Transcriptomic responses of Bulinus globosus to extreme temperature and drought stress

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO—a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations—evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)—mechanistic models of molecular “pathways” (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Previous studies have shown that asthma is a risk factor for lung cancer, while the mechanisms involved remain unclear. We attempted to further explore the association between asthma and non-small cell lung cancer (NSCLC) via bioinformatics analysis. We obtained GSE143303 and GSE18842 from the GEO database. Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) groups were downloaded from the TCGA database. Based on the results of differentially expressed genes (DEGs) between asthma and NSCLC, we determined common DEGs by constructing a Venn diagram. Enrichment analysis was used to explore the common pathways of asthma and NSCLC. A protein-protein interaction (PPI) network was constructed to screen hub genes. KM survival analysis was performed to screen prognostic genes in the LUAD and LUSC groups. A Cox model was constructed based on hub genes and validated internally and externally. Tumor Immune Estimation Resource (TIMER) was used to evaluate the association of prognostic gene models with the tumor microenvironment (TME) and immune cell infiltration. Nomogram model was constructed by combining prognostic genes and clinical features. 114 common DEGs were obtained based on asthma and NSCLC data, and enrichment analysis showed that significant enrichment pathways mainly focused on inflammatory pathways. Screening of 5 hub genes as a key prognostic gene model for asthma progression to LUAD, and internal and external validation led to consistent conclusions. In addition, the risk score of the 5 hub genes could be used as a tool to assess the TME and immune cell infiltration. The nomogram model constructed by combining the 5 hub genes with clinical features was accurate for LUAD. Five-hub genes enrich our understanding of the potential mechanisms by which asthma contributes to the increased risk of lung cancer.

Background:The adult stage is an important period in the life cycle of Angiostrongylus cantonensis, as it is at this stage that male and female worms produce thousands of fertilized eggs daily.Methods:To explore the transcriptional details of adult male and female A. cantonensis, three groups of male and female adult worms were collected, and their transcriptome profiles were analyzed using an Illumina next-generation sequencing platform. A total of 283,910,174 clean reads were obtained, and 137,626 unigenes and 237,059 transcripts were then generated. Unigenes were successfully annotated by querying the Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG), NCBI non-redundant protein sequences (NR), PFAM, STRING, and SWISS-PROT databases. Then, differentially expressed genes (DEGs) between the 2 genders were identified. The GO and KEGG databases were used for DEG annotation, and a number of DEG annotations were enriched.Results:The results obtained from querying DEGs using the GO and KEGG databases revealed that male and female adult worms exhibited differences in metabolism and production. Protein phosphorylation, ion transport, and calcium transport were all significantly enriched according to GO annotation. A number of other pathways were also enriched according to KEGG enrichment annotation, including the pentose phosphate pathway, nitrogen metabolism, oocyte meiosis pathway, neuroactive ligand-receptor interaction, calcium signaling pathway, transforming growth factor β (TGF-β) signaling pathway etc.Conclusion:We hypothesized that the nervous system of the worm plays a key role in the physiological regulation of adult A. cantonensis, and based on this, the function of the calcium-signaling pathway should be investigated.

Buzura suppressaria Guenee (Lepidoptera: Geometridae) is a defoliator that seriously harms eucalyptus trees in South China. Buzura suppressaria nuclear polyhedrosis virus (BsNPV) is a baculovirus that infects B. suppressaria with high specificity and efficiency. Transcriptomes of B. suppressaria were sequenced before and after BsNPV infection using an Illumina-based platform to probe for differentially expressed genes (DEGs) of B. suppressaria after viral infection. On average, ∼57.4 million high-quality clean reads were generated and assembled de novo into 69,761 unigenes. The NCBI nonredundant protein, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene ontology (GO), and Cluster of Orthologous Groups databases were used to annotate unigenes through NCBI BLAST; 33,575 unigenes (48.1%) were then mapped to at least one of these databases, and 4,366 unigenes (6.3%) were mapped to all databases. Differential expression analysis showed that 25,212 unigenes were upregulated and 22,880 unigenes were downregulated in at least one pairwise comparison. Control versus 48 h had more DEGs than other two pairwise comparisons in either the GO or KEGG database, because the number of regulated gene would increase as BsNPV infected more tissues and would decrease as more tissues were disabled. To ascertain B. suppressaria immune response to BsNPV infection, DEGs were annotated to the GO and KEGG databases. In total, 89 GO categories are related to immune response and 1,007 DEGs are annotated to these GO categories. Furthermore, 7 downregulated DEGs and 37 upregulated were obtained simultaneously in all three groups. These DEGs were considered to possess a central role throughout viral infection.

