SRA Database Research Articles

Oral probiotics increased the proportion of Treg, Tfr, and Breg cells to inhibit the inflammatory response and impede gestational diabetes mellitus

BackgroundChildren of mothers with gestational diabetes mellitus (GDM) are more prone to acquire type 2 diabetes and obesity as adults. Due to this link, early intervention strategies that alter the gut microbiome may benefit the mother and kid long-term. This work uses metagenomic and transcriptome sequencing to investigate how probiotics affect gut microbiota dysbiosis and inflammation in GDM.MethodsGDM and control metagenomic sequencing data were obtained from the SRA database. This metagenomic data helped us understand gut microbiota abundance and function. KEGG detected and extracted functional pathway genes. Transcriptome sequencing data evaluated GDM-related gene expression. Finally, GDM animal models were given probiotics orally to evaluate inflammatory response, regulatory immune cell fractions, and leptin protein levels.ResultsGDM patients had more Fusobacteria and Firmicutes, while healthy people had more Bacteroidetes. Gut microbiota composition may affect GDM by altering the L-aspartate and L-asparagine super pathways. Mannan degradation and the super pathway of L-aspartate and L-asparagine synthesis enhanced in GDM mice with leptin protein overexpression. Oral probiotics prevent GDM by lowering leptin. Oral probiotics increased Treg, Tfr, and Breg cells, which decreased TNF-α and IL-6 and increased TGF-β and IL-10, preventing inflammation and preserving mouse pregnancy.ConclusionDysbiosis of the gut microbiota may increase leptin expression and cause GDM. Oral probiotics enhance Treg, Tfr, and Breg cells, which limit the inflammatory response and assist mice in sustaining normal pregnancy. Thus, oral probiotics may prevent GDM, enabling targeted gut microbiota modulation and maternal and fetal health.

Mining Public Data to Investigate the Virome of Neglected Pollinators and Other Floral Visitors.

This study reports the virome investigation of pollinator species and other floral visitors associated with plants from the south of Bahia: Aphis aurantii, Atrichopogon sp., Dasyhelea sp., Forcipomyia taiwana, and Trigona ventralis hoozana. Studying viruses in insects associated with economically important crops is vital to understand transmission dynamics and manage viral diseases that pose as threats for global food security. Using literature mining and public RNA next-generation sequencing data deposited in the NCBI SRA database, we identified potential vectors associated with Malvaceae plant species and characterized the microbial communities resident in these insects. Bacteria and Eukarya dominated the metagenomic analyses of all taxon groups. We also found sequences showing similarity to elements from several viral families, including Bunyavirales, Chuviridae, Iflaviridae, Narnaviridae, Orthomyxoviridae, Rhabdoviridae, Totiviridae, and Xinmoviridae. Phylogenetic analyses indicated the existence of at least 16 new viruses distributed among A. aurantii (3), Atrichopogon sp. (4), Dasyhelea sp. (3), and F. taiwana (6). No novel viruses were found for T. ventralis hoozana. For F. taiwana, the available libraries also allowed us to suggest possible vertical transmission, while for A. aurantii we followed the infection profile along the insect development. Our results highlight the importance of studying the virome of insect species associated with crop pollination, as they may play a crucial role in the transmission of viruses to economically important plants, such as those of the genus Theobroma, or they will reduce the pollination process. This information may be valuable in developing strategies to mitigate the spread of viruses and protect the global industry.

Identification and functional prediction of long non-coding RNAs related to oxidative stress in the jejunum of piglets.

