Gene Function Prediction Research Articles

RNA interference-mediated knockdown of genes involved in sugar transport and metabolism disrupts psyllid Bactericera cockerelli (Order: Hemiptera) gut physiology and results in high mortality.

The causal agent of zebra chip of potato and vein-greening diseases of tomato is "Candidatus Liberibacter solanacearum" (CLso), a fastidious bacterium transmitted by the potato psyllid. In the absence of disease-resistant cultivars, disease management has relied on minimizing vector population size to reduce CLso transmission, which requires frequent insecticide applications. There is growing interest in the use of RNA interference (RNAi) technology to supplant traditional insecticides with biopesticides. This requires knowledge of genes essential for insect livelihood whose knockdown leads to significant mortality or other phenotypes. Such candidate genes can be evaluated by reverse genetics approaches to further corroborate predicted gene function. Here, five potato psyllid genes involved in sugar homeostasis in the potato psyllid gut, α-glucosidase1 (AGLU1), aquaporin2 (AQP2), facilitated trehalose transporter1 (TRET1), Trehalase1 (TRE1), and Trehalase2 (TRE2), were investigated as candidates for effective gene silencing. Potato psyllid dsRNAs were designed to optimize knockdown of gene targets. Third instar PoP nymphs were given a 48-hr ingestion-access period (IAP) on individual or groups of dsRNA in 20% sucrose. Mortality was recorded 0, 3, 5, 7, and 9 days post-IAP. Gene knockdown was analyzed 9 days post-IAP by quantitative real-time reverse-transcriptase polymerase chain reaction amplification. The individual or stacked dsRNA combinations resulted in 20-60% and 20-40% knockdown, respectively, while subsequent psyllid mortality ranged from 20-40% to >60% for single and stacked dsRNA combinations, respectively. Reverse genetics analysis showed that simultaneous knockdown of the five selected candidate genes with predicted functions in pathways involved in sugar-homeostasis, metabolism, and -transport yielded the highest mortality, when compared with single or combinations of targets. Results confirmed the functions afforded by psyllid gut genes responsible for osmotic homeostasis and sugar metabolism/transport are essential for livelihood, identifying them as potentially lucrative RNAi biopesticide targets and highlighted the translational relevance of targeting multiple nodes in a physiological pathway simultaneously.

Long-term maintenance rate fertilisation increases soil bacterial-archaeal community diversity in the subsoil and N-cycling potentials in a humid crop season

Among agronomical practices, fertilisation greatly influences soil microbial diversity and functionality and severely disturbs the global nitrogen (N) cycle. In this study, we assessed the effect of 16 years of mineral fertilisation (NPS) on soil bacterial-archaeal communities in a no-tillage experiment in a humid climate season. We used 16S rRNA amplicon sequencing and functional prediction of marker genes involved in the N cycle at two soil depths (0–5 and 5–10 cm). Samples were taken after soybean harvest in a wheat/soybean-maize crop sequence. At both soil depths, fertilisation increased the abundance of Proteobacteria while reducing the abundance of Verrucomicrobiota. Indicator species analyses revealed that MB-A2–108 (Actinobacteriota) and Nitrososphaeraceae (Archaea) were indicators of the low fertiliser rates at 0–5 cm. Instead, Rokubacteriales (Methylomirabilota) and Nitrolancea (Chloroflexi) were indicators of low and high rates, respectively, at 5–10 cm. Biological N–fixation genes (nifA, nifV nifHD1, and nifHD2) showed an inconsistent response depending on the soil depth. Yet, the high abundance of nifA revealed the presence of N-fixing microorganisms even at high levels of N fertilisation. The predominance of genes involved in the dissimilatory (nirB and nirK) and assimilatory (nirA) reduction of nitrate was steadily found at higher fertilisation. Given that the predecessor crop was a legume that did not receive N, our results revealed the substantial legacy of long-term N inputs on soil bacterial-archaeal diversity and N-cycling genes that might have been umpired by the current humid conditions.