To screen differentially expressed genes (DEGs) associated with chronic schistosomiasis japonica-induced hepatic fibrosis and analyze their functions. The dataset of gene expression profiles of patients with chronic schistosomiasis japonica-induced hepatic fibrosis was downloaded from the Gene Expression Omnibus (GEO) database, and DEGs were screened using R package. The biological functions of DEGs were characterized using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. In addition, the protein-protein interaction (PPI) network of DEGs was created to screen the hub genes. A total of 62 DEGs were identified, including 12 down-regulated genes and 50 up-regulated genes. GO enrichment analysis showed that DEGs were mainly enriched in 116 biological processes, including fatty acid, sulfur compound, acyl-coenzyme A and thioester metabolism; 19 cellular components, including mitochondrial matrix, outer mitochondrial membrane and organelle outer membrane; and 7 molecular functions, including insulin-like growth factor binding and oxidoreductase activity. KEGG pathway enrichment analysis that the DEGs were significantly enriched in phosphatidylinositol-3-kinase/serine/threonine protein kinase (PI3K/Akt), mitogen-activated protein kinase (MAPK), calcium metabolism and cyclic adenosine monophosphate (cAMP) signaling. PPI network analysis identified six hub genes involved in the development of chronic schistosomiasis japonica-induced hepatic fibrosis, including ACACA, ACSL1, GPAM, THRSP, PLIN1 and DGAT2, and ACSL1, ACACA and PLIN1 were the top 3 hub genes. ACSL1, ACACA and PLIN1 may be the hub genes associated with the development of chronic schistosomiasis japonica-induced hepatic fibrosis, and abnormal lipid metabolism mediated by these DEGs may play an important role in the development of chronic schistosomiasis japonica-induced hepatic fibrosis.

Objective: To screen the differentially expressed genes (DEGs) in diabetic foot ulcers (DFUs), and to perform functional analysis and clinical validation of them, intending to lay a theoretical foundation for epigenetic therapy of chronic refractory wounds. Methods: An observational study was conducted. The gene expression profile dataset GSE80178 of DFU patients in Gene Expression Omnibus (GEO) was selected, and the DEG between three normal skin tissue samples and six DFU tissue samples in the dataset was analyzed and screened using the GEO2R tool. For the screened DEG, ClusterProfiler, org.Hs.eg.db, GOplot, and ggplot2 in the R language packages were used for Gene Ontology (GO) enrichment analysis of biological processes, molecular functions, and cellular components, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, respectively. Protein-protein interaction (PPI) analysis was performed using STRING database to screen key genes in the DEG, and GO enrichment analysis of key genes was performed using Cytohubba plug-in in Cytoscape 3.9.1 software. DFU tissue and normal skin tissue discarded after surgery were collected respectively from 15 DFU patients (7 males and 8 females, aged 55-87 years) and 15 acute wound patients (6 males and 9 females, aged 8-52 years) who were admitted to Xiang'an Hospital of Xiamen University from September 2018 to March 2021. The mRNA and protein expressions of small proline-rich repeat protein 1A (SPRR1A) and late cornified envelope protein 3C (LCE3C) were detected by real-time fluorescent quantitative reverse transcription polymerase chain reaction and immunohistochemistry, respectively. Data were statistically analyzed with independent sample t test. Results: Compared with normal skin tissue, 492 statistically differentially expressed DEGs were screened from DFU tissue of DFU patients (corrected P<0.05 or corrected P<0.01), including 363 up-regulated DEGs and 129 down-regulated DEGs. GO terminology analysis showed that DEGs were significantly enriched in the aspects of skin development, keratinocyte (KC) differentiation, keratinization, epidermal development, and epidermal cell differentiation, etc. (corrected P values all <0.01). KEGG pathway analysis showed that DEGs were significantly enriched in the aspects of tumor-associated microRNA, Ras related protein 1 signaling pathway, and pluripotent stem cell regulatory signaling pathway, etc. (corrected P values all <0.01). PPI analysis showed that endophial protein, SPRR1A, SPRR1B, SPRR2B, SPRR2E, SPRR2F, LCE3C, LCE3E, keratin 16 (all down-regulated DEGs), and filoprotein (up-regulated DEG) were key genes of DEGs screened from DFU tissue of DFU patients, which were significantly enriched in GO terms of keratinization, KC differentiation, epidermal cell differentiation, skin development, epidermis development, and peptide cross-linking, etc. (corrected P values all <0.01). The mRNA expressions of SPRR1A and LCE3C in DFU tissue of DFU patients were 0.588±0.082 and 0.659±0.098, respectively, and the protein expressions were 0.22±0.05 and 0.24±0.04, respectively, which were significantly lower than 1.069±0.025 and 1.053±0.044 (with t values of 20.91 and 13.66, respectively, P values all <0.01) and 0.38±0.04 and 0.45±0.05 (with t values of 9.69 and 12.46, respectively, P values all <0.01) in normal skin tissue of acute wound patients. Conclusions: Compared with normal skin tissue, there is DEG profile in DFU tissue of DFU patients, with DEGs being significantly enriched in the aspects of KC differentiation and keratin function. Key DEGs are related to the biological function of KC, and their low expressions in DFU tissue of DFU patients may impede ulcer healing.