Oxidative stress (OS) is a pathological process arising from the excessive production of free radicals in the body. It has the potential to alter animal gene expression and cause damage to the jejunum. However, there have been few reports of changes in the expression of long noncoding RNAs (lncRNAs) in the jejunum in piglets under OS. The purpose of this research was to examine how lncRNAs in piglet jejunum change under OS. The abdominal cavities of piglets were injected with diquat (DQ) to produce OS. Raw reads were downloaded from the SRA database. RNA-seq was utilized to study the expression of lncRNAs in piglets under OS. Additionally, six randomly selected lncRNAs were verified using quantitative real-time polymerase chain reaction (qRT‒PCR) to examine the mechanism of oxidative damage. A total of 79 lncRNAs were differentially expressed (DE) in the treatment group compared to the negative control group. The target genes of DE lncRNAs were enriched in gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes (KEGG) signaling pathways. Chemical carcinogenesis-reactive oxygen species, the Foxo signaling pathway, colorectal cancer, and the AMPK signaling pathway were all linked to OS. Our results demonstrated that DQ-induced OS causes differential expression of lncRNAs, laying the groundwork for future research into the processes involved in the jejunum's response to OS.

RoseAP: an analytical platform for gene function of Rosa rugosa.

Rosa rugosa, a perennial shrub belonging to family Rosaceae, is a well-known ornamental plant. Its petals contain an abundance of essential oils and anthocyanins with enormous economic and health benefits when used as edible or cosmetic ingredients. The whole genome of R. rugosa was sequenced in 2021, which provided opportunities and challenges for gene regulation. However, many gene functions remain unknown. Therefore, an analytical platform named RoseAP (http://www.gzybioinformatics.cn/RoseAP/index.php) for the functional analysis of R. rugosa genes was constructed. It improved the gene annotation rate by integrating and analyzing genomic and transcriptomic datasets. First, 38,815 genes, covering 97.76% of the coding genes, were annotated functionally and structurally using a variety of algorithms and rules. Second, a total of 33 transcriptome samples were integrated, including 23 samples from our lab and 10 samples from the SRA database. A co-expression network containing approximately 29,657 positive or negative gene pairs, covering 74.7% of the coding genes, was constructed based on PCC and MR algorithms. Network analysis revealed that the DFR function was closely related to anthocyanin metabolism. It demonstrated the reliability of the network. Several SAUR genes of R. rugosa shared similar expression patterns. RoseAP was used to determine the sequence, structure, functional annotation, expression profile, regulatory network, and functional modules at the transcriptional and protein levels by inputting gene IDs. In addition, auxiliary analytical tools, including BLAST, gene set enrichment, orthologue conversion, gene sequence extraction, gene expression value extraction, and JBrowse, were utilized. Regular updates to RoseAP are expected to facilitate mining of gene function and promote genetic improvement in R. rugosa.

In Silico Comparative Metagenomic Analysis of Microbial Communities of Chromium Contaminated Sites

Chromium is one of the highly toxic and carcinogenic heavy metals. Due to increased anthropogenic activities, high concentration of chromium is found in many areas. Many microorganisms have the ability to detoxify chromium. Metagenomics allow us to comprehensively study microbial communities present at different sites without culturing them. The objective of this study was to analyze the abundance of microbial groups in different environments contaminated with chromium. For this purpose, chromium contaminated soil, anaerobic sludge and reactor samples were chosen. 16S rRNA data of these samples was retrieved from NCBI SRA database. The sequences were analyzed by Mothur software accessed via Galaxy server, and were classified using SILVA database. Venn diagram, phylogenetic tree, heatmap, relative abundance graphs and Krona pie charts were generated. Statistical analysis was also performed in the form of AMOVA and HOMOVA tests. According to results of our study, Proteobacteria, Leucobacter, Actinomycetales, Actinobacteria, Arthrobacter, Rhizobiales, Sphingomonas, Bradyrizobium and Nucardioidaceae were present in all the samples. Firmicutes, Planctomycetes, Verrucomicrobia and Bacteroidetes were more abundant in chromium contaminated samples as compared to control samples. The results were also found to be statistically significant. The above-mentioned bacteria can be targeted and studied to discover their roles in bioremediation of chromium contaminated sites.

Discovery of two novel tilapia lake virus-like virus isolates in the transcriptomic data of guppy fish (Poecilia reticulata).

