy of Panicle-3D reaches 93.4%, which is higher than PointNet. Panicle-3D is suitable for other similar crop point cloud segmentation tasks.

Sea urchins (Echinoidea) are key components of marine benthic communities and many are commercially important fishery resources as luxury and healthy seafood. However, despite their high ecological and economic value, the mitochondrial genomes of all sea urchins have yet to be analyzed. In this study, we report the first complete mitochondrial genome of Stomopneustidae from Stomopneustes variolaris. The mitogenome has 15,767 base pairs (59.77% A + T content) and contains 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), plus a putative control region. This study provides useful molecular resources for clarifying evolutionary and phylogenetic histories of sea urchins.

Ditylenchus destructor is a migratory plant-parasitic nematode that causes huge damage to global root and tuber production annually. The main plant hosts of D. destructor contain plenty of starch, which makes the parasitic environment of D. destructor to be different from those of most other plant-parasitic nematodes. It is speculated that D. destructor may harbor some unique pathogenesis-related genes to parasitize the starch-rich hosts. Herein, we focused on the multi-copy alpha-amylase genes in D. destructor, which encode a key starch-catalyzing enzyme. Our previously published D. destructor genome showed that it has three alpha-amylase encoding genes, Dd_02440, Dd_11154, and Dd_13225. Comparative analysis of alpha-amylases from different species demonstrated that the other plant-parasitic nematodes, even Ditylenchus dipsaci in the same genus, harbor only one or no alpha-amylase gene, and the three genes from D. destructor were closely clustered in the phylogenetic tree, indicating that there was a unique expansion of the alpha-amylase gene in D. destructor. The enzymatic activity of the three alpha-amylase proteins was verified by an enzyme assay. Quantitative real-time PCR assay showed that the expression of the three alpha-amylase genes in the post-hatching stage of D. destructor was found to be significantly higher than that in eggs. In the in situ hybridization assay, the expression of the genes was localized to the intestine, implying the association of these genes with nematode digestion. An infection assay in sweet potato demonstrated that RNA interference of any one alpha-amylase gene had no influence on the infectivity of D. destructor. Using the multi-target dsRNA cocktail method, it was found that silencing of two of the three genes inhibited nematode infection, and the infectivity of worms treated with three dsRNA simultaneously changed the most, which decreased by 76.6%. Thus, the multi-copy alpha-amylase genes in D. destructor are compensatory and crucial for nematodes to parasitize the plant host.

Drought is the main abiotic stress that constrains sugarcane growth and production. To understand the molecular mechanisms that govern drought stress, we performed a comprehensive comparative analysis of physiological changes and transcriptome dynamics related to drought stress of highly drought-resistant (ROC22, cultivated genotype) and weakly drought-resistant (Badila, wild genotype) sugarcane, in a time-course experiment (0 h, 4 h, 8 h, 16 h and 32 h). Physiological examination reviewed that ROC22, which shows superior drought tolerance relative to Badila, has high performance photosynthesis and better anti-oxidation defenses under drought conditions. The time series dataset enabled the identification of important hubs and connections of gene expression networks. We identified 36,956 differentially expressed genes (DEGs) in response to drought stress. Of these, 15,871 DEGs were shared by the two genotypes, and 16,662 and 4423 DEGs were unique to ROC22 and Badila, respectively. Abscisic acid (ABA)-activated signaling pathway, response to water deprivation, response to salt stress and photosynthesis-related processes showed significant enrichment in the two genotypes under drought stress. At 4 h of drought stress, ROC22 had earlier stress signal transduction and specific up-regulation of the processes response to ABA, L-proline biosynthesis and MAPK signaling pathway–plant than Badila. WGCNA analysis used to compile a gene regulatory network for ROC22 and Badila leaves exposed to drought stress revealed important candidate genes, including several classical transcription factors: NAC87, JAMYB, bHLH84, NAC21/22, HOX24 and MYB102, which are related to some antioxidants and trehalose, and other genes. These results provide new insights and resources for future research and cultivation of drought-tolerant sugarcane varieties.