ABSTRACTObjective: The purpose of this study was to investigate critical genes in multiple sclerosis (MS) using microarray data from brain tissue in MS.Materials: The expression profile data set of MS (GSE38010) downloaded from the Gene Expression Omnibus database contained gene information from five plaque tissues from MS brains and two white matter tissues from healthy controls. An R package was applied to process these raw chip data. Gene Ontology (GO) functional analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and protein–protein interaction (PPI) network analysis were performed to investigate interactions between differentially expressed genes (DEGs) in MS brain tissues.Results: This study identified a total of 1065 DEGs, including 530 up-regulated genes and 535 down-regulated genes, in MS brain tissue samples compared to those in normal white matter tissue samples. GO and KEGG pathway enrichment analyses showed that the up-regulated DEGs were mainly related to neuron development, neuron projection morphogenesis and neuron differentiation. Furthermore, the down-regulated DEGs were largely related to axon ensheathment, ensheathment of neurons and nervous system development. Seven key genes were found as hub genes in the maintenance of the PPI network.Conclusion: Several key target genes and their GO and KEGG pathway enrichment identified in the present study may serve as feasible targets for MS therapies.

Objective To characterize the changes in transcriptome of mouse enteroids exposed to indomethacin. Methods The viability of enteroids exposed to indomethacin was measured using MTT staining. The differentially expressed genes (DEGs) between the control group and the indomethacin group were identified using Illumina Hiseq sequencing systems. The functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of DEGs were mapped in Gene Ontology (GO) and KEGG pathway database, respectively. Results The MTT results showed that the survival rates of mouse enteroids exposed to indomethacin at concentrations of 100, 250, 300, 400 and 500 μM for 48 h were 80.34%, 70.17%, 61.94%, 54.38% and 42.22%. The survival rates of enteroids were 80.56%, 70.17% and 59.30% at 250 μM of indomethacin treatment for 24 h, 48 h and 72 h respectively. For cellular component, several GO terms were identified, especially those associated with microbody and peroxisome (P<0.01). The GO terms for biological process with DEGs were mostly in the category of organic acid metabolic process, oxoacid metabolic process and carboxylic acid metabolic process (P<0.01). Most of the molecular functional GO terms associated with DEGs fell into the category of oxidoreductase activity, glutathione transferase activity and carboxylic acid binding (P<0.01). The KEGG pathway enrichment analyses revealed that the DEGs were primarily associated with chemical carcinogenesis, metabolism of xenobiotics by cytochrome P450, drug metabolism-cytochrome P450, PPAR signaling pathway (P<0.01). Conclusions Indomethacin inhibits the growth of mouse enteroids. There may be some mechanisms of defence against oxidative stress to protect enteroids from NSAIDs-induced injury. Targeting oxidative stress with anti-oxidant therapy would be an effective therapeutic strategy. Key words: Indomethacin; Enteroids; High-throughput sequencing

Transcriptional regulation mechanism of reduced accumulation of chlorogenic acid and luteoloside in Lonicera japonica under drought stress

