Construction of comprehensive and comparative multi-omics database for animal evo-devo (EDomics) and cross-species analysis
Penghui Liu#, Jiankai Wei#, Fuyun Liu#, Yuli Li*, Shi Wang*, Bo Dong*
Abstract: Despite the rapid accumulation of omics data provides unprecedented opportunities to answer many interesting but unresolved evo-devo questions, the access and utilization of these resources are hindered by challenges particularly in non-model animals. Here, we established the first comparative multi-omics database for animal evo-devo (EDomics, http://edomics.qnlm.ac) containing comprehensive genomes, bulk transcriptomes, and single-cell data across 40 representative species, many of which are generally used as model organisms for animal evo-devo study. EDomics provides a systematic view of genomic/transcriptomic information from various aspects, including genome assembly statistics, gene features and families, transcription factors, transposable elements, and gene expressional profiles/networks. It also exhibits spatiotemporal gene expression profiles at a single-cell level, such as cell atlas, cell markers, and spatial-map information. Moreover, we conducted cross-species analysis at genomic, transcriptomic and single-cell transcriptomic levels. 34 species were analyzed for the gene family expansion/contraction and pan-gene set. In the macrosynteny analysis module, the genomes of 40 species are analyzed by comparing with bilaterian ALGs represented by three ancient animal genomes. Comparative transcriptomic analysis was also displayed. The developmental correlation provided analysis of developmental transcriptome correlations between two species. By comparing the single cell RNA sequencing data of 9 species with 84 major cell types, we demonstrate the conservation and divergence of cell types. EDomics represents a comprehensive and comparative multi-omics platform for animal evo-devo community to decipher the whole history of developmental evolution across the tree of life. Our results provide a useful tool for the evolutionary development of important species at the molecular and cellular levels respectively.