Rhizosphere microbial characteristics of pioneer plant Oxyria sinensis Hemsl. in abandoned Pb-Zn mining area

Oxyria sinensis has the characteristics of drought resistance, barren resistance, pollution resistance and clonal reproduction, and has the potential to be developed as a restoration plant (pioneer plant) for vegetation restoration and heavy metal pollution control in mining wasteland. In this study, the rhizosphere microbial communities of the pioneer plant O. sinensis growing in a lead-zinc mine wasteland and the rhizosphere microbial communities of O. sinensis growing in adjacent non-mining areas were studied by field investigation. There were significant differences in the composition of microbial communities between the rhizosphere soil of O. sinensis and the bare soil. There were significant differences in the composition of soil microbial communities between the non-mining area control and the lead-zinc mine wasteland. Compared with the non-mining area control, the rhizosphere soil of O. sinensis in the lead-zinc mine wasteland had a unique microbial community. The dominant bacteria were Nitrospirae, Chloroflexi, Proteobacteria, Actinobacteria, Ascomycota and Kickxellomycota. Further gene function prediction showed that the metabolic pathway sequences related to heavy metal ion transport, heavy metal resistance and repair in the rhizosphere soil of O. sinensis were more abundant than those in the control. The dominant ecological functional groups of fungi in the rhizosphere soil of O. sinensis were saprophytic flora and pathological flora. Plenodomus, Surfurifusis, Sphingomonas, Filobasidium and Articulospora were enriched in the rhizosphere soil of O. sinensis in the abandoned land of lead-zinc mining area, and had high tolerance to heavy metals in the soil, indicating that O. sinensis can recruit heavy metal-tolerant microbial groups to promote its survival and adaptation in the abandoned land of the mining area.

Structure analysis and in vitro evaluation of probiotic properties for polysaccharides from Phellinus baumii extracted with phosphotungstic acid assistance

Heteropolysaccharides were extracted from Phellinus baumii using hot water assisted by phosphotungstic acid, and their physicochemical properties and structures were analyzed. Two isolated components (SPB and SPC) were composed of fucose, galactose, glucose and mannose, with molecule weight of 12.6 kDa and 9.4 kDa, respectively. Structural analysis showed that →6)-Galp-(1→ and →4)-Glcp-(1→ were the main 2D structural fragments in SPB, while →6)-Galp-(1→ and →6)-Glcp-(1→ predominated in SPC. After 48 h of in vitro fermentation with human fecal inoculum, the concentration of propionic acid was extensively boosted (166.3–538.0 μg/mL) by SPB. In addition, the heteropolysaccharides could promote the abundance and diversity of gut microbiota. SPB markedly promoted proliferation of Limosilactobacillus, Megamonas and Bifidobacterium. KEGG-based functional gene prediction implied that biosynthesis of antibiotics, secondary metabolites and ribosome were promoted by SPB component, indicating a stronger probiotic proliferative ability compared to SPA. Overall, these findings emphasized the potential of these heteropolysaccharides possess to maintain the gut health as a potential prebiotic supplemented in foods and nutraceuticals.

Changes in stoichiometric ratio of carbon and sulfate affect methanogenesis pathways in sulfate-rich sewers

