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

Abstract

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.

Species Delimitation of the Eisenia nordenskioldi Complex (Oligochaeta, Lumbricidae) Using Transcriptomic Data

“…Genetic lineage is an established term among earthworm scientists (King et al, 2008 ; Martinsson and Erséus, 2017 ; Marchán et al, 2018 ) that refers to intraspecific clades that are highly genetically diverged from other clades within the species. At least 15 distinct lineages are currently recognized within E. nordenskioldi , and deep genetic divergence between some of them were verified by the phylogenomic approach (Shekhovtsov et al, 2019 ). On the whole, the gathered evidence implies that this taxon encompasses several distinct species.…”

Генетическое разнообразие и антиоксидантный потенциал сортов перца сладкого (Capsicum annuum L.) сибирской селекции

“…Большинство изученных видов этой группы состоит из нескольких (от двух до десяти) филогенетических линий, различающихся 5-20 % нуклеотидных замен в митохондриальной ДНК (King et al, 2008;Porco et al, 2013;Shekhovtsov et al, 2016). При этом степень различий между ядерными геномами этих линий, как правило, неизвестна, хотя имеющиеся данные свидетельствуют в пользу того, что их можно считать отдельными видами (Shekhovtsov et al, 2019(Shekhovtsov et al, , 2020. Морфологические различия между филогенетическими линиями в некоторых случаях также наблюдаются (Dupont et al, 2011).…”

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“…Genetic lineage is an established term among earthworm scientists (King et al, 2008;Martinsson and Erséus, 2017;Marchán et al, 2018) that refers to intraspecific clades that are highly genetically diverged from other clades within the species. At least 15 distinct lineages are currently recognized within E. nordenskioldi, and deep genetic divergence between some of them were verified by the phylogenomic approach (Shekhovtsov et al, 2019). On the whole, the gathered evidence implies that this taxon encompasses several distinct species.…”

“…For transcriptomic analysis, live earthworm individuals were collected in 2016-2019 (see Table 1). RNA was extracted by the Trizol method as described in Shekhovtsov et al (2019). For large worms, RNA was extracted from a section of the body containing the clitellum; for small individuals, the whole body was used.…”

“…In this study, we performed low-depth Illumina singe-end transcriptomes for 12 specimens of E. nordenskioldi and outgroup species, and combined this data with five Ion Torrent transcriptomes from our earlier study (Shekhovtsov et al, 2019). The final dataset contained transcriptomes for 12 E. nordenskioldi lineages, as well as five outgroup species of the genus Eisenia.…”