The author declares no conflict of interest. All raw datasets (SRR6377113–SRR6377114) reanalysed in this study are accessible via the SRA database. The assembled genome sequences (BK063200–BK063219) are available in Supplementary material and also in the Third Party Annotation (TPA) section of the GenBank database. Appendix S1. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Genome comparison reveals that Halobacterium salinarum 63-R2 is the origin of the twin laboratory strains NRC-1 and R1.

The genome of Halobacterium strain 63-R2 was recently reported and provides the opportunity to resolve long-standing issues regarding the source of two widely used model strains of Halobacterium salinarum, NRC-1 and R1. Strain 63-R2 was isolated in 1934 from a salted buffalo hide (epithet "cutirubra"), along with another strain from a salted cow hide (91-R6T , epithet "salinaria," the type strain of Hbt. salinarum). Both strains belong to the same species according to genome-based taxonomy analysis (TYGS), with chromosome sequences showing 99.64% identity over 1.85 Mb. The chromosome of strain 63-R2 is 99.99% identical to the two laboratory strains NRC-1 and R1, with only five indels, excluding the mobilome. The two reported plasmids of strain 63-R2 share their architecture with plasmids of strain R1 (pHcu43/pHS4, 99.89% identity; pHcu235/pHS3, 100.0% identity). We detected and assembled additional plasmids using PacBio reads deposited at the SRA database, further corroborating that strain differences are minimal. One plasmid, pHcu190 (190,816 bp) corresponds to pHS1 (strain R1) but is even more similar in architecture to pNRC100 (strain NRC-1). Another plasmid, pHcu229, assembled partially and completed in silico (229,124 bp), shares most of its architecture with pHS2 (strain R1). In deviating regions, it corresponds to pNRC200 (strain NRC-1). Further architectural differences between the laboratory strain plasmids are not unique, but are present in strain 63-R2, which contains characteristics from both of them. Based on these observations, it is proposed that the early twentieth-century isolate 63-R2 is the immediate ancestor of the twin laboratory strains NRC-1 and R1.

Investigating the clinical relevance of RNA editing events and their derived neoantigens in patients with melanoma treated with immunotherapy.

e21580 Background: RNA editing (RE) is a post-transcriptional modification occurring in RNA, which promotes transcriptome and proteome diversity. Peptides translated from RE sites may represent a new source of neoantigens in cancer (RE-derived neoantigens, RED-neoantigens) that could be presented on tumor surface by human-leukocyte-antigen (HLA) and recognized by specific T-cells, leading to an improved response to immune checkpoint inhibitors (ICIs). However, the clinical significance of both RE events and RED-neoantigens in melanoma patients with ICIs therapy has not been systematically characterized. Methods: The WES and transcriptome data with immunotherapy response of melanoma were obtained from the GEO and SRA database. Vardict and VEP were used to identify and annotate the somatic mutations. Polysover was applied to identify the HLA genotype. RNA editing events were identified by Reditools2 and filtered by a custom pipeline. miRTar2GO was implemented to predict the RE event whether located in miRNA targets within the 3' UTR region. NetMHCpan and NetCTLpan were used to identify and characterize RED-neoantigens. K-M survival analysis was performed on the training set to investigate the clinical relevance of RNA editing events and RED-neoantigens in melanoma patients treated with immunotherapy. The independent melanoma dataset was used to validate this clinical relevance. Results: In total, 7,116 RE events were identified, most of which were A-to-I events. 34% of RE sites in 3'UTR and 15% in 5' UTR were located in the seed regions of miRNA targets and transcription factor binding sites (TFBS), respectively, suggesting the different functional effects of the RE events. Furthermore, using our custom pipeline, 631 RED-neoantigens were identified that show a significantly greater peptide-MHC affinity, and facilitate epitope processing and presentation than wild-type peptides. Meanwhile, we found that patients exhibiting a high RED-neoantigens burden correlated with an increased OS, and a significantly higher RED-neoantigens burden was observed in responders. The area under the curve (AUC) of the RED-neoantigen was 0.831 of OS and 0.686 of responsiveness. Conclusions: The findings in this study provide a more insightful view and resource for investigating the neoantigens in cancer as well as for novel cancer immunotherapies and biomarker development.