Methane emissions from sewer systems have been a major concern in terms of posing safety risks and aggravating the greenhouse effect. Discharging a large amount of sulfate-rich wastewater produced by industrial manufacture into municipal sewers breaks the balance between organic matter and sulfate, and has a significant influence on methanogenesis. However, the direct impact of sulfate-rich wastewater on the interactions between methane and sulfate metabolism in sewers remains unclear. In this study, methane production, microbial community and functional genes of the sewers with different chemical oxygen demand/sulfate ratios (C/S) were studied by 33 sampling sites collected in full-scale field investigation. The concentrations of chemical oxygen demand in the sewers were 10.0–378.0 mg/L, while the concentrations of sulfate fluctuated in a wider range of 4.1–758.4 mg/L, which distinguished the sewers into different C/S of 0.3, 2.5 and 5.8. With the average sulfate concentrations of 37.9 mg/L, the methane-production capabilities of sewers were reduced as the decreased C/S from 5.8 to 2.5. In contrast, the sewers with low C/S of 0.3 and high sulfate concentration of 368.2 mg/L exhibited twice as much methane concentrations (1.2 mL/L) than the sewers (0.6 mL/L) with C/S of 2.5 and 5.8. Genera showing a positive correlation (Enterobacter, Prevotella_9 and Acinetobacter) and a negative correlation (Bacteroidetes vadinHA17_norank, Smithella and Thiobacillus) with methanogenesis contributed significant variations of methane in the sewers with different C/S. The results of functional gene prediction suggested that the main pathways of methanogenesis in sewers with C/S of 5.8 and 2.5 were acetoclastic (ACSS and ackA) and hydrogenotrophic methanogenesis (mtrA, mtrH and K00400), whereas methylotrophic methanogenesis (mttB) was dominant in sewers with C/S of 0.3. The genes expressed by methylotrophic methanogens in sewer with low C/S and higher sulfate concentration refrained from the competitive inhibition by SRB, which contributed to the superior methane-production of the sewers. These results bridge the knowledge gap of methanogenesis with different sulfate levels and improve the understanding of methane cycle driven by microorganisms, facilitating more accurate prediction and assessment of methane in sewers.

Manual correction of genome annotation improved alternative splicing identification of Artemisia annua.

Gene annotation is essential for genome-based studies. However, algorithm-based genome annotation is difficult to fully and correctly reveal genomic information, especially for species with complex genomes. Artemisia annua L. is the only commercial resource of artemisinin production though the content of artemisinin is still to be improved. Genome-based genetic modification and breeding are useful strategies to boost artemisinin content and therefore, ensure the supply of artemisinin and reduce costs, but better gene annotation is urgently needed. In this study, we manually corrected the newly released genome annotation of A. annua using second- and third-generation transcriptome data. We found that incorrect gene information may lead to differences in structural, functional, and expression levels compared to the original expectations. We also identified alternative splicing events and found that genome annotation information impacted identifying alternative splicing genes. We further demonstrated that genome annotation information and alternative splicing could affect gene expression estimation and gene function prediction. Finally, we provided a valuable version of A. annua genome annotation and demonstrated the importance of gene annotation in future research.

Comprehensive Analysis and Characterization of the GATA Gene Family, with Emphasis on the GATA6 Transcription Factor in Poplar.

GATA transcription factors are ubiquitously present in eukaryotic organisms and play a crucial role in multiple biological processes, such as plant growth, stress response, and hormone signaling. However, the study of GATA factors in poplar is currently limited to a small number of proteins, despite their evident functional importance. In this investigation, we utilized the most recent genome annotation and stringent criteria to identify 38 GATA transcription factor genes in poplar. Subsequently, we conducted a comprehensive analysis of this gene family, encompassing phylogenetic classification, protein characterization, analysis of promoter cis-acting elements, and determination of chromosomal location. Our examination of gene duplication events indicated that both tandem and segmental duplications have contributed to the expansion of the GATA gene family in poplar, with segmental duplication potentially being a major driving force. By performing collinearity analysis of genes across six different species, we identified 74 pairs of co-linear genes, which provide valuable insights for predicting gene functions from a comparative genomics perspective. Furthermore, through the analysis of gene expression patterns, we identified five GATA genes that exhibited differential expression in leaf-stem-root tissues and eight genes that were responsive to salt stress. Of particular interest was GATA6, which displayed strong induction by salt stress and overlapped between the two gene sets. We discovered that GATA6 encodes a nuclear-localized protein with transcription activation activity, which is continuously induced by salt stress in leaf and root tissues. Moreover, we constructed a co-expression network centered around GATA6, suggesting the potential involvement of these genes in the growth, development, and response to abiotic stress processes in poplar through cell transport systems and protein modification mechanisms, such as vesicle-mediated transport, intracellular transport, ubiquitination, and deubiquitination. This research provides a foundation for further exploration of the functions and mechanisms of GATA transcription factors in poplar.

