Project description:DNA, RNA and protein were extracted from the culture and subjected to massive parallel sequencing and nano-LC-MS-MS respectively Combination of these methods enabled the reconstruction of the complete genome sequence of M oxyfera from the metagenome and identification of the functionally relevant enzymes and genes
Project description:Apple is one of the most important fruits that is propagated vegetatively, facilitating frequent transmission of viruses. The causative agent of the apple rubbery wood disease, apple rubbery wood virus 2 (ARWV2), can infect apple and pear. The branches of ARWV2-infected, symptomatic trees are flexible due to the decreased lignification of the xylem. In this research, we reanalysed our sRNA HTS datasets to survey the presence of ARWV2 in Hungary. Validation of HTS using RT-PCR revealed infection in several cultivars. The following RT-PCR-based survey revealed the infection of 15 trees, including pear and quince, without showing any rubbery wood symptoms. Analysis of the sRNA datasets allowed us to profile the sRNA pattern of ARWV2-infected and non-infected trees, and characterise the differential expression pattern of vsiRNAs and miRNAs targeting the lignin biosynthetic pathway. The results confirmed that neither the symptoms nor the gene-expression changes in the ARWV2-infected trees can be directly correlated with the presence of the virus, which can explain its frequent latent presence. Its variable concentration, sequence, and the mixed-infection status of the trees, make difficult its reliable diagnostics, which, although it would be highly needed, could be achieved as a result of further research.
Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
Project description:Metagenome sequencing All specimens were collected and immediately stored in a -80 freezer. All BALF samples were subjected to MS. DNA was extracted from BALF using the TIANamp Micro DNA kit (DP316, Tiangen Biotech). DNA libraries were constructed with the end-repair method and then sequenced on the BGI Sequencer platform (BGI Genomics, Shenzhen, China). Bioinformatic pipeline analysis Low-quality and short (<35 bp) reads were removed from raw data using fastp [10]. Remaining reads were mapped to the human reference genome (hg19) using the Burrows-Wheeler method to remove sequences of human origin. Filtered reads were classified with RefSeq, downloaded from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/).
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.