Foremost report of the whole genome of Spirabiliibacterium mucosae from India and comparative genomics of the novel genus Spirabiliibacterium

Several Pasteurella like organisms isolated from various avian species were recently reclassified into new genus based on whole genome sequence analysis. One such Pasteurella like organism, Bisgaard taxon 14 was classified as Spirabiliibacterium mucosae. In the present study, a Gram-negative organism was isolated from ailing pigeons with respiratory infection from a farm in Tamil Nadu, India and the organism was misidentified as Burkholderia mallei by Vitek 2 compact system based on biochemical characterization. Since, B. mallei is highly pathogenic and zoonotic, to further confirm, 16S rDNA sequencing and analysis was carried out which revealed that the strain belonged to Bisgaard taxon 14 (Spirabiliibacterium mucosae). To further confirm the findings, whole genome sequencing of the isolate was performed. Whole genome phylogeny and average nucleotide identity (ANI) analysis showed that the genome was closely matching with Spirabiliibacterium mucosae type strain 20,609 /3. Hence, the strain from pigeon was named as Spirabiliibacterium mucosae TN_CUL_2021 and the genome was submitted in NCBI SRA database. The genome of S. mucosase TN_CUL_2021 is only the second genome available worldwide in the NCBI database. Comparative genome analysis of 26 Pasteurellaceae family strains revealed 1101 genes specific for Spirabiliibacterium mucosae. Similarly, luxS virulence gene was found only in S. mucosae and Bisgaardia hudsonensis strains. Since there are only 2 genomes available in the NCBI genome database, further studies on isolation of S. mucosae needs to be carried out to identify its epidemiology and pathogenesis so as to develop better diagnostic assays and vaccines.

Differential gene expression analysis in germinating and dormant teliospores of Tilletia indica using RNA seq approach

Karnal bunt of wheat is an important quarantine disease that interrupts India’s wheat trade in the international market. The whole transcriptome of germinating and dormant teliospores of Tilletia indica was performed using the RNA Seq approach to identify germination-related genes. Approximately 63 million reads were generated using the RNA sequencing by the Illumina NextSeq500 platform. The high-quality reads were deposited in NCBI SRA database (accession: PRJNA522347). The unigenes from the pooled teliospores were 16,575 having unigenes length of 28,998,753 bases. The high-quality reads of germinating teliospores mapped on to 21,505 predicted CDSs. 9,680 CDSs were common between dormant and germinating teliospores of T. indica. 11,825 CDSs were found to be in germinating teliospores while only 91 were unique in dormant spores of pathogen. The pathway analysis showed the highest number of pathways was found in germinating spores than dormant spores. The highest numbers of CDSs were found to be associated with translation (431 in number), transport and catabolism (340), signal transduction (326), and carbohydrate metabolism (283). The differential expression analysis (DESeq) of germinating and dormant teliospores showed that 686 CDS were up-regulated and 114 CDS were down-regulated in the germinating teliospores. Significant germination-related genes in the spores were validated using qPCR analysis. Ten genes viz. Ti3931, Ti6828, Ti7098, Ti7462, Ti7522, Ti 9289, Ti 8670, Ti 7959, Ti 7809,and Ti10095 were highly up-regulated in germinated teliospores which may have role in germination of spores.Further, these differentially expressed genes provide insights into the molecular events. This first study of transcriptome will be helpful to devise better management strategies to manage Karnal bunt disease.

