Bioinformatic methods for the analysis of high-throughput RNA sequencing in arbuscular mycorrhizal fungi

F Venice, A Salvioli di Fossalunga… - … Mycorrhizal Fungi: Methods …, 2020 - Springer
RNA-seq is a powerful method for transcriptome profiling that allows the detection of total
RNA present in a single cell, tissues, or organs. mRNA-seq is focused on protein-coding …

Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi

D Beaudet, ECH Chen, S Mathieu, G Yildirir… - DNA …, 2018 - academic.oup.com
Arbuscular mycorrhizal fungi (AMF) are a group of soil microorganisms that establish
symbioses with the vast majority of land plants. To date, generation of AMF coding …

Utility of large subunit for environmental sequencing of arbuscular mycorrhizal fungi: a new reference database and pipeline.

CS Delavaux, SL Sturmer, MR Wagner… - New …, 2021 - search.ebscohost.com
Keywords: amplicon sequencing; bioinformatics; eDNA; Glomeromycota; large subunit EN
amplicon sequencing bioinformatics eDNA Glomeromycota large subunit 3048 3052 5 …

Fungal gene expression levels do not display a common mode of distribution

M Nowrousian - BMC Research Notes, 2013 - Springer
Background RNA-seq studies in metazoa have revealed a distinct, double-peaked (bimodal)
distribution of gene expression independent of species and cell type. However, two studies …

Barcoded NS31/AML2 primers for sequencing of arbuscular mycorrhizal communities in environmental samples

BST Morgan… - Applications in plant …, 2017 - Wiley Online Library
Premise of the study: Arbuscular mycorrhizal fungi (AMF) are globally important root
symbioses that enhance plant growth and nutrition and influence ecosystem structure and …

Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi

M Vasar, R Andreson, J Davison, T Jairus, M Moora… - Mycorrhiza, 2017 - Springer
The arrival of 454 sequencing represented a major breakthrough by allowing deeper
sequencing of environmental samples than was possible with existing Sanger approaches …

User‐friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences

M Vasar, J Davison, L Neuenkamp… - Molecular Ecology …, 2021 - Wiley Online Library
High‐throughput sequencing (HTS) of multiple organisms in parallel (metabarcoding) has
become a routine and cost‐effective method for the analysis of microbial communities in …

[PDF][PDF] Developing a bioinformatics pipeline gDAT to analyse arbuscular mycorrhizal fungal communities using sequence data from different marker regions

M Vasar - 2020 - core.ac.uk
Arbuscular mycorrhizal (AM) fungi (Phylum Mucoromycota, Subphylum Glomeromycotina,
Spatafora et al. 2016) are widespread soil microorganisms that are obligate symbionts of the …

Navigating the labyrinth: a guide to sequence‐based, community ecology of arbuscular mycorrhizal fungi

MM Hart, K Aleklett, PL Chagnon, C Egan… - New …, 2015 - Wiley Online Library
Data generated from next generation sequencing (NGS) will soon comprise the majority of
information about arbuscular mycorrhizal fungal (AMF) communities. Although these …

Widespread polycistronic transcripts in mushroom-forming fungi revealed by single-molecule long-read mRNA sequencing

SP Gordon, E Tseng, A Salamov, J Zhang, X Meng… - bioRxiv, 2014 - biorxiv.org
Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into
polycistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some …