The orientation of plant roots responds to gravity and influences nutrient acquisition. Here the authors show that the formin RMD buffers movement of specialized gravity-sensing organelles and report enhanced RMD expression during phosphate deficiency that could alter root angle to improve phosphate uptake.

Plant root architecture can adapt to different nutrient conditions in the soil. Here Giri et al. show that the rice auxin influx carrier AUX1 mobilizes auxin from the root apex to the differentiation zone and promotes root hair elongation when roots encounter low external phosphate.

Venus clams (Veneridae) including Antigona lamellaris are commercially important fishery resources by their dominance in local benthic communities. However, despite their great diversity, the phylogenetic and taxonomic relationships in venus clams remain poorly understood. In this study, we report the first complete mitochondrial genome of A. lamellaris. The mitogenome has 17,532 base pairs (67.9% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), plus a putative control region. This study will provide useful molecular resources for clarifying taxonomic and phylogenetic confusion in venus clams.

The true crabs (Brachyura) including Calappidea are one of the most diverse groups of Decapod crustaceans However, despite their great diversity and commercial importance, phylogenetic and classification relationships within Calappidea are still complicated and controversial. In this study, we report the first complete mitochondrial genome of Matuta victos. The mitogenome has 17,782 base pairs (70.1% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and two ribosomal RNAs), plus a putative control region. This study will provide useful molecular resources for clarifying evolutionary and phylogenetic confusion within Calappidea.

The common frogsnail Bufonaria rana, is an ecologically and economically important Tonnoideans in China due to valuable nutrition and pharmacological compounds. However, the taxonomy and phylogeny of the Bursidae have been debated and synonyms among Bursidae species have been reported recently. In this study, we report the first complete mitochondrial genome of Bursidae from B. rana. The mitogenome has 15,510 base pairs (69.0% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a putative control region. This study was the first available complete mitogenomes of Bursidae and will provide useful genetic information for future phylogenetic and taxonomic classification of Tonnoideans.

Miters including Mitra chinensis are important fishery resources in China. However, the phylogenetic and taxonomic studies in Mitridae have been limited. In this study, we report the first complete mitochondrial genome of M. chinensis. The mitogenome has 16,238 base pairs (66.9% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs, and two ribosomal RNAs), plus a putative control region. This study will provide useful molecular resources for addressing taxonomic and evolutionary issues in Neogastropoda.

Phascolosoma is one of the most important genera of Sipuncula, many species of which including P. scolops are economic important species in the fishery of southeast China. However, the synonym and misidentification of species in Phascolosoma have been reported repeatedly. Here, we report the complete mitochondrial genome sequence of P. scolops. The mitogenome has 15,515 base pairs and made up of total of 38 genes (13 protein-coding, 23 transfer RNAs and 2 ribosomal RNAs), and a putative control region. The complete mitogenomes of P. scolops will contribute to further phylogenetic and taxonomic study in the genus Phascolosoma.

Chicoreus asianus is an ecologically and economically important species of Muricidae, which comprises a highly diverse group of carnivorous marine snails. However, the taxonomic classification and phylogenetic studies have so far been limited. In this study, we report the complete mitochondrial genome of C. asianus. The mitogenome has 15,361 base pairs (65.2% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a control region. The complete mitogenomes of C. asianus. will provide useful genetic information for future taxonomic and phylogenetic classification of Neogastropoda.

The deep-water redfish, Actinopyga echinites, is an ecologically and economically important holothuroid in China due to its valuable nutrition and pharmacological compounds. However, the taxonomy and phylogeny of the Actinopyga have been debated and misidentifications have been reported recently. Moreover, there remain considerable doubts about cryptic species complex within Actinopyga. In this study, we report the first complete mitochondrial genome of Actinopyga from A. echinites. The mitogenome has 15,619 base pairs (62.9% A + T content) and made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs, and 2 ribosomal RNAs), and a putative control region. This study was the first available complete mitogenome of Actinopyga and will provide useful genetic information for future phylogenetic and taxonomic classification of Holothuriidae.

