Two telomere-to-telomere genome assemblies and comparative genomics reveal the conserved "toolkit" genes associated with sugar accumulation in Rubus genus
Here, we assembled two telomere-to-telomere reference genomes of the Rubus subgenus: Rubus hirsutus Thunb. 'Penglei' (XMM) and Rubus eustephanos Focke ex Diels 'Dahongpao' (DHP), which exhibit similar phenotypic traits, yet distinct sugar accumulation levels in ripe fruits, making them ideal comparative system to elucidate the "toolkit" genes and the molecular mechanisms underlying sugar accumulation in the Rubus genus. The XMM and DHP genomes exhibit close evolutionary relationships, diverging approximately 3.21 Mya. Comparative genomics identified extensive synteny, interspecific structural variations (SV), and presence/absence variation (PAV). Additionally, we identified a sugar transporter gene (MFS1), which is present in XMM but absent in DHP and act as a positive regulator for total soluble solids accumulation in Rubus. Combined analysis of the gene family expansion/contraction and transcriptome identified two conserved "toolkit" sugar transporter genes, STP13 and STP7, displayed distinct roles in sugar accumulation via transient expression assay in Rubus fruits.
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