Transcriptomics has significantly grown as a functional genomics tool for understanding the expression of biological systems. The generated transcriptomics data can be utilised to produce a gene co-expression network that is one of the essential downstream omics data analyses. To date, several gene co-expression network databases that store correlation values, expression profiles, gene names and gene descriptions have been developed. Although these resources remain scattered across the Internet, such databases complement each other and support efficient growth in the functional genomics area. This review presents the features and the most recent gene co-expression network databases in crops and summarises the present status of the tools that are widely used for constructing the gene co-expression network. The highlights of gene co-expression network databases and the tools presented here will pave the way for a robust interpretation of biologically relevant information. With this effort, the researcher would be able to explore and utilise gene co-expression network databases for crops improvement.

In recent years, the advance in whole-genome sequencing technology has changed the study of infectious diseases. The emergence of genome sequencing has improved the understanding of infectious diseases, which has revamped many fields, such as molecular microbiology, epidemiology, infection control, and vaccine production. In this review we discuss the findings of Salmonella enterica serovar Typhi genomes, publicly accessible from the initial complete genome to the recent update of Salmonella enterica serovar Typhi genomes, which has greatly improved Salmonella enterica serovar Typhi and other pathogen genomic research. Significant information on genetic changes, evolution, antimicrobial resistance, virulence, pathogenesis, and investigation from the genome sequencing of S. Typhi is also addressed. This review will gather information on the variation of the Salmonella enterica serovar Typhi genomes and hopefully facilitate our understanding of their genome evolution, dynamics of adaptation, and pathogenesis for the development of the typhoid point-of-care diagnostics, medications, and vaccines.

Pathogenic fungi belonging to the genera Botrytis, Phaeomoniella, Fusarium, Alternaria and Aspergillus are responsible for vines diseases that affect the growth, grapevine yield and organoleptic quality. Among innovative strategies for in-field plant disease control, one of the most promising is represented by biocontrol agents, including wild epiphytic yeast strains of grapevine berries. Twenty wild yeast, isolated and molecularly identified from three different Malaysian regions (Perlis, Perak and Pahang), were evaluated in a preliminary screening test on agar to select isolates with inhibition against Botrytis cinerea. On the basis of the results, nine yeasts belonging to genera Hanseniaspora, Starmerella, Metschnikowia, Candida were selected and then tested against five grape berry pathogens: Aspergillus carbonarius, Aspergillus ochraceus, Fusarium oxysporum, Alternaria alternata and Phaeomoniella chlamydospora.Starmerella bacillaris FE08.05 and Metschnikowia pulcherrima GP8 and Hanseniaspora uvarum GM19 showed the highest effect on inhibiting mycelial growth, which ranged between 15.1 and 4.3 mm for the inhibition ring. The quantitative analysis of the volatile organic compound profiles highlighted the presence of isoamyl and phenylethyl alcohols and an overall higher presence of low-chain fatty acids and volatile ethyl esters. The results of this study suggest that antagonist yeasts, potentially effective for the biological control of pathogenic moulds, can be found among the epiphytic microbiota associated with grape berries.

Stevia rebaudiana (S. rebaudiana) is a herbaceous and perennial plant belonging to Asteraceae family. The genus stevia is well known as a natural producer of sweetener comprising non-caloric and non-carcinogenic steviol glycosides. In recent years, the capability in producing natural sweetner has increased the demand for S. rebaudiana as substitute of processed sugars. Flowering phase of S. rebaudiana has shown to affect the content of steviol glycosides in the leaves. Steviol glycosides level is the highest at the time of flower bud formation and lowest at time preceding and following flower bud formation. Therefore, sequencing and analysing the genes that are involved in flowering phase will provide platform for gene manipulation in increasing steviol glycosides content. The Stevia transcriptome data that include two stages of growth (before flowering and after flowering), were obtained using Illumina RNA-seq technology and can be accessed at NCBI Sequence Read Archive under Accession No. SRX6362785 and SRX6362784.

Purpose: Bacillus megaterium strain BHS1, isolated from an alkaline water sample taken from Mavi Gölü (Blue Lake, Turkey), can grow on minimal medium containing 2,2-dichloropropionic acid. We characterized this bacterium at the genomic level. Methods: The HiSeq platform was used to carry out genome sequencing, de novo assembly, and scaffolding with strain BHS1. Next, genome data were analyzed to demarcate DNA regions containing protein-coding genes and determine the function of certain BHS1 genes. Finally, results from a colorimetric chloride ion–release assay demonstrated that strain BHS1 produces dehalogenase. Results: De novo assembly of the BHS1 genomic sequence revealed a genome size of ~ 5.37 Mb with an average G+C content of 38%. The predicted nuclear genome harbors 5509 protein-coding genes, 1353 tRNA genes, 67 rRNA genes, and 6 non-coding (mRNA) genes. Genomic mapping of strain BHS1 revealed its amenability to synthesize two families of dehalogenases (Cof-type haloacid dehalogenase IIB family hydrolase and haloacid dehalogenase type II), suggesting that these enzymes can participate in the catabolism of halogenated organic acids. The mapping identified seven Na⁺/H⁺ antiporter subunits that are vital for adaptation of the bacterium to an alkaline environment. Apart from a pairwise analysis to the well-established L-2-haloacid dehalogenases, whole-cell analysis strongly suggested that the haloacid dehalogenase type II might act stereospecifically on L-2-chloropropionic acid, D,L-2-chloropropionic acid, and 2,2-dichloropropionic acid. Whole-cell studies confirmed the utilization of these three substrates and the gene’s role in dehalogenation. Conclusions: To our knowledge, this is the first report of the full genome sequence for strain BHS1, which enabled the characterization of selected genes having specific metabolic activities and their roles in the biodegradation of halogenated compounds.