Genome and transcriptome Saxifraga stolonifera

Saxifraga stolonifera is a shade-tolerant species with significant ornamental and medicinal properties. Here, we present for the first time a chromosome-level draft genome for S. stolonifera. The genome assembly was 2.01 Gb, with 2,139 contigs and a contig N50 of 3,535,068 bp, which was ordered into 18 pseudochromosomes based on Hi-C analysis. Morphological, physiological, and transcriptome data were then used to study the underlying formation mechanism of the purple-variegated type. The structural basis of the purple-variegated type was mainly due to the uneven distribution of anthocyanins in the palisade tissue cells. The purple-variegated type was more sensitive to light than the green leaf type under the same light conditions. Under relatively high-light conditions, the expression of photosynthesis-related genes (FD3, LIL3:1, TKL2, PsbX, and CRR7) and flavonoid synthesis-related genes (PAL, C4H, 4CL, CHS, F3H, ANS, and CYP75A) was suppressed. Meanwhile, the expression of photoprotection-related genes (GLDP2, HCEF1, CP12, OHP2, and RbcX) and anthocyanidin 3-O-glucosyltransferase (SS_010223_BZ1) gene was up-regulated. The accumulation of anthocyanins in the purple-variegated type was mainly associated with the high expression of anthocyanidin 3-O-glucosyltransferase (SS_010223_BZ1). This study provides a new high-quality S. stolonifera genome and insights into the molecular mechanism underlying the formation of the purple-variegated types. Our findings have implications for genetic improvements of S. stolonifera, which would promote the understanding of how the pigment-type variegation originates and evolves.