Study question Does transcriptome of remaining trophectoderm (TE) reflect the developmental potential of mosaic blastocysts after preimplantation genetic testing for aneuploidy (PGT-A)? Summary answer: TE from low-degree mosaic (Low-mos) and high-degree mosaic (High-mos) blastocysts are transcriptionally equivalent, standing between euploid and aneuploid categories and displaying key deregulated developmental processes. What is known already Blastocysts classified as mosaic by PGT-A are associated with lower implantation and higher miscarriage rates than those classified as euploid, yet they still lead to healthy babies. Unveiling the true developmental identity of these embryos faces a dilemma: understanding to which extent they represent technical artefacts or whether they hold own potential to implant and give rise to normal pregnancies. Current RNA sequencing (RNA-seq) techniques allow for the determination of whole transcriptomic profiles even from single cells, which paves the way for the identification of new molecular keys of embryonic competence. Study design, size, duration Prospective study comparing RNA-seq data of remaining TE from blastocysts classified as euploid (n = 4), Low-mos (n = 5), High-mos (n = 4) and aneuploid (n = 6) by PGT-A. Participants were recruited between October 2018 and November 2019 at IVI-RMA Valencia. Participants/materials, setting, methods Chromosomal mosaicism was defined in the range 30%-&amp;lt;50% (Low-mos) and 50%-&amp;lt;70% (High-mos) using a next-generation sequencing (NGS) validated algorithm. Whole TE fractions were separately collected and processed for RNA-seq. Differentially expressed genes (DEGs) were calculated with DESeq2 package [Benjamini-Hochberg (BH)-adjusted p &amp;lt; 0.01 &amp; abs(log2FoldChange)&amp;gt;2 significant]. Fgsea algorithm was used for enrichment analysis on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene Ontology (GO) terms (BH-adjusted p &amp;lt; 0.01 significant). Main results and the role of chance For comparisons, TE from euploid blastocysts were used as control. At the gene level, 15 DEGs were found in Low-mos, 20 DEGs in High-mos, and 64 DEGs in aneuploid blastocysts. To address the functional implications of these differences, pathways significantly deregulated according to KEGG and GO categories were identified. TE from aneuploid blastocysts displayed significant downregulation in up to 115 KEGG and GO processes directly involved in processing and integrity maintenance of nuclear and mitochondrial genomes, a reflection of their aberrant chromosomal identity. In addition, TE from High-mos and Low-mos were transcriptionally equivalent (0 DEGs between both groups), with 23 overlapping KEGG and GO processes significantly downregulated compared with control. Importantly, main significantly-affected processes included mitotic sister chromatid segregation, NIK NF-kB activity, regulation of apoptosis, and pathways related to the biosynthesis and metabolism of proteins, fatty acids, carbohydrates and steroid hormones. These findings indicate that mosaic embryos comprise a unique developmental entity, which swims between the euploid and aneuploid waterfronts and may regulate survival by diverse mechanisms, including cell proliferation and apoptosis. Limitations, reasons for caution This is a descriptive, single-center study with limited sample size. TE fractions were obtained by micromanipulation, which may have led to potential cross-contamination with the inner cell mass. Wider implications of the findings: Transcriptomic equivalence between Low-mos and High-mos TE fractions questions the biological significance of inferring mosaicism degrees from single biopsies. Deregulated processes in these embryos support their reduced developmental and live birth potential, pointing to mechanisms that may mediate survival in the presence of aneuploid cells, as shown in the mouse. Trial registration number Not applicable

