Intragenomic variation of rDNA internal transcribed spacers in the endemic Baikal sponge Lubomirskia baikalensis (Pallas, 1776) (Spongillida, Lubomirskiidae): Implications for Porifera barcoding

Abstract

Baikal endemic sponges are a species group for which species identification is difficult and the taxonomy is insufficiently developed. The rDNA ITS (internal transcribed spacers) are practical molecular markers for sponges. However, intragenomic polymorphism of the ITS spacers has recently been detected in many organisms including marine and freshwater sponges. We for the first time demonstrate intragenomic polymorphism of the ITS region in the sponge family Lubomirskiidae. We identified 27 new ITS1 and ITS2 haplotypes. The level of intragenomic polymorphism of the ITS1 and ITS2 regions in Lubomirskia baikalensis was 0.1–2.0%, which overlaps with the intraspecific polymorphism of L. baikalensis and to the interspecific polymorphism within Lubomirskiidae. Thus, the detected level of intragenomic polymorphism of Lubomirskiidae suggests species identification of Baikal sponges using ITS sequences would be difficult. The reasons for the lack of concerted evolution of the ITS spacers in Lubomirskiidae may be hybridization or insufficient divergence time. Our work contributes to the development of sponge barcoding markers.