Molecular and FISH analysis of 45S rDNA on BAC molecule of Saccharina japonica

IGS is abundant in polymorphism, which is widely used in the analysis of intraspecific genetic diversity and phylogenetic relationships among geographical populations. In this study, the 45S rDNA repeat unit of Saccharina japonica was obtained for the first time by BAC clone sequencing. The total length of the 45S rDNA repeat unit of S. japonica was 8 995 bp, including 5 420 bp of 18S-5.8S–25S rDNA, and 3 575 bp of IGS (Intergenic Spacer), with the GC content of 51.4 %. The IGS was composed of a 465 bp of 3′-outer transcribed spacer (ETS), an 874 bp 5′-ETS, and a 2 236 bp non-transcribed spacer (NTS), with the GC content of 50.1 %. Fiber-FISH (fiber-fluorescence in situ hybridization) analysis of the distribution of 45S rDNA repeat units on the bacterial artificial chromosome illustrated that each fiber had at least five continuously moniliform hybridization signal points. This study provided a new candidate molecular marker for detecting intraspecific polymorphisms of S. japonica. In addition, the successful fiber-FISH analysis of the 45S rDNA on BAC molecule would contribute to the construction of the physical map and map-based cloning of this kelp.