Muscari commutatum genome sequences reveal genetic basis of flower pigmentation

Flower colour is an important component of floral signaling, yet the genetic basis of naturally occurring colour variation remains poorly understood in many non-model plant groups. Here, we compare genome sequences of a normally pigmented and a largely unpigmented individual of Muscari commutatum, a species typically characterized by very dark violet flowers. Both assemblies were approximately 3.5 Gbp in size, with contig N50 values exceeding 130 Mbp and BUSCO completeness of about 99%. Most structural genes of the flavonoid biosynthesis and the corresponding transcriptional regulators were identified in both plants. Strikingly, no flavanone 3-hydroxylase (F3H) gene was detected in the genome sequence of the unpigmented plant, and additional manual searches provided no evidence for a bona fide F3H copy. Comparison of the two genome sequences revealed a lack of local synteny around the F3H locus of the anthocyanin-pigmented plant, suggesting that F3H might have been lost in the unpigmented plant in association with a genomic rearrangement.