How voles adapt to subterranean lifestyle: Insights from RNA-seq

Life under the earth surface is highly challenging and associated with a number of morphological, physiological and behavioral modifications. Subterranean niche protects animals from predators, fluctuations in environmental parameters, but is characterized by high levels of carbon dioxide and low levels of oxygen and implies high energy requirements associated with burrowing. Moreover, it lacks most of the sensory inputs available above ground. The current study describes results from RNA-seq analysis of four subterranean voles from subfamily Arvicolinae:Prometheomys schaposchnikowi,Ellobius lutescens,Terricola subterraneus, andLasiopodomys mandarinus. Original RNA-seq data were obtained for eight species, for nine species, SRA data were downloaded from the NCBI SRA database. Additionally assembled transcriptomes of Mynomes ochrogaster and Cricetulus griseus were included in the analysis. We searched for the selection signatures and parallel amino acid substitutions in a total of 19 species. Even within this limited data set, we found significant changes ofdN/dSratio by free-ratio model analysis for subterranean Arvicolinae. Parallel substitutions were detected in genesRAD23BandPYCR2. These genes are associated with DNA repair processes and response to oxidative stress. Similar substitutions were discovered in theRAD23genes for highly specialized subterraneanHeterocephalus glaberandFukomys damarensis. The most pronounced signatures of adaptive evolution related to subterranean niche within species of Arvicolinae subfamily were detected forEllobius lutescens. Our results suggest that genomic adaptations can occur very quickly so far as the amount of selection signatures was found to be compliant with the degree of specialization to the subterranean niche and independent from the evolutionary age of the taxon. We found that the number of genomic signatures of selection does not depend on the age of the taxon, but is positively correlated with the degree of specialization to the subterranean niche.

Metagenomics reveals an abundance of black yeast-like fungi in the skin microbiome.

The skin is the first line of defence against communities of resident viruses, bacteria and fungi. The composition of the microbiome might change with factors related to the environment and host. The microbiome is dominated by bacteria. Dermatophytes and yeasts are the predominant fungi that are also involved in opportunistic infections of skin, hair and nails. Among environmental fungi, Chaetothyriales (black yeasts and relatives) are enriched by hydrocarbon pollution in domesticated habitats and comprise numerous species that cause mild-to-severe disease. We investigated the presence of black fungi in the skin microbiome by conducting an analysis in the publicly available metagenomic SRA database (NCBI). We focused on the causative agents of chromoblastomycosis and phaeohyphomycosis and used barcodes and padlock probe sequences as diagnostic tools. A total of 132,159,577 MB was analysed and yielded 18,360 reads that matched with 24 species of black fungi. Exophiala was the most prevalent genus, and Cyphellophora europaea was the most abundant species. This study reveals the abundant presence of Chaetothyriales on the skin without necessarily being associated with infection. Most of the detected causal agents are known from mild skin diseases, while also species were revealed that had been reported from CARD9-deficient patients.

ESCCdb: A comprehensive database and key regulator exploring platform based on cross dataset comparisons for esophageal squamous cell carcinoma

Esophageal cancer is the seventh most prevalent and the sixth most lethal cancer. Esophageal squamous cell carcinoma (ESCC) is one of the major esophageal cancer subtypes that accounts for 87 % of the total cases. However, its molecular mechanism remains unclear. Here, we present an integrated database for ESCC called ESCCdb, which includes a total of 56 datasets and published studies from the GEO, Xena or SRA databases and related publications. It helps users to explore a particular gene with multiple graphical and interactive views with one click. The results comprise expression changes across 20 datasets, copy number alterations in 11 datasets, somatic mutations from 12 papers, related drugs derived from DGIdb, related pathways, and gene correlations. ESCCdb enables directly cross-dataset comparison of a gene’s mutations, expressions and copy number changes in multiple datasets. This allows users to easily assess the alterations in ESCC. Furthermore, survival analysis, drug-gene relationships, and results from whole-genome CRISPR/Cas9 screening can help users determine the clinical relevance, derive functional inferences, and identify potential drugs. Notably, ESCCdb also enables the exploration of the correlation structure and identification of potential key regulators for a process. Finally, we identified 789 consistently differential expressed genes; we summarized recurrently mutated genes and genes affected by significant copy number alterations. These genes may be stable biomarkers or important players during ESCC development. ESCCdb fills the gap between massive omics data and users’ needs for integrated analysis and can promote basic and clinical ESCC research. The database is freely accessible at http://cailab.labshare.cn/ESCCdb.