Study question Does transcriptome of remaining trophectoderm (TE) reflect the developmental potential of mosaic blastocysts after preimplantation genetic testing for aneuploidy (PGT-A)? Summary answer TE from low-degree mosaic (Low-mos) and high-degree mosaic (High-mos) blastocysts are transcriptionally equivalent, standing between euploid and aneuploid categories and displaying key deregulated developmental processes. What is known already Blastocysts classified as mosaic by PGT-A are associated with lower implantation and higher miscarriage rates than those classified as euploid, yet they still lead to healthy babies. Unveiling the true developmental identity of these embryos faces a dilemma: understanding to which extent they represent technical artefacts or whether they hold own potential to implant and give rise to normal pregnancies. Current RNA sequencing (RNA-seq) techniques allow for the determination of whole transcriptomic profiles even from single cells, which paves the way for the identification of new molecular keys of embryonic competence. Study design, size, duration Prospective study comparing RNA-seq data of remaining TE from blastocysts classified as euploid (n = 4), Low-mos (n = 5), High-mos (n = 4) and aneuploid (n = 6) by PGT-A. Participants were recruited between October 2018 and November 2019 at IVI-RMA Valencia. Participants/materials, setting, methods Chromosomal mosaicism was defined in the range 30%- &amp;lt; 50% (Low-mos) and 50%- &amp;lt; 70% (High-mos) using a next-generation sequencing (NGS) validated algorithm. Whole TE fractions were separately collected and processed for RNA-seq. Differentially expressed genes (DEGs) were calculated with DESeq2 package [Benjamini-Hochberg (BH)-adjusted p &amp;lt; 0.01 &amp; abs(log2FoldChange)&amp;gt;2 significant]. Fgsea algorithm was used for enrichment analysis on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene Ontology (GO) terms (BH-adjusted p &amp;lt; 0.01 significant). Main results and the role of chance For comparisons, TE from euploid blastocysts were used as control. At the gene level, 15 DEGs were found in Low-mos, 20 DEGs in High-mos, and 64 DEGs in aneuploid blastocysts. To address the functional implications of these differences, pathways significantly deregulated according to KEGG and GO categories were identified. TE from aneuploid blastocysts displayed significant downregulation in up to 115 KEGG and GO processes directly involved in processing and integrity maintenance of nuclear and mitochondrial genomes, a reflection of their aberrant chromosomal identity. In addition, TE from High-mos and Low-mos were transcriptionally equivalent (0 DEGs between both groups), with 23 overlapping KEGG and GO processes significantly downregulated compared with control. Importantly, main significantly-affected processes included mitotic sister chromatid segregation, NIK NF-kB activity, regulation of apoptosis, and pathways related to the biosynthesis and metabolism of proteins, fatty acids, carbohydrates and steroid hormones. These findings indicate that mosaic embryos comprise a unique developmental entity, which swims between the euploid and aneuploid waterfronts and may regulate survival by diverse mechanisms, including cell proliferation and apoptosis. Limitations, reasons for caution This is a descriptive, single-center study with limited sample size. TE fractions were obtained by micromanipulation, which may have led to potential cross-contamination with the inner cell mass. Wider implications of the findings Transcriptomic equivalence between Low-mos and High-mos TE fractions questions the biological significance of inferring mosaicism degrees from single biopsies. Deregulated processes in these embryos support their reduced developmental and live birth potential, pointing to mechanisms that may mediate survival in the presence of aneuploid cells, as shown in the mouse. Trial registration number Not applicable

Series-temporal transcriptome profiling of cotton reveals the response mechanism of phosphatidylinositol signaling system in the early stage of drought stress

Robust statistical tools such as the Skellam model and Bayesian networks can capture the count properties of transcriptome sequencing data and clusters of genes among treatments, thereby improving our knowledge of gene functions and networks. In this study, we successfully implemented a model to analyze a transcriptome dataset of Cucumis sativus and Botrytis cinerea before and after their interaction. First, 4200 differentially expressed genes (DEGs) from C. sativus were clustered into 17 distinct groups, and 670 DEGs from B. cinerea were clustered into 12 groups. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were applied on these DEGs to assess the interactions between C. sativus and B. cinerea. In C. sativus, more DEGs were divided into terms in the molecular function and biological process domains than into cellular components, and 277 DEGs were allocated to 19 KEGG pathways. In B. cinerea, more DEGs were divided into terms in the biological process and cellular component domains than into molecular functions, and 150 DEGs were allocated to 26 KEGG pathways. In this study, we constructed networks of genes that interact with each other to screen hub genes based on a directed graphical model known as Bayesian networks. Through a detailed GO analysis, we excavated hub genes which were biologically meaningful. These results verify that availability of Skellam model and Bayesian networks in clustering gene expression data and sorting out hub genes. These models are instrumental in increasing our knowledge of gene functions and networks in plant–pathogen interaction.

