Community transcriptomics, genomics and the problem of species co-occurrence

1. Genomic and transcriptomic information has been largely leveraged in ecological investigations of primarily model species and their relatives. The amount of infrastructure and financing necessary for such investigations has meant that analyses of assemblages full of non-model species were impossible. These barriers have rapidly eroded over the past few years to the point where community ecology will soon see a large influx of genomic and transcriptomic investigations. The hope is that such studies will greatly refine or even transform our inferences regarding the distribution and co-occurrence of plant species. 2. This special feature presents five studies that use cutting-edge 'omic concepts and approaches in assemblages of non-model species. All studies focus on the drivers of species co-occurrence. The work blends functional phylogenomic, differential gene expression and metagenomic approaches in observational and experimental frameworks. 3. Two studies demonstrate of functional phylogenomic approaches that can be used in conjunction with neighbourhood demographic models to understand the role of neighbouring heterospecific species on focal tree demography. Two additional papers demonstrate how genes are differentially expressed in different competitive contexts and how this is related to species coexistence. The final study uses a metabarcoding approach to document whether the incredible levels of soil fungal and tree biodiversity in the tropics are linked. 4. Synthesis. The articles presented in this special feature clearly demonstrate that 'omic toolkits can now be readily integrated into community ecology. While there are still many obstacles facing this integration, it seems clear that the amounts and types of data provided by such approaches will lead to a rapid transformation in how we study plant communities.