Genome and single-cell RNA-sequencing of the earthworm Eisenia andrei identifies cellular mechanisms underlying regeneration

Abstract

The earthworm is particularly fascinating to biologists because of its strong regenerative capacity. However, many aspects of its regeneration in nature remain elusive. Here we report chromosome-level genome, large-scale transcriptome and single-cell RNA-sequencing data during earthworm (Eisenia andrei) regeneration. We observe expansion of LINE2 transposable elements and gene families functionally related to regeneration (for example, EGFR, epidermal growth factor receptor) particularly for genes exhibiting differential expression during earthworm regeneration. Temporal gene expression trajectories identify transcriptional regulatory factors that are potentially crucial for initiating cell proliferation and differentiation during regeneration. Furthermore, early growth response genes related to regeneration are transcriptionally activated in both the earthworm and planarian. Meanwhile, single-cell RNAsequencing provides insight into the regenerative process at a cellular level and finds that the largest proportion of cells present during regeneration are stem cells.

Resolving Transcriptional States and Predicting Lineages in the Annelid Capitella teleta Using Single-Cell RNAseq

“…As a result, we used stringent quality control metrics to screen out such doublets. Similar background noise and a considerable amount of cell-free RNA can be detected in another 10X dataset obtained from the blastema of the headregenerating adult earthworm Eisenia andrei although clustering analysis was able to generate 12 discrete clusters, the majority of which appeared to be undifferentiated stem cells (Shao et al, 2020). Our second attempt with more careful quantification of cells failed to yield enough cDNA to create high-quality libraries for sequencing probably because of low RNA content in C. teleta cells.…”

Amynthas corticis genome reveals molecular mechanisms behind global distribution

“…17 ), and homeostatic process (Supplementary Fig. 18 ) in the genome A. corticis compared to those in the genome of Eisenia fetida 34 or Eisenia andrei 46 (Supplementary data file 7 ).…”

de novo transcriptome profile of two earthworms Lampito mauritii and Drawida calebi during regeneration

“…During regeneration of tail in both DE_RE and LM_RE samples, Wnt-signaling components encoding Wnt1, Dishevelled , transcription factors hox4, lox2, post2 were up-regulated along with induction of transcription of early growth response genes. Besides, expression of genes such as slit known for ventral surface formation, netrin gene for axon guidance and cell migration during development of regenerated tissue observed in planarians and earthworm Eisenia andrei were also found to be similarly upregulated in both DE_RE and LM_RE samples [ 4 , 20 ]. In both DC_RE and LM_RE samples, up-regulation of gene run was observed which promotes gut formation in Caenorhabditis elegans and heterogeneity in neoblasts near wounds in planarians and earthworm, Eisenia andrei [ 4 , 20 , 21 ].…”

“…Comparison of differential expression of genes between intact and regenerated samples show up-regulation of specific genes meant for promoting regeneration and immunity. In DC_RE samples, there was up-regulation of Na,K-ATPase activity that plays an important role in regulating both the structure and function of polarized epithelial cells during regeneration in newts, planarians [ 13 , 20 ]. There was up-regulation of notch protein expression to carry out cell-cell signaling needed for self renewal in regenerated tissue [ 22 ].…”