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Background  Many earthworm species demonstrate significant cryptic diversity, with several highly diverged mitochondrial lineages found within most of the taxa studied to date. The status of differences between these lineages on the nuclear level is still unclear. Because of widespread polyploidy in earthworms, most studies were limited to two nuclear loci, the ribosomal and the histone clusters. Here we attempted to elucidate the status of a set of genetic lineages within  Eisenia nordenskioldi nordenskioldi , an earthworm species from Northern Asia with high intraspecific diversity. We performed RNA-seq on an IonTorrent platform for five specimens of this species belonging to five genetic lineages, as well as two outgroups from the family Lumbricidae, the congenetic  E. andrei , and  Lumbricus rubellus .    Results  We de novo assembled transcriptomes and constructed datasets of genes present in all seven specimens using broad (ProteinOrtho; 809 genes) and narrow (HaMStR; 203 genes) ortholog assignment. The majority of orthologs had identical amino acid sequences in all studied specimens, which we believe was due to strong bias towards the most conserved genes. However, for the rest of genes the differences among the lineages were lower than those between them and the congeneric  E. andrei . Both datasets yielded phylogenetic trees with the same topology.  E. n. nordenskioldi  was found to be monophyletic. The differences on the genetic level had no concordance with geography, implying complex history of dispersal.    Conclusions  We found that genetic lineages of  E. n. nordenskioldi  are genetically distinct on nuclear level and probably diverged long ago. Current data implies that they might even represent distinct species within the  E. nordenskioldi  species complex.    Electronic supplementary material  The online version of this article (10.1186/s12862-019-1370-y) contains supplementary material, which is available to authorized users.

Transcriptomic analysis confirms differences among nuclear genomes of cryptic earthworm lineages living in sympatry