FungiExp: A Comprehensive Platform For Exploring Fungal Gene Expression and Alternative Splicing Based On 35,821 RNA-Seq Experiments From 220 Fungi

Background: RNA-seq has become a standard tool in biology and has produced large and diverse transcriptomic datasets for users to explore fungal expression regulation. Fungal alternative splicing, which is attracting increasing attention because of evolutionary adaptations to changing external conditions has not been thoroughly investigated in previous studies, unlike that of animals and plants. However, the analyses of RNA-seq datasets are made difficult by the heterogeneity of study design and complex bioinformatics approaches. Comprehensive analyses of these published datasets should contribute new insights into fungal expression regulation.Results: We have developed a web-based platform called FungiExp hosting fungal gene expression levels and alternative splicing profiles in 35,821 curated RNA-seq experiments from 220 species. It allows users to perform retrieval via diverse terms and sequence similarity. Moreover, users can customize experimental groups to perform differential and specific expression analyses. The wide range of data visualization is an additional important feature that should help users intuitively understand retrieval and analysis results.Conclusions: With its uniform data processing, easy data accessibility, convenient retrieval, and analysis functions, FungiExp is a valuable resource and tool that allows users to (re)use published RNA-seq datasets. It is accessible at http://bioinfo.njau.edu.cn/fungiExp.

Availability of carbon and nitrogen in soil affects Metarhizium robertsii root colonization and transfer of insect-derived nitrogen

ABSTRACT The endophytic, insect pathogenic fungus, Metarhizium, exchanges insect-derived nitrogen for photosynthate as part of a symbiotic association similar to well-known mycorrhizal relationships. However, little is known about this nitrogen transfer in soils where there is an abundance of nitrogen and/or carbon. Here, we applied D-glucose and ammonium nitrate to soil to examine the effect on root colonization and transfer of labelled nitrogen (15N) from an insect (injected with 15N-ammonium sulfate) to Metarhizium robertsii, into leaves of the common bean, Phaseolus vulgaris, over the course of 28 days. Application of exogenous carbon and/or nitrogen to soils significantly reduced detectable 15N in plant leaves. Metarhizium root colonization, quantified with real-time PCR, revealed colonization persisted under all conditions but was significantly greater on roots in soil supplemented with glucose and significantly lower in soil supplemented with ammonium nitrate. Fungal gene expression analysis revealed differential expression of sugar and nitrogen transporters (mrt, st3, nrr1, nit1, mep2) when Metarhizium was grown in pure broth culture or in co-culture with plant roots under various carbon and nitrogen conditions. The observation that Metarhizium maintained root colonization in the absence of nitrogen transfer, and without evidence of plant harm, is intriguing and indicates additional benefits with ecological importance.