Unveiling the Human Brain Virome in Brodmann Area 46: Novel Insights Into Dysbiosis and Its Association With Schizophrenia.

Whole-genome sequencing raw data from postmortem Brodmann Area 46 (BA46) tissue from 49 individuals (20 healthy controls [HCs], 29 with schizophrenia [SCZs]) obtained from the NCBI SRA database from BioProject: PRJNA422380.Virome profiles were retrieved using Metaphlan3, and viral signatures were identified using linear discriminant analysis effect size (LEfSe). Mann-Whitney tests and receiver operating characteristic curve validated the viral signatures. In BA46, 30 distinct species representing 9 phyla, 10 classes, 10 orders, 13 families, and 19 genera were identified. HCs exhibited greater alpha diversity, and there were significant differences in beta diversity between the groups. LEfSe analysis highlighted distinct viral levels, including Escherichia virus Lambda, Escherichia virus phiV10, Human endogenous retrovirus K, Taterapox virus, Alcelaphine gammaherpesvirus 1, and Bovine gammaherpesvirus 4 in HCs, while Glypta fumiferanae ichnovirus and unknown virus showed higher levels in schizophrenia. This is the first study to identify a human brain virome associated with schizophrenia in BA46. Brain virome dysbiosis may be associated with mental illness, and viral signatures may serve as biomarkers for the early detection of schizophrenia.

ARA: a flexible pipeline for automated exploration of NCBI SRA datasets.

One of the most effective and useful methods to explore the content of biological databases is searching with nucleotide or protein sequences as a query. However, especially in the case of nucleic acids, due to the large volume of data generated by the next-generation sequencing (NGS) technologies, this approach is often not available. The hierarchical organization of the NGS records is primarily designed for browsing or text-based searches of the information provided in metadata-related keywords, limiting the efficiency of database exploration. We developed an automated pipeline that incorporates the well-established NGS data-processing tools and procedures to allow easy and effective sampling of the NCBI SRA database records. Given a file with query nucleotide sequences, our tool estimates the matching content of SRA accessions by probing only a user-defined fraction of a record's sequences. Based on the selected parameters, it allows performing a full mapping experiment with records that meet the required criteria. The pipeline is designed to be easy to operate-it offers a fully automatic setup procedure and is fixed on tested supporting tools. The modular design and implemented usage modes allow a user to scale up the analyses into complex computational infrastructure. We present an easy-to-operate and automated tool that expands the way a user can access and explore the information contained within the records deposited in the NCBI SRA database.

Integrative Meta-Analysis of Huntington’s Disease Transcriptome Landscape

Huntington's disease (HD) is a neurodegenerative disorder with autosomal dominant inheritance caused by glutamine expansion in the Huntingtin gene (HTT). Striatal projection neurons (SPNs) in HD are more vulnerable to cell death. The executive striatal population is directly connected with the Brodmann Area (BA9), which is mainly involved in motor functions. Analyzing the disease samples from BA9 from the SRA database provides insights related to neuron degeneration, which helps to identify a promising therapeutic strategy. Most gene expression studies examine the changes in expression and associated biological functions. In this study, we elucidate the relationship between variants and their effect on gene/downstream transcript expression. We computed gene and transcript abundance and identified variants from RNA-seq data using various pipelines. We predicted the effect of genome-wide association studies (GWAS)/novel variants on regulatory functions. We found that many variants affect the histone acetylation pattern in HD, thereby perturbing the transcription factor networks. Interestingly, some variants affect miRNA binding as well as their downstream gene expression. Tissue-specific network analysis showed that mitochondrial, neuroinflammation, vasculature, and angiogenesis-related genes are disrupted in HD. From this integrative omics analysis, we propose that abnormal neuroinflammation acts as a two-edged sword that indirectly affects the vasculature and associated energy metabolism. Rehabilitation of blood-brain barrier functionality and energy metabolism may secure the neuron from cell death.