Siphonosoma cumanense is economic important species in the fishery of southeast China. However, the current classification and the phylogeny of genus Siphonosoma had not been verified yet. Here, we report the complete mitochondrial genome sequence of S. Siphonosoma. The mitogenome has 15,917 base pairs and made up of total of 38 genes (13 protein-coding, 23 transfer RNAs and 2 ribosomal RNAs), and a putative control region. This study was the first available complete mitogenomes of Siphonosoma and will provide useful genetic information for future phylogenetic and taxonomic classification of Sipuncula.

Mammilla mammata is an ecologically and economically important species of Caenogastropoda, which is the largest and most evolutionary successful group of marine gastropods. However, the phylogenetic relationships between the families and superfamilies within Caenogastropoda have been debated. In this study, we report the first complete mitochondrial genome of Mammilla from M. mammata. The mitogenome has 15,300 base pairs (71.4% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a control region. This study was the first available complete mitogenomes of Mammilla and will provide useful genetic information for future phylogenetic and taxonomic classification of Naticidae.

Eukaryotic translation initiation factor 4E (eIF4E) plays a key role in the infection of potyviruses in susceptible plants by interacting with viral genome-linked protein (VPg). Sugarcane (Saccharum spp.) production is threatened by mosaic disease caused by Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV), and Sugarcane streak mosaic virus (SCSMV). In this study, two eIF4Es and their isoform eIF(iso)4E and 4E-binding protein coding genes were cloned from sugarcane cultivar ROC22 and designated SceIF4Ea, SceIF4Eb, SceIF(iso)4E, and ScnCBP, respectively. Real-time quantitative PCR analysis showed different expression profiles of these four genes upon SCMV challenge. A subcellular localization assay showed that SceIF4Ea, SceIF4Eb, SceIF(iso)4E, and ScnCBP were distributed in the nucleus and cytoplasm. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that SceIF4Ea/b and SceIF(iso)4E were selectively employed by different sugarcane mosaic pathogens, i.e., SCMV-VPg interacted with SceIF4Ea/b and SceIF(iso)4E, SrMV-VPg interacted with both SceIF4Eb and SceIF(iso)4E, and SCSMV-VPg interacted only with SceIF(iso)4E. Intriguingly, the BiFC assays, but not the Y2H assays, showed that ScnCBP interacted with the VPgs of SCMV, SrMV, and SCSMV. Competitive interaction assays showed that SCMV-VPg, SrMV-VPg, and SCMV-VPg did not compete with each other to interact with SceIF(iso)4E, and SceIF(iso)4E competed with SceIF4Eb to interact with SrMV-VPg but not SCMV-VPg. This study sheds light on the molecular mechanism of sugarcane mosaic pathogen infection of sugarcane plants and benefits sugarcane breeding against the sugarcane mosaic disease.

Phosphate is an essential macro-element for plant growth accumulated in the topsoil. The improvement of phosphate uptake efficiency via manually manipulating root system architecture is of vital agronomic importance. This review discusses the molecular mechanisms of root patterning in response to external phosphate availability, which could be applied on the alleviation of phosphate-starvation stress. During the long time evolution, plants have formed sophisticated mechanisms to adapt to environmental phosphate conditions. In terms of root systems, plants would adjust their root system architecture via the regulation of the length of primary root, the length/density of lateral root and root hair and crown root growth angle to cope with different phosphate conditions. Finally, plants develop shallow or deep root system in low or high phosphate conditions, respectively. The plasticity of root system architecture responds to the local phosphate concentrations and this response was regulated by actin filaments, post-translational modification and phytohormones such as auxin, ethylene and cytokinin. This review summarizes the recent progress of adaptive response to external phosphate with focus on integrated physiological, cellular and molecular signaling transduction in rice and Arabidopsis.