Niche Differentiation of Biofilm Microorganisms in a Full-scale Municipal Drinking Water Distribution System in China and Their Implication for Biofilm Control.

Biofilms on the inner surface of a drinking water distribution system (DWDS) affect water quality and stability. Understanding the niche differentiation of biofilm microbial communities is necessary for the efficient control of DWDS biofilms. However, biofilm studies are difficult to conduct in the actual DWDS because of inaccessibility to the pipes buried underground. Taking the opportunity of infrastructure construction and relevant pipeline replacement in China, biofilms in a DWDS (a water main and its branch pipes) were collected in situ, followed by analysis on the abundances and community structures of bacterial and archaeal using quantitative PCR and high-throughput sequencing, respectively. Results showed that archaea were detected only in the biofilms of the water main, with a range of 9.4×103~1.1×105 copies/cm2. By contrast, bacteria were detected in the biofilms of branch pipes and the distal part of the water main, with a range of 8.8×103~9.6×106 copies/cm2. Among the biofilm samples, the archaeal community in the central part of the water main showed the highest richness and diversity. Nitrosopumilus was found to be predominant (86.22%) in the biofilms of the proximal part of the water main. However, Methanobrevibacter (87.15%) predominated in the distal part of the water main. The bacterial community of the water main and branch pipes was primarily composed of Firmicutes and Proteobacteria at the phylum level, respectively. Regardless of archaea or bacteria, only few operational taxonomic units (OTUs) (<0.5% of total OTUs) were shared by all the biofilms, indicating the niche differentiation of biofilm microorganisms. Moreover, the high Mn content in the biofilms of the distal sampling location (D3) in the water main was linked to the predominance of Bacillus. Functional gene prediction revealed that the proportion of infectious disease-related genes was 0.44-0.67% in the tested biofilms. Furthermore, functional genes related to the resistance of the bacterial community to disinfections and antibiotics were detected in all the samples, that is, glutathione metabolism-relating genes (0.14-0.65%) and beta-lactam resistance gene (0.01-0.05%). The results of this study indicate the ubiquity of archaea and bacteria in the biofilms of water main and branch pipes, respectively, and pipe diameters could be a major influencing factor on bacterial community structure. In the water main, the key finding was the predominant existence of archaea, particularly Nitrosopumilus and methanogen. Hence, their routine monitoring and probable influences on water quality in pipelines with large diameter should be given more attention. Besides, since Mn-related Bacillus and suspected pathogenic Enterococcus were detected in the biofilm, supplementation of disinfectant may be a feasible strategy for inhibiting their growth and ensuring water quality. In addition, the monitoring on their abundance variation could help to determine the frequency and methods of pipeline maintenance.

Identification of an Immune-Related Gene Diagnostic Model and Potential Drugs in Sepsis Using Bioinformatics and Pharmacogenomics Approaches.

