Species-specific transcriptomic network inference of interspecies interactions

A cyanobacterium, Thermosynechococcus elongatus BP1, was cultured with a heterotroph, Meiothermus ruber strain A, under a variety of conditions. A gene co-expression approach was used to infer a network of T. elongatus and M. ruber genes, with a focus on those genes from different species that were co-expressed, highlighting potential points of coordination and interaction. Overall design: Both species were co-cultured together under 20 different culturing conditions, RNA-seq data was collected for each condition and combined with previously existing RNA-seq data. CLR was then used to infer a network of co-expressed genes.