The green tiger prawn, Penaeus semisulcatus, is one of the economically important penaeid shrimp due to its larger body size compared with other shrimps in Penaeidae family. However, the taxonomic revision studies of Penaeidae have been one of the most controversial issues in recent years. Moreover, there are at least two morphotypes of the green tiger prawn, one with banded antenna, another with non-banded antenna. In this study, we report the complete mitochondrial genome of P. semisulcatus. The mitogenome has 16,002 base pairs (68.6% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a control region. This study adds one more available complete mitogenomes of Penaeus and will provide useful genetic information for future evolutionary and taxonomic classification of Penaeidae.

The black sea cucumber, Holothuria leucospilota, is an ecologically and economically important holothuroid in China due to broader environmental adaptation and valuable pharmacological compounds. However, the wild stocks of H. leucospilota, have been declining steadily due to overexploitation in recent years. The stock enhancement programme has become an increasingly important priority. In this study, we report the complete mitochondrial genome of H. leucospilota. The mitogenome has 15,839 base pairs (57.6% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a putative control region. The complete mitogenomes of H. leucospilota will provide useful genetic information for future conservation and management of this valuable and vulnerable species.

The sea cucumber, Stichopus monotuberculatus, is an economically important holothuroid in China due to its larger body size and valuable nutrition. However, the taxonomic revision studies of Stichopodidae have been one of the most controversial issues in recent years. Moreover, there remain considerable doubts about a complex of cryptic species within S. monotuberculatus. In this study, we report the complete mitochondrial genome of S. monotuberculatus. The mitogenome has 16,274 base pairs (60.4% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a putative control region. This study adds one more available complete mitogenomes of Stichopus and will provide useful genetic information for future evolutionary and taxonomic classification of Stichopodidae.

The rare-spined murex (Murex trapa) is an ecologically and economically important species of Muricidae, which comprises a highly diverse group of predatory marine snails. However, the taxonomic classification and phylogenetic studies have so far been limited. In this study, we report the first complete mitochondrial genome of Murex from M. trapa. The mitogenome has 15,408 bp (66.3% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs, and 2 ribosomal RNAs), and a control region. This study provided the first complete mitogenome of Murex and will provide useful genetic information for future phylogenetic and taxonomic classification of Muricidae.

Hemifusus tuba is an ecologically and economically important species of Buccinoidea, which comprises an ecologically diverse group of carnivorous marine gastropods. However, the taxonomic classification and phylogenetic studies have so far been limited. In this study, we report the first complete mitochondrial genome of Melongenidae from H. tuba. The mitogenome has 15,483 bp (68.2% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs, and 2 ribosomal RNAs), and a control region. This study was the first to provide complete mitogenome of Melongenidae and will provide useful genetic information for future phylogenetic and taxonomic classification of Buccinoidea.

Melo melo is an ecologically and economically important species of Neogastropoda, which is an ecologically diverse group of carnivorous marine gastropods. However, the taxonomic classification and phylogenetic studies have so far been limited. In this study, we report the second complete mitochondrial genome of Volutidae from M. melo. The mitogenome has 15,721 base pairs (68.3% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a control region. This study was the second available complete mitogenomes of Volutidae and will provide useful genetic information for future phylogenetic and taxonomic classification of Neogastropoda.

The evolution of interfacial morphology and shear strengths of the joints soldered with Sn-0.3Ag-0.7Cu (SAC0307) and SAC0307-0.05Pr aged at 150 °C for different times (h; up to 840 h) were investigated. The experiments showed the electronic joint soldered with SAC0307-0.05Pr has a much higher shear strength than that soldered with SAC0307 after each period of the aging process. This contributes to the doping of Pr atoms, “vitamins in alloys”, which tend to be adsorbed on the grain surface of interfacial Cu6Sn5 IMCs, inhibiting the growth of IMCs. Theoretical analysis indicates that doping 0.05 wt.% Pr can evidently lower the growth constant of Cu6Sn5 (DCu6), while the growth constant of Cu3Sn (DCu3) decreased slightly. In addition, the electronic joint soldered with SAC0307-0.05Pr still has better ductility than that soldered with SAC0307, even after a 840-h aging process.