Genomes shed light on the evolution of Begonia, a mega-diverse genus

DATA AVAILABILTY : All of the raw sequence data including whole-genome sequencing and transcriptome have been deposited in China National GeneBank Sequence Archive (CNSA) database (https://db.cngb. org/cnsa) under accession number CNP0001056 and National Center for Biotechnology Information (NCBI) under accession number PRJNA791490. The assemblies, gene sequences and annotation data are available at the CNSA database with accession nos. CNA0013973, CNA0013974, CNA0013975 and CNA0013976 for B. darthvaderiana, B. loranthoides, B. masoniana and B. peltatifolia, respectively.Clarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with c. 2000 species, most of which are shade-adapted. Here, we present chromosome-scale genome assemblies for four species of Begonia (B. loranthoides, B. masoniana, B. darthvaderiana and B. peltatifolia), and whole genome shotgun data for an additional 74 Begonia representatives to investigate lineage evolution and shade adaptation of the genus. The four genome assemblies range in size from 331.75 Mb (B. peltatifolia) to 799.83 Mb (B. masoniana), and harbor 22 059–23 444 protein-coding genes. Synteny analysis revealed a lineage-specific whole-genome duplication (WGD) that occurred just before the diversification of Begonia. Functional enrichment of gene families retained after WGD highlights the significance of modified carbohydrate metabolism and photosynthesis possibly linked to shade adaptation in the genus, which is further supported by expansions of gene families involved in light perception and harvesting. Phylogenomic reconstructions and genomics studies indicate that genomic introgression has also played a role in the evolution of Begonia. Overall, this study provides valuable genomic resources for Begonia and suggests potential drivers underlying the diversity and adaptive evolution of this mega-diverse clade.The National Key R&D Program of China, the Shenzhen Municipal Government of China, the Shenzhen Urban Administration, the Fairy Lake Botanical Garden, the Public Welfare Forestry Industry Project of State Forestry Administration of China, the National Natural Science Foundation of China, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program and from Ghent University (Methusalem funding).https://nph.onlinelibrary.wiley.com/journal/14698137am2023BiochemistryGeneticsMicrobiology and Plant Patholog