Evolutionary Perspective of Fungal Pathogenic Genes

Fungal pathogenesis has been vastly investigated in recent years and the phylogenic studies of fungal genome reveal that unique genes are responsible for pathogenesis. It has been found that the pathogenesis is caused by genes responsible for DNA repair, vegetative growth and sporulation. In the recent past, studies on filamentous pathogenic fungi playing an important role in establishing a pathogenic relationship with the host was well described

Genome-wide characterization of small RNA, gene expression and DNA methylation changes in response to salt stress in Musa acuminata / Gudimella Ranganath

Banana, a commercially important crop which serves as a staple food in several countries worldwide, faces threats from abiotic stress especially related to soil and water salinity due to climate change. Most banana cultivars are salt sensitive, which results in low productivity and fruit of low quality. Physiological responses to salt stress are regulated by underlying gene expression which is influenced by microRNA, small interfering RNA and methylations of genic regions. This study integrated data from transcriptomes, small RNA transcriptomes, degradomes and methylomes using high-throughput sequencing of RNA and DNA extracted from the roots of salt-stressed and non-salt-stressed banana plantlets. Various bioinformatics approaches were adopted for analysis of multi-omics data, for miRNA prediction using small RNA transcriptome a customized pipeline was designed using miRDeep2, miRNA target validation using degradomes was performed by cleaveland4 tool, methylomes were analysed using Bismark and MethPipe tools. Data integration for small RNA and degradome data was performed using network mapping by cytoscape tool. Similarly, data integration for small RNA, transcriptome and methylomes was performed by using statistical approach by custom scripts and visualized data using genome browser. Genome-wide microRNAs were annotated using small RNA transcriptome data and the most recent banana genome sequence. A total of 180 mature miRNAs belonging to 20 orthologous miRNA families and 39 Musa-specific miRNA families were identified. Candidate microRNA targets genes were predicted using bioinformatics tools and validated using degradome data. Profiling of transcription factor binding sites (TFBS) motifs across miRNA promoter regions showed that transcription factors belonging to TCP, AP2; ERF, GATA, NF-YB, DOF, B3, bZIP, trihelix, ZF-HD, bHLH and Dehydrin are likely abundant in the Musa acuminata genome. A putative miRNA-mediated regulatory network is proposed for miR156, miR164, miR166, miR171, miR319 miR396, miR528, mac-miR6, mac-miR-new14 and mac-miR-new20 and their respective transcription factor targets. Genome-wide association between DNA methylation, expression of genes and of 21nt and 24nt small RNAs in response to salt stress was determined using methylome, transcriptome and small RNA transcriptome libraries. DNA methylation in genic regions showed transcriptional repression in several stress-responsive gene candidates such as DRE2, DHN1, AP2, ion-transport related genes, i.e. calcium permeable stress-gated cation channel 1-like and cation/H+ antiporter 20-like, and peroxidases (PER1, PER67 and PNC1), which are ROS-related antioxidants during salt stress. Salt-stressed root samples displayed symmetric CG methylation and CHH demethylation adjacent to differentially expressed genes, while 21 and 24nt siRNA clusters on genomic loci showed increased methylation levels in CG, CHG and CHH contexts. This research contributes Musa- specific miRNA”ome” and small RNA-targeted differentially methylated genic regions which serve as molecular and epigenetic markers to support improvement of banana to address cultivation in salinized soil. Musa-specific genomic markers will serve as an important knowledge base for crop improvement and plant breeding programs

Molecular Characterization and Comparative Sequence Analysis of Defense-Related Gene, Oryza rufipogon Receptor-Like Protein Kinase 1

Abstract: Many of the plant leucine rich repeat receptor-like kinases (LRR-RLKs) have been found to regulate signaling during plant defense processes. In this study, we selected and sequenced an LRR-RLK gene, designated as Oryza rufipogon receptor-like protein kinase 1 (OrufRPK1), located within yield QTL yld1.1 from the wild rice Oryza rufipogon (accession IRGC105491). A 2055 bp coding region and two exons were identified. Southern blotting determined OrufRPK1 to be a single copy gene. Sequence comparison with cultivated rice orthologs (OsI219RPK1, OsI9311RPK1 and OsJNipponRPK1, respectively derived from O. sativa ssp. indica cv. MR219, O. sativa ssp. indica cv. 9311 and O. sativa ssp. japonica cv. Nipponbare) revealed the presence of 12 single nucleotide polymorphisms (SNPs) with five non-synonymous substitutions, and 23 insertion/deletion sites. The biological role of the OrufRPK1 as a defense related LRR-RLK is proposed on the basis of cDNA sequence characterization, domain subfamily classification, structura

Comparative genomic analysis of ten clinical Streptococcus pneumoniae collected from a Malaysian hospital reveal 31 new unique drug-resistant SNPs using whole genome sequencing

