A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily
attainable proxy catalog of protein-coding genes when genome assembly is unnecessary …

Alternaria is an important fungus to study due to their different life style from saprophytes to
endophytes and a very successful fungal pathogen that causes diseases to a number of …

Even though automated functional annotation of genes represents a fundamental step in
most genomic and metagenomic workflows, it remains challenging at large scales. Here, we …

Mutualistic interactions between host plants and their microbiota have the potential to
provide disease resistance. Most research has focused on the rhizosphere, but it is unclear …

Modern tomatoes have narrow genetic diversity limiting their improvement potential. We
present a tomato pan-genome constructed using genome sequences of 725 …

Orthology assignment is ideally suited for functional inference. However, because predicting
orthology is computationally intensive at large scale, and most pipelines are relatively …

Abstract InterPro (http://www. ebi. ac. uk/interpro/) is a freely available database used to
classify protein sequences into families and to predict the presence of important domains …

The pathogen–host interactions database (PHI-base) is available at www. phi-base. org. PHI-
base contains expertly curated molecular and biological information on genes proven to …

Antimicrobial peptides (AMPs) play a key role in the innate immunity, the first line of defense
against bacteria, fungi, and viruses. AMPs are small molecules, ranging from 10 to 100 …

Plant‐pathogenic fungi secrete effector proteins to facilitate infection. We describe extensive
improvements to EffectorP, the first machine learning classifier for fungal effector prediction …