Whole mitochondrial genome phylogeny of Drosophilidae

A total of 241 mitochondrial genomes were assembled and annotated from the SRA database to reconstruct a mtDNA genome phylogeny for the genus Drosophila, the family Drosophilidae, and close relatives. The resulting mtDNA genome phylogeny is largely congruent with previous higher-level analyses of Drosophila species with the exception of the relationships between the melanogaster, montium, anannassae, saltans and obscura groups. Although relationships within these species groups are congruent between nuclear and mtDNA studies, the mtDNA genome phylogeny of the groups is different when compared to earlier studies. Monophyly of known species groups within the genus Drosophila are highly supported and, as in previous work, the genera Lordiphosa, Hirtodrosophila, Zaprionus and Scaptomya are all imbedded within the genus Drosophila. Incongruence and partitioned support analyses indicate that DNA sequences are better at resolving the phylogeny than their translated protein sequences. Such analyses also indicate that genes on the minus strand of the circular molecule (Lrrna, Srrna, ND4, ND4L and ND5) provide most of the support for the overall phylogenetic hypothesis.

Transcriptome Analysis of Wheat-Tilletia indica Interaction Provides Defense and Pathogenesis-Related Genes.

Karnal bunt (Tilletia indica Mitra) is an internationally quarantined disease of wheat. Until now, very little information has been available on the molecular basis of resistance and pathogenicity of T. indica. To investigate the molecular basis of host-pathogen interaction, the transcriptome of T. indica inoculated resistant (HD29) and susceptible (WH542) genotypes of wheat were analyzed. Approximately 58 million reads were generated using RNA sequencing by the Illumina NextSeq500 platform. These sequence reads were aligned to a reference genome of wheat to compare the expression level of genes in resistant and susceptible genotypes. The high-quality reads were deposited in the NCBI SRA database (SRP159223). More than 80,000 genes were expressed in both the resistant and susceptible wheat genotypes. Of these, 76,088 were commonly expressed genes, including 3184 significantly upregulated and 1778 downregulated genes. Four thousand one hundred thirteen and 5604 genes were exclusively expressed in susceptible and resistant genotypes, respectively. Based on the significance, 503 genes were upregulated and 387 genes were downregulated. Using gene ontology, the majority of coding sequences were associated with response to stimuli, stress, carbohydrate metabolism, developmental process, and catalytic activity. Highly differentially expressed genes (integral component of membrane, exonuclease activity, nucleic acid binding, DNA binding, metal ion binding) were validated in resistant and susceptible genotypes using qPCR analysis and similar expression levels were found in RNA-Seq. Apart from the wheat, the mapping of T. indica was 7.07% and 7.63% of resistant and susceptible hosts, respectively, upon infection, which revealed significant pathogenesis-related genes. This first study provided in-depth information and new insights into wheat-T. indica interaction for managing Karnal bunt disease of wheat.

Bioinformatic analysis of the RNA expression patterns in microgravity-induced bone loss.

Researchers have linked microgravity in space to the significant imbalance between bone formation and bone resorption that induces persistent bone loss in load-bearing bones. However, the underlying molecular mechanisms are still unclear, which hinders the development of therapeutic measures. The aim of this study was to identify hub genes and explore novel molecular mechanisms underlying microgravity-induced bone loss using transcriptome datasets obtained from the GEO and SRA databases. In summary, comparative RNA expression pattern studies that differ in species (Homo or Mus), models (in vitro or in vivo), microgravity conditions (real microgravity or ground-based simulators) and microgravity duration showed that it is difficult to reach a consistent conclusion about the pathogenesis of microgravity-induced bone loss across these studies. Even so, we identified 11 hub genes and some miRNA-mRNA interactions mainly based on the GSE100930 dataset. Also, the expression of CCL2, ICAM1, IGF1, miR-101-3p and miR-451a markedly changed under clinorotation-microgravity condition. Remarkedly, ICAM1 and miR-451a were key mediators of the osteogenesis of hMSCs under clinorotation-microgravity condition. These findings provide novel insights into the molecular mechanisms of bone loss during microgravity and could indicate potential targets for further countermeasures against this condition.

