FungiExp: a user-friendly database and analysis platform for exploring fungal gene expression and alternative splicing

Abstract

Summary Fungi form a large and heterogeneous group of eukaryotic organisms with diverse ecological niches. The high importance of fungi contrasts with our limited understanding of fungal lifestyle and adaptability to environment. Over the last decade, the high-throughput sequencing technology produced tremendous RNA-sequencing (RNA-seq) data. However, there is no comprehensive database for mycologists to conveniently explore fungal gene expression and alternative splicing. Here, we have developed FungiExp, an online database including 35,821 curated RNA-seq samples derived from 220 fungal species, together with gene expression and alternative splicing profiles. It allows users to query and visualize gene expression and alternative splicing in the collected RNA-seq samples. Furthermore, FungiExp contains several online analysis tools, such as differential/specific, co-expression network and cross-species gene expression conservation analysis. Through these tools, users can obtain new insights by re-analyzing public RNA-seq data or upload personal data to co-analyze with public RNA-seq data. Availability and implementation The FungiExp is freely available at https://bioinfo.njau.edu.cn/fungiExp. Supplementary information Supplementary data are available at Bioinformatics online.

Revealing Hidden Genes in Botrytis cinerea: New Insights into Genes Involved in the Biosynthesis of Secondary Metabolites

“…FungiDB, part of the EuPathDB platform, integrates diverse data types including genomic, transcriptomic, proteomic, and phenotypic information. It supports custom in silico analyses through advanced bioinformatics tools and a Galaxy-based workspace for comprehensive data analyses like RNA sequencing (RNA-Seq) and variant calling [ 45 , 46 , 47 ]. This integration enhances the utility of FungiDB for comparative genomics and evolutionary studies, complementing the resources provided by Ensembl Fungi [ 48 , 49 ].…”

Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs

“…To address these challenges, the development of unified platforms for cataloguing, curating, and retrieving AS isoforms and GE quantification data is important. In this context, multiple attempts to generate a unified platform for GE and AS have been published to the date [217][218][219][220][221][222]. The aim of such platforms is to provide researchers with a centralized resource for accessing comprehensive and high-quality data across different biological contexts and investigations.…”

“…This can allow researchers to better explore and analyze complex AS patterns and transcript expression dynamics. Advanced algorithms and computational tools are being implemented to enable a more comprehensive data analysis, allowing researchers to uncover novel insights into AS and transcript expression [217][218][219][220][221][222]. For instance, the PlantExp platform integrates plant transcript expression and AS profiles from 131,423 uniformly processed publicly available RNA-seq samples that belong to 85 plant species across 24 plant orders [219].…”

“…By integrating fragmented data, ensuring data quality and accessibility, and providing powerful analysis tools, such platforms empower researchers to explore the intricate relationship between AS and transcript expression. In addition, scientists can flexibly customize sample groups to re-analyze publicly available RNA-seq datasets and obtain new insights [217][218][219][220][221][222].…”

A comprehensive workflow for optimizing RNA-seq data analysis

“…Fungal diseases account for a significant proportion of plant diseases, estimated at 70%-80%, adversely affecting agricultural and forestry crop yields and quality [34]. With the development of high-throughput sequencing technologies, RNA-seq has become a common method for researchers studying fungal diseases [35]. Transcriptome analysis identifies disease resistance genes [36] and related pathways [37], providing a foundation for resistant breeding [38][39][40].…”