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

BMC Evolutionary Biology
S V ShekhovtsovSergey E Peltek

Abstract

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. 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...Continue Reading

References

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Citations

Mar 1, 2019·BMC Evolutionary Biology·Yuriy L OrlovLeonid L Moroz
Mar 5, 2021·Vavilovskiĭ Zhurnal Genetiki I Selekt︠s︡ii·S V ShekhovtsovS E Peltek

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Methods Mentioned

BETA
nucleic acid extraction
chips
RNA-Seq
Chip

Software Mentioned

Ion Torrent
ProteinOrtho
HIT
MAFFT
TransDecoder
FastTreeMP
CD
PhyloTreePruner
RADseq
HMMER

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