Sepsis is an organ dysfunction with high mortality. Early identification, diagnosis, and effective treatment of sepsis are beneficial to the survival of patients. This study aimed to find potential diagnosis and immune-related genes, and drug targets, which could provide novel diagnostic and therapeutic markers for sepsis. The GSE69063, GSE154918 and GSE28750 datasets were integrated to evaluate immune infiltration and identify differentially expressed genes (DEGs) and immune-related genes. Weighted gene co-expression network analysis (WGCNA) was applied to find the hub module related to immune score and sepsis. Immune-related key genes were screened out by taking interaction of DEGs, immune-related genes, and genes in hub module. Protein-protein interaction (PPI) analysis was used to further screen immune-related hub genes, followed by construction of a diagnostic model based on immune-related hub genes. Functional analysis and drug prediction of immune-related hub genes were, respectively, performed by David software and DGIdb database, followed by expression validation by reverse transcriptase polymerase chain reaction (RT-PCR). Totally, 93 immune-related key genes were identified between 561 DEGs, 1793 immune-related genes and 12,459 genes in the hub module of WGCNA. Through PPI analysis, a total of 5 diagnose and immune-related hub genes were further obtained, including IL7R, IL10, CD40LG, CD28 and LCN2. Relationship pairs between these 5 genes and immune cell were identified, including LCN2/IL7R/CD28-activated dendritic cell and IL10-immature B cell. Based on pharmacogenomics, 17 candidate drugs might interact with IL 10, including CYCLOSPORINE. Six candidate drugs might interact with CD28 and 11 with CD40LG, CD40LG and CD28 were drug targets of ALDESLEUKIN. Four significantly enriched signaling pathways were identified, such as T cell receptor signaling pathway, NF-kappa B signaling pathway and JAK-STAT signaling pathway. The 5-gene diagnostic model could be used to diagnose and guide clinical immunotherapy for sepsis.

Morphological, Histological, and Transcriptome Analysis of Doubled Haploid Plants in Poplars (Populus simonii × Populus nigra)

In this study, the poplar doubled haploid (DH) plants were used as the experimental material to explore the huge phenotypic differences between homozygous DH plants and the paternal plants, and the molecular regulation mechanism of the differential phenotypes. In this experiment, through morphological and histological observation and statistics, we found that the double haploid plants had significantly reduced plant height and ground diameter, increased leaf aspect ratio, premature senescence phenotype of top bud, and significant changes in the shape and cell area of the shoot apical meristem. Significantly differentially expressed genes were obtained using RNA-seq transcriptome sequencing. They were subjected to GO enrichment and KEGG analysis. Transcription factors with key functions were screened out for qRT-PCR to verify gene expression changes to predict gene function. The results showed that after the IAA and ABA treatment, the expression levels of some hormone-responsive genes in wild type plants were significantly changed with different treatment time. In the dihaploid plants, the corresponding genes also changed to different degrees, which reflected the changes in the response of the dihaploid plants to hormones. Compared to in WT, the differential expressed genes in the double haploids were involved in multiple physiological process such as response to oxidative stress, response to salicylic acid, plant pathogen interaction, and plant hormone signal transduction. A TF–centered gene regulatory network for phytohormone synthesis and plant senescence was constructed with the expression patterns of differentially expressed transcription factors (TFs). This study increases researchers’ understanding of the regulation of poplar growth and development and provides new research ideas for the creation of new species of poplar.

A survey on graph embedding techniques for biomedical data: Methods and applications

As a result of the expeditious advancement of biomedical technologies, a plethora of relational data linking biomedical entities such as genes, proteins, and drugs have been collected for modern biomedical research. Biomedical graphs, one of the most popular ways to represent relational data, can easily describe different complex biomedical systems, including molecular-level, multi-omics-level, therapeutics-level, and healthcare-level interactions. However, traditional graph analysis methods still suffer from two difficulties (i.e., heterogeneities and dynamic properties of biomedical graphs) when handling high-dimensional, multi-modal, and sparsely interconnected biomedical data. To address these issues, graph embedding methods that can effectively analyze biomedical graphs have received a significant amount of attention recently. Generally, graph-based data is converted into a low-dimensional vector space with its structural properties and well-reserved information. These vectorized representations are used for further computation in various downstream biomedical tasks, such as gene function prediction and drug–target interaction prediction. In this article, we focus on the application of graph data in the biomedical domain and mainly introduce recent developments of graph embedding techniques (homogeneous, heterogeneous, and dynamic graph embedding techniques), including methodologies and related biomedical tasks. We also summarize relevant biomedical datasets and open-source implementations. We further discuss existing limitations and potential solutions. We hope this survey can provide useful directions for researchers who are interested in using graph embedding methods to solve problems in the biomedical field.

