NEW INSIGHTS INTO THE PHYLOGENY AND SPECIATION OF KUMQUAT ( FORTUNELLA SPP.) BASED ON CHLOROPLAST SNP, NUCLEAR SSR AND WHOLE-GENOME SEQUENCING

● Fortunella genus consists of two populations: cultivated kumquat and wild Hong Kong kumquat. ● Artificial selection might involve in the origin of cultivated Fortunella species. ● A hypothesis for the differentiation and speciation of Fortunella species is proposed. Kumquat ( Fortunella spp.) is a fruit and ornamental crop worldwide due to the palatable taste and high ornamental value of its fruit. Although Fortunella is classified into the economically important true citrus fruit tree group together with Citrus and Poncirus, few studies have been focused on its evolutionary scenario. In this study, analysis of five chloroplast loci and 47 nuclear microsatellites (nSSR) loci from 38 kumquat and 10 citrus accessions revealed the independent phylogeny of Fortunella among citrus taxa, and that Fortunella mainly comprises two populations: CUL, cultivated Fortunella spp. ( F. margarita, F. crassifolia and F. japonica); and HK, wild Hong Kong kumquat ( Fortunella hindsii). Genomic analysis based on whole-genome SNPs indicated that the allele frequency of both pupations deviated from the neutral selection model, suggesting directional selection was a force driving their evolutions. CUL exhibited lower genomic diversity and higher linkage strength than HK, suggesting artificial selection involved in its origin. A high level of genetic differentiation ( Fst = 0.364) was detected and obviously asynchronous demographic changes were observed between CUL and HK. Based on these results, a new hypothesis for the speciation of Fortunella is proposed.