The techniques of DNA microarray and bioinformatic analysis have exhibited efficiency in identifying dysregulated gene expression in human cancers. In this study, we used integrated bioinformatics analysis to improve our understanding of the pathogenesis of papillary thyroid cancer (PTC). In this study, we integrated four Gene Expression Omnibus (GEO) datasets, GSE33630, GSE35570, GSE60542 and GSE29265, including 136 normal samples and 157 PTC specimens. The contents of the four datasets are based on GPL570, an Affymetrix Human Genome U133 Plus 2.0 array. Gene ontology (GO) analysis was used to identify characteristic the biological attributes of differentially expressed genes (DEGs) between PTC and normal samples. GO annotation was performed on the DEGs obtained, and the process relied on the DAVID online tool. Kyoto Encyclopedia of Genes and Genomes (KEGG) approach enrichment analyses were adopted to obtain the basic functions of the DEGs. The KOBAS online analysis database was used to complete DEG KEGG pathway comparison and analysis. The search tool (STRING) database was mainly used to search for interacting genes and complete the construction of protein-protein interaction (PPI) networks. Five hundred-ninety DEGs were consistently expressed in the four datasets; 327 of them were upregulated, while 263 were downregulated. Ten DEGs, including five upregulated (ENTPD1, THRSP, KLK10, ADAMTS9, MIR31HG) and five downregulated (SCARA5, EPHB1, CHRDL1, LOC440934, FOXP2) genes, were randomly selected for q-PCR in our own tissue samples to validate the integrated data. The most highly enriched GO terms were extracellular exosome (GO:0070062), cell adhesion (GO:0070062), positive regulation of gene expression (GO:0010628), and extracellular matrix (ECM) organization (GO:0030198). KEGG pathway analysis was performed, and it was found that abnormally expressed genes effectively participated in pathways such as tyrosine metabolism, complement and coagulation cascades, cell adhesion molecules (CAMs), transcriptional misregulation and ECM-receptor interaction pathways. Five hundred-ninety DEGs were identified in PTC by integrated microarray analysis. The GO and KEGG analyses presented here suggest that the DEGs were enriched in extracellular exosome, tyrosine metabolism, CAMs, complement and coagulation cascades, transcriptional misregulation and ECM-receptor interaction pathways. Functional studies of PTC should focus on these pathways.

With the continuous change of climate, drought stress has emerged as the primary constraint on crop growth, posing a significant threat to the stability of global grain reserves. Arbuscular mycorrhizal fungi (AMF), as a kind of widely distributed root endophytes, enhance the drought tolerance of maize (Zea mays L.) through regulating the physiological and molecular responses. However, comprehensive transcriptome analysis to reveal the molecular mechanism of drought tolerance in the symbiotic process between AMF and maize is still limited. In the potted plant experiment, maizes inoculated with and without arbuscular mycorrhizal fungus Funneliformis mosseae were grown under well-watered (WW) or drought-stressed (DS) conditions. By using RNA-Seq and transcriptome analysis on maize roots and leaves, this work aimed to investigate the differential expressed genes (DEGs) related to the Ca2+ signaling pathway induced by AMF symbiosis under drought stress. Our findings indicated that F. mosseae inoculation resulted in a decrease in the net fluxes of Ca2+, while simultaneously elevating Ca2+ contents in the maize roots and leaves under well-watered or drought-stressed conditions. Notably, 189 DEGs were regulated not only by AMF symbiosis and drought stress, but also exhibited preferential expression in either leaves or roots. The annotation and enrichment of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that most of the DEGs were significantly enriched in Ca2+ signaling pathway genes, related to signal transduction, cellular process, and defense response. A high number of DEGs with this function (including calcineurin B-like protein (CBL), CBL-interacting protein kinase (CIPK), mitogen-activated protein kinase (MAPK), and calcium-dependent protein kinase (CDPK) receptor kinases) were upregulated-DEGs or downregulated-DEGs in F. mosseae-inoculated maizes under drought stress. Furthermore, some DEGs belong to transcription factor (TF) families, including bHLH ERF, and, MYB, were speculated to play key roles in improving the drought tolerance of maize. Based on the expression data and co-expression analysis between TF and Ca2+ signaling pathway genes, Whirly1 with CBL11, and BRI1-EMS-SUPPRESSOR 1 (BES1) with CBL10, CIPK24, CDPK1, CDPK14, CDPK19, and MAPK9 genes showed significant positive correlations, while B3 domain-containing transcription factors (B3 TFs) with MAPK1 and both CBL9 genes showed significant negative correlations in response to both F. mosseae inoculation and drought stress. The regulation of Ca2+ signaling pathways by AMF symbiosis was an important response mechanism of maize to improve their drought resistance. This study provides insightful perspectives on how AMF-induced modulation of gene expression within the Ca2+ signaling pathway can enhance the drought tolerance of mycorrhizal maize in the future.