Revealing the roles of carbonized humic acid in biohydrogen production

For low yield in dark fermentation (DF), in this study, the carbonized humic acid (CHA) was produced and added to DF for enhancing biohydrogen (bioH2) yield at mesophilic condition. The highest bioH2 yield was 151.08 mL/g glucose with the addition of CHA at 80 mg/L, which was 35.27% and 16.53% higher than those of 0 mg/L CHA and 80 mg/L mineral humic acid (MHA) groups, respectively. Electrons preferentially conducted via the butyrate pathway due to CHA amendments, which corresponded to the prediction of relevant functional genes. Furthermore, CHA possessed distinctive advantages over MHA, which acted as an electron shuttle to facilitate electron transfer, released metal ions as an essential signal mediator and favored the reduction of ferredoxin, obtaining more H2. The use of CHA in the field of H2-DF depicted the high-value utilization and industrial chain extension of MHA.

The utility of transcriptomics in the conservation of sensitive and economically important species

The utility of transcriptomics in the conservation of sensitive and economically important species

A stable quantitative trait locus on chromosome A10 improves the oil content of a backbone parent in Brassica napus L.

One of the most important breeding goals for rapeseed (Brassica napus L.) is improving the oil content (OC) to increase edible or industrial oil quality. Using backbone parents as research materials to excavate OC genetic loci is not only helpful in enhancing the understanding of the genetic basis of OC in rapeseed but also offers a promising approach to improve backbone parents. In this study, a doubled haploid population constructed using the backbone parent 19514 A (with low OC) and the inbred line ZY50 (with high OC) were investigated in eight environments. A total of 30 quantitative trait loci (QTLs) were identified, among which qOC.A10 was detected in six environments. Local QTL scanning for the BC4F2 population showed that qOC.A10 accounted for 22.77% of the phenotypic variance and 0.97% of the additive effect. Further, we improved the parent 19514 A on qOC.A10 by marker-assisted selection, and the background response rate of the improved line A10–19514A reached 97.5%. The phenotypic identification results showed that the OC of A10–19514A and its hybrid significantly increased compared with that of the control, with no negative effects on other agronomic traits. Transcriptome analysis and sequence difference analysis facilitated the prediction of potential functional genes of qOC.A10. This study increases the knowledge regarding the genetic foundation of OC in rapeseed. Furthermore, it identified and confirmed a stable QTL that can be detected in various studies and possesses practical breeding significance.

Effects of Chromium Propionate and Calcium Propionate on Lactation Performance and Rumen Microbiota in Postpartum Heat-Stressed Holstein Dairy Cows.

Chromium propionate (Cr-Pro) and calcium propionate (Ca-Pro) are widely applied in dairy production, especially in the alleviation of heat stress (HS). HS can reduce the abundance of rumen microbiota and the lactation performance of dairy cows. The present work mainly focused on evaluating the effects of Cr-Pro and Ca-Pro on the performance, ruminal bacterial community, and stress of postpartum HS dairy cows as well as identifying the differences in their mechanisms. Fifteen multiparous postpartum Holstein cows with equivalent weights (694 ± 28 kg) and milk yields (41.2 ± 1.21 kg/day) were randomly divided into three groups: control (CON), Cr-Pro (CRPR), and Ca-Pro (CAPR). The control cows received the basal total mixed ration (TMR) diet, while the CRPR group received TMR with 3.13 g/day of Cr-Pro, and the CAPR group received TMR with 200 g/day of Ca-Pro. The rumen microbial 16S rRNA was sequenced using the Illumina NovaSeq platform along with the measurement of ruminal volatile fatty acids (VFAs) and milking performance. Cr-Pro and Ca-Pro improved lactation performance, increased the rumen VFA concentration, and altered the rumen microbiota of the HS dairy cows. Cr-Pro significantly improved the milk yield (p < 0.01). The richness and diversity of the microbial species significantly increased after feeding on Ca-Pro (p < 0.05). Gene function prediction revealed increased metabolic pathways and biological-synthesis-related function in the groups supplemented with Cr-Pro and Ca-Pro. Our results indicate that the application of Cr-Pro or Ca-Pro can provide relief for heat stress in dairy cows through different mechanisms, and a combination of both is recommended for optimal results in production.

