LGRPv2: A high-value platform for the advancement of Fabaceae genomics.

Fabaceae, as one of the most diverse angiosperm families, plays a crucial role in maintaining global ecosystems and advancing human civilization. With the rapid accumulation of legume genomes, we developed LGRPv2 (https://fabaceae.cgrpoee.top), an updated version of the Legume Genomics Research Platform. LGRPv2 integrates 414 genomes, covering all published legume genomes and containing our latest deciphered Tamarindus indica genome from early-diverging legumes and three outgroup genomes (Euscaphis pleiosperma, Vitis vinifera, and Platycodon tenuifolia). It features user-friendly interactive interfaces for studying functional annotations, gene duplications, regulatory proteins, N-methyladenosine modifications, and transposable elements. For easily exploring genome evolution associated with polyploidizations, we incorporated DotView, SynView, and DecoBrowse with genome synteny (GenS) to establish a central GenS database for legumes. Specialized web services for ancestral legume genomes enable scientists to analyse the role of paleogenome reshuffling in shaping genomic diversity. The platform offers 184 511 synteny-based orthogroups and 1 086 836 genes from 139 families, and tools to explore agronomic trait origins. LGRPv2 integrates 40 550 transcriptomes, 5091 pan-genomes, 12 136 metabolomes, species encyclopaedias, ecological resources, and literature for exploring legume genomics comprehensively. Furthermore, LGRPv2 implemented 58 window-based operating tools (31 new) to efficiently support new mining, especially in advancing assembling pipelines for polyploidization identification, ancestral genome reconstruction, and gene family evolution. Finally, we provided detailed usage guides and community support to empower LGRPv2 with user-friendly and continuously updated features.