Abstract Background Streptococcus pneumoniae or pneumococcus is a leading cause of morbidity and mortality worldwide, specifically in relation to community-acquired pneumonia. Due to the overuse of antibiotics, S. pneumoniae has developed a high degree of resistance to a wide range of antibacterial drugs. Methods In this study, whole genome sequencing (WGS) was performed for 10 clinical strains of S. pneumoniae with different levels of sensitivity to standard antibiotics. The main objective was to investigate genetic changes associated with antibiotic resistance in S. pneumoniae. Results Our results showed that resistant isolates contain a higher number of non-synonymous single nucleotide polymorphisms (SNPs) as compared to susceptible isolates. We were able to identify SNPs that alter a single amino acid in many genes involved in virulence and capsular polysaccharide synthesis. In addition, 90 SNPs were only presented in the resistant isolates, and 31 SNPs were unique and had not been previously reported, suggesting that these unique SNPs could play a key role in altering the level of resistance to different antibiotics. Conclusion Whole genome sequencing is a powerful tool for comparing the full genome of multiple isolates, especially those closely related, and for analysing the variations found within antibiotic resistance genes that lead to differences in antibiotic sensitivity. We were able to identify specific mutations within virulence genes related to resistant isolates. These findings could provide insights into understanding the role of single nucleotide mutants in conferring drug resistance

CoVigator—A Knowledge Base for Navigating SARS-CoV-2 Genomic Variants

Background: The outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulted in the global COVID-19 pandemic. The urgency for an effective SARS-CoV-2 vaccine has led to the development of the first series of vaccines at unprecedented speed. The discovery of SARS-CoV-2 spike-glycoprotein mutants, however, and consequentially the potential to escape vaccine-induced protection and increased infectivity, demonstrates the persisting importance of monitoring SARS-CoV-2 mutations to enable early detection and tracking of genomic variants of concern. Results: We developed the CoVigator tool with three components: (1) a knowledge base that collects new SARS-CoV-2 genomic data, processes it and stores its results; (2) a comprehensive variant calling pipeline; (3) an interactive dashboard highlighting the most relevant findings. The knowledge base routinely downloads and processes virus genome assemblies or raw sequencing data from the COVID-19 Data Portal (C19DP) and the European Nucleotide Archive (ENA), respectively. The results of variant calling are visualized through the dashboard in the form of tables and customizable graphs, making it a versatile tool for tracking SARS-CoV-2 variants. We put a special emphasis on the identification of intrahost mutations and make available to the community what is, to the best of our knowledge, the largest dataset on SARS-CoV-2 intrahost mutations. In the spirit of open data, all CoVigator results are available for download. The CoVigator dashboard is accessible via covigator.tron-mainz.de. Conclusions: With increasing demand worldwide in genome surveillance for tracking the spread of SARS-CoV-2, CoVigator will be a valuable resource of an up-to-date list of mutations, which can be incorporated into global efforts

Identifying protein biomarkers in predicting disease severity of dengue virus infection using immune-related protein microarray

Dengue virus is one of the most widespread flaviviruses that re-emerged throughout recent decades. The progression from mild dengue to severe dengue (SD) with the complications such as vascular leakage and hemorrhage increases the fatality rate of dengue. The pathophysiology of SD is not entirely clear. To investigate potential biomarkers that are suggestive of pathogenesis of SD, a small panel of serum samples selected from 1 healthy individual, 2 dengue patients without warning signs (DWS-), 2 dengue patients with warning signs (DWS+), and 5 patients with SD were subjected to a pilot analysis using Sengenics Immunome protein array. The overall fold changes of protein expressions and clustering heat map revealed that PFKFB4, TPM1, PDCL3, and PTPN20A were elevated among patients with SD. Differential expression analysis identified that 29 proteins were differentially elevated greater than 2-fold in SD groups than DWS- and DWS+. From the 29 candidate proteins, pathways enrichment analysis also identified insulin signaling and cytoskeleton pathways were involved in SD, suggesting that the insulin pathway may play a pivotal role in the pathogenesis of SD

Transcripts and MicroRNAs Responding to Salt Stress in <i>Musa acuminata</i> Colla (AAA Group) cv. Berangan Roots

<div><p>Physiological responses to stress are controlled by expression of a large number of genes, many of which are regulated by microRNAs. Since most banana cultivars are salt-sensitive, improved understanding of genetic regulation of salt induced stress responses in banana can support future crop management and improvement in the face of increasing soil salinity related to irrigation and climate change. In this study we focused on determining miRNA and their targets that respond to NaCl exposure and used transcriptome sequencing of RNA and small RNA from control and NaCl-treated banana roots to assemble a cultivar-specific reference transcriptome and identify orthologous and <i>Musa</i>-specific miRNA responding to salinity. We observed that, banana roots responded to salinity stress with changes in expression for a large number of genes (9.5% of 31,390 expressed unigenes) and reduction in levels of many miRNA, including several novel miRNA and banana-specific miRNA-target pairs. Banana roots expressed a unique set of orthologous and <i>Musa</i>-specific miRNAs of which 59 respond to salt stress in a dose-dependent manner. Gene expression patterns of miRNA compared with those of their predicted mRNA targets indicated that a majority of the differentially expressed miRNAs were down-regulated in response to increased salinity, allowing increased expression of targets involved in diverse biological processes including stress signaling, stress defence, transport, cellular homeostasis, metabolism and other stress-related functions. This study may contribute to the understanding of gene regulation and abiotic stress response of roots and the high-throughput sequencing data sets generated may serve as important resources related to salt tolerance traits for functional genomic studies and genetic improvement in banana.</p></div