Responses of Soil Microbial Communities in Soybean–Maize Rotation to Different Fertilization Treatments

Rotation and fertilization are important methods used to improve crop yield. In particular, crop rotation is an effective means of enhancing ecosystem diversity; however, there exist relatively few studies regarding the effects of long-term maize–soybean rotation and fertilization on soil microbial communities. To further understand the changes in soil microbial community structure under long-term maize–soybean rotation and fertilization, we used a 9-year-old experimental site with maize–soybean rotation as the research object and soybean continuous cropping as a control. We explored the growth effects of soybean and the changes in soil microbial communities under the soybean–maize rotation system and fertilization treatments by analyzing the physicochemical properties of the soil, crop agronomic traits, yield, and changes in soil microbial community structure. The results show that, in comparison with soybean continuous cropping, the yield of soybeans was increased by 12.11% and 21.42% under maize–soybean rotation with different fertilization treatments, respectively. Additionally, there was a significant increase in the agronomic effects of nitrogen following rotation combined with fertilization. Moreover, the soil pH, SOM, and nutrient status were also improved. Bryobacter, Gemmatimonas, and Rhodanobacter were the dominant bacteria. Rotation treatment increased the relative abundance of Bryobacter and Rhodanobacter, and fertilization treatment increased the relative abundance of Gemmatimonas. Rotation also increased the stability of the bacterial community structure and strengthened the symbiotic relationship between species. The prediction of nitrogen-related functional genes indicates that rotation increased soil ammonification and nitrification. Heterocephalacria and Mrakia were the dominant fungal genera under crop rotation. The abundance of Saccharomyces Mrakia was significantly positively correlated with ammonium nitrogen levels and crop yield. Crop rotation increased the abundance of Saccharomyces Mrakia and reduced the abundance of Fusarium, but fertilization increased the abundance of Fusarium. Functional gene prediction also indicates that the relative abundance of plant pathogens was significantly reduced. This study provides a theoretical basis for soil microbial diversity and ecosystem service function in long-term soybean–maize rotation.

Identification and characterization of pathogens causing saffron corm rot in China.

Corm rot is the most important disease of saffron, for which fungi from several genus such as Fusarium spp. Penicillium spp. and Botrytis spp., have been previously reported to be the pathogens. In this research, we used a combination of amplicon sequencing and traditional isolation methods to identify the causal agents, main infection source. The diversity of microbial communities in diseased saffron corms and soil decreased significantly compared with healthy corms and soil. The contents of Penicillium and Botrytis in healthy and diseased corms were similarly high, indicating that them were not directly related to the occurrence of corm rot. But the relative abundance of Fusarium, Cadophora and Fusicolla were significantly higher in the diseased corms than healthy ones. The abundance of Fusarium increased, while the abundance of Oidiodendron, Paraphaeosphaeria and the endophytic beneficial bacteria Pseudomonas decreased, which may relate to the occurrence of the disease. The co-occurrence network diagram showed that the correlation between fungal and bacterial communities was mainly positive. Plant pathogens were relatively abundant in the diseased soil, according to functional gene prediction. At the same time, we also collected 100 diseased corms from the fields in Jiande, where is known as the "hometown of saffron." All isolated pathogenic strains were identified as Fusarium oxysporum through morphological observation and phylogenetic tree analysis of ITS, Tef-1α and β-tubulin. To better clarify the biological characteristics of F. oxysporum, we cultured the isolates at different temperatures and pH values. The optimum temperature for mycelial growth and sporulation was 25°C, pH 6，carbon sources sorbitol and nitrogen sources, peptone. In short, our results suggests that F. oxysporum was the pathogen causing corm rot in Jiande and corms other than soils are the main primary infection source. These new understanding of saffron corm rot will provide the theoretical basis for its better and efficiently management.

