Abstract

Summary 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.

Highlights

  • The following Supporting Information is available for this article: Methods S1: Supplemental methods Cytology 10×Genomics ChromiumTM Genome library preparation Hi-C library preparation SMART library preparation Raw data processing and estimation of genome size Genome assembly Assessment of assembly completeness Genome annotation Genome evolution Principal component analysis (PCA) analysis of transposable elements (TEs) diversity Plastome assembly Genetic variation and admixture pattern Identification of orthologs of the light regulatory network Transcriptome analysis of light/dark-responsive genes

  • Cytology Young root tips of the four Begonia species were collected at 8:00~10am, immediately pretreated for 4 hr with 0.1% colchicine solution at 4°C, and fixed overnight in ethanol: acetic acid (3:1) at 4°C

  • The features of predicted genes for four Begonia species, including number of genes, exon per gene, average length of mRNA, coding sequence (CDS), exon, intron, were compared with those of other genomes whose gene sets were used for homology-based method (Table S5)

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Summary

Methods

The features of predicted genes for four Begonia species, including number of genes, exon per gene, average length of mRNA, CDS, exon, intron, were compared with those of other genomes whose gene sets were used for homology-based method (Table S5). Considering good presentation of BUSCOs in genome assembly and gene set (Table S4), we inferred that they came from genes associated with Begonia specific features not shared by genes used in homology-based annotation. For a given gene list, such as the B. loranthoides specific genes or conserved genes between B. loranthoides and other three Begonia species (B. masoniana, B. darthvaderiana and B. peltatifolia) that were used for GO enrichment analysis: the given gene list was carried out based on the algorithm implemented in GOstat, with the whole annotated gene set as the background. Gene expression levels were calculated as fragments-per-kilobase-of-transcript-per-million-fragments-mapped (FPKM)

Genome Size
Total Unmapped Reads
BBE Protein kinase domain Dehydrin
Findings
ACBP MATE
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