Taxon-specific small RNA loci are widespread in eukaryotic genomes, yet their role in lineage-specificadaptation, phenotypic diversification, and speciation is poorly understood. Here, we report that aspeciation locus in monkeyflowers (Mimulus), YELLOW UPPER (YUP), contains an inverted repeat region that produces small interfering RNAs (siRNAs) in a phased pattern. Although the inverted repeat is derived from a partial duplication of a protein-coding gene that is not involved in flower pigmentation, one of the siRNAs targets and represses a master regulator of floral carotenoid pigmentation. YUP emerged with two protein-coding genes that control other aspects of flower coloration as a “superlocus in a subclade of Mimulus and has contributed to subsequent phenotypic diversification and pollinatormediated speciation in the descendant species.

Fig. 1. Flower color phenotypes of different genotypic combinations of YUP and PELAN. (A to G) The front view (left image) and dissected view (middle image) of the corollas of the three parental species [(A) to (C)] and various NILs [(D) to (G)]. The dissected view was produced by cutting the corolla along the junction between the two dorsal (upper) petals 1 day before anthesis. The white arrow in (A) indicates the yellow nectar guides (NG) of M. lewisii; the dashed line in (B) marks the boundary between the petal lobes (PL) and corolla tube (CT). Phase separation of pigment extracts from petal lobes of equal area are also shown (right image). Anthocyanins and carotenoids were separated into the upper and lower layer, respectively, following the protocol described in (25). The Mpar_DPKC/C homozygous NIL (F) accumulates more anthocyanins than the Mpar_DPKP/C heterozygous NIL (G) in the petal lobes because the PELANC allele is semidominant (21). Scale bars are 10 mm. (H) Genotypic combinations of YUP and PELAN and pigment compositions of the parental species and NILs shown in (A) to (G). Inter, intermediate. (I) The 70-kb candidate interval for YUP is part of the 337-kb introgressed fragment in the Mpar_DPKC/C NIL. Chr4, chromosome 4.

This result was published in Science with the title of “Taxon-specific, phased siRNAs underlie a speciation locus in monkeyflowers ".

The link below will guide you to the reading:
https://www.science.org/doi/epdf/10.1126/science.adf1323