Unraveling the Positive Effect of Soil Moisture on the Bioaugmentation of Petroleum-Contaminated Soil Using Bioinformatics.

Petroleum contamination is a severe threat to the soil environment. Previous studies have demonstrated that petroleum degradation efficiency is promoted by enhancing soil moisture content (MC). However, the effects of MC on soil microbial ecological functions during bioremediation remain unclear. Here, we investigated the impacts of 5% and 15% of moisture contents on petroleum degradation, soil microbial structures and functions, and the related genes using high-throughput sequencing and gene function prediction. Results indicated that petroleum biodegradation efficiency was increased by 8.06% in the soils with 15% MC when compared to that with 5% of MC. The complexity and stability of soil microbial community structures with 15% MC were higher than those in the soils with 5% MC when hydrocarbon-degrading bacterial flora (HDBF) were inoculated into the soils. Fifteen percent of moisture content strengthened the interaction of the bacterial community network and reduced the loss of some key bacteria species including Mycobacterium, Sphingomonas, and Gemmatimonas. Some downregulated gene pathways relating to bioaugmentation were enhanced in the soils with 15% MC. The results suggested that the dynamic balances of microbial communities and the metabolic interactions by 15% MC treatment are the driving forces for the enhancement of bioremediation in petroleum-contaminated soil.

Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks.

In this paper, we introduce Gene Knockout Inference (GenKI), a virtual knockout (KO) tool for gene function prediction using single-cell RNA sequencing (scRNA-seq) data in the absence of KO samples when only wild-type (WT) samples are available. Without using any information from real KO samples, GenKI is designed to capture shifting patterns in gene regulation caused by the KO perturbation in an unsupervised manner and provide a robust and scalable framework for gene function studies. To achieve this goal, GenKI adapts a variational graph autoencoder (VGAE) model to learn latent representations of genes and interactions between genes from the input WT scRNA-seq data and a derived single-cell gene regulatory network (scGRN). The virtual KO data is then generated by computationally removing all edges of the KO gene-the gene to be knocked out for functional study-from the scGRN. The differences between WT and virtual KO data are discerned by using their corresponding latent parameters derived from the trained VGAE model. Our simulations show that GenKI accurately approximates the perturbation profiles upon gene KO and outperforms the state-of-the-art under a series of evaluation conditions. Using publicly available scRNA-seq data sets, we demonstrate that GenKI recapitulates discoveries of real-animal KO experiments and accurately predicts cell type-specific functions of KO genes. Thus, GenKI provides an in-silico alternative to KO experiments that may partially replace the need for genetically modified animals or other genetically perturbed systems.

Global dissection of R2R3-MYB in Pogostemon cablin uncovers a species-specific R2R3-MYB clade

MYB family is one of the largest transcription factor families in plants and plays a crucial role in regulating plant biochemical and physiological processes. However, R2R3-MYBs in patchouli have not been systematically investigated. Here, based on the gene annotation of patchouli genome sequence, 484 R2R3-MYB transcripts were detected. Further in-depth analysis of the gene structure and expression of R2R3-MYBs supported the tetraploid hybrid origin of patchouli. When combined with R2R3-MYBs from Arabidopsis, a phylogenetic tree of patchouli R2R3-MYBs was constructed and divided into 31 clades. Interestingly, a patchouli-specific R2R3-MYB clade was found and confirmed by homologous from other Lamiaceae species. The syntenic analysis demonstrated that tandem duplication contributed to its evolution. This study systematically analysed the R2R3-MYB family in patchouli, providing information on its gene characterization, functional prediction, and species evolution.