HEMU: an integrated Andropogoneae comparative genomics database and analysis platform
The Andropogoneae tribe encompasses various crops with substantial agronomic value such as maize (Zea mays) and sorghum (Sorghum bicolor). Despite the prevalence in released multi-omics data resources, there is a dearth of comprehensive, tribe-level integration and multi-layer omics dataset platform within the tribe, assisting inter- and intra-species comparative analysis from a multi-omics aspect. Here, we first collected a comprehensive atlas of multi-omics datasets within the tribe, including 75 genomes from 20 unique species, transcriptomes from 4,747 samples comprising more than 50 tissues, epigenome data from 90 ChIP-seq samples and 39 ATAC-seq samples, as well as transposable element (TE) annotation for all the genomes. Then, an integrated database and analysis platform, HEMU (http://shijunpenglab.com/HEMUdb/), was constructed. HEMU comprises six sophisticated toolkits, namely genome analysis toolkit, transcriptome-derived analysis toolkit, gene family analysis toolkit, transposable element (TE) analysis toolkit, epigenome analysis toolkit and miscellaneous analysis toolkit, facilitating convenient inter- and intra-species comparative analysis taking advantage of the multi-omics data. Three case studies substantiated the capability of HEMU in conducting gene-centered analysis, transcriptome derived analysis and gene family analysis from a both multi-omics and comparative perspective. In a nutshell, HEMU lowers the barrier of traditional code-based analysis workflow, providing novel insights into modern genetic breeding in the tribe Andropogoneae.