P421 Whole-transcriptome analysis of Sporothrix brasiliensis grown in mold- and yeast-inducing conditions

Poster session 3, September 23, 2022, 12:30 PM - 1:30 PM Objectives Sporothrix brasiliensis is an emerging Sporothrix species limited to Brazil capable of causing sporotrichosis in humans and animals, especially in cats. Like other pathogenic Sporothrix species, S. brasiliensis exhibits a temperature-dependent dimorphic switch and is therefore, able to undergo a reversible morphological transition (mold and yeast), in response to environmental thermal stimuli.While dimorphism appears to be essential for virulence in Sporothrix spp, the molecular mechanisms involved in this phenomenon have not yet been fully elucidated.In this study, we used the strand-specific RNA-Seq technique and bioinformatics analysis to investigate the transcriptomic signatures associated with mold and yeast phases of S. brasiliensis. Furthermore, we generated an accurate version of the S. brasiliensis genome annotation in order to perform high-quality gene expression analysis and other functional or structural genomic studies.MethodsThe whole transcriptome of S. brasiliensis ATCC-MYA-4823, grown in both yeast-inducing (YPD medium at 37°C) and mold-inducing (YPD medium at 25°C) conditions, was sequenced in this study. High-quality RNA was used to prepare Illumina TruSeq Stranded mRNA-paired-end sequencing libraries (2 × 150 bp) that were sequenced using the HiSeq-2500 platform. A total of three biological replicates were sequenced for each condition.Before transcriptome assembly, adapters and low-quality reads (Phred-score <25) were removed. The StringTie software was used to assemble the transcriptomes imported into the Apollo webtool to manually curate the genome annotation. Transcripts were investigated using TransDecoder and CPC2 programs to determine whether a gene was potentially protein-coding or non-coding. Finally, differential gene expression analysis between yeast and mold forms of S. brasiliensis was conducted using the edgeR package.ResultsIllumina sequencing resulted in a total of ∼217 million raw reads. After quality filtering and trimming, ∼99.5% of reads were used for downstream bioinformatics analysis. The updated S. brasiliensis genome annotation consisted of a total of 14 664 genes of which 10 243 protein-coding genes, 4259 lncRNAs, 140 tRNAs, and 22 rRNAs.Gene expression analysis revealed a total of 13 838 and 13 938 transcripts expressed in mold- and yeast-form, respectively. Of these, 192 and 292 were expressed exclusively in the mold and yeast-phase, respectively. Moreover, a total of 6802 genes (FDR <0.05) were differentially expressed between the two examined conditions. In particular, 3420 of these genes were up-regulated in the yeast-form (2450 coding, 970 non-coding), and 3382 genes in the filamentous form (2507 coding, 875 non-coding). The raw reads have been deposited into the SRA database and are available under BioProjectID: PRJNA646214.ConclusionsThe characterization of the whole-transcriptome of S. brasiliensis mycelial and yeast-like forms represents an essential starting point for investigating the molecular pathways and regulatory frameworks associated with these two morphological stages. Our results provide new insight into global gene expression profiles of S. brasiliensis, emphasizing the role of non-coding RNAs in its complex transcriptional network.All transcriptomic data have also been integrated into the ‘Sporothrix Genome DataBase’ (www. sporothrixgenomedatabase.unime.it) in order to expand the current knowledge of Sporothrix genomics and to allow a more in-depth structural exploration of S. brasiliensis gene models, including gene expression patterns related to its saprophytic and pathogenic lifestyle.