#36 · Genomics

Multi-omics and genome resources map candidate genes in plant and fungal systems

The dominant thread is computational integration of heterogeneous omics data to prioritize candidate genes and interactions in plant and fungal systems. The Taxus study benchmarks 35 RNA-seq preprocessing pipelines (six normalizations, five batch-effect corrections) across 45 samples and nominates ABC transporters as candidates for taxane export. MagNet constructs a genome-wide protein-protein interaction network for Magnaporthe oryzae by combining interolog, co-expression, and domain-domain evidence. The Phyllanthus niruri chromosome-scale genome reports 19,254 annotated genes and 305 candidate phyllanthin biosynthesis genes, providing a putative biosynthetic framework. The Colletotrichum sublineola study is more experimental, using MPLEx-based integrative proteomics and metabolomics to examine growth under different PDA media strengths. Several items report candidate lists and predicted networks rather than confirmed function, so the new contribution is largely methodological and resource-oriented.