Large scale changes in the transcriptome of Eisenia fetida during regeneration

Abstract

Earthworms show a wide spectrum of regenerative potential with certain species like Eisenia fetida capable of regenerating more than two-thirds of their body while other closely related species, such as Paranais litoralis seem to have lost this ability. Earthworms belong to the phylum Annelida, in which the genomes of the marine oligochaete Capitella telata and the freshwater leech Helobdella robusta have been sequenced and studied. Herein, we report the transcriptomic changes in Eisenia fetida (Indian isolate) during regeneration. Following injury, E. fetida regenerates the posterior segments in a time spanning several weeks. We analyzed gene expression changes both in the newly regenerating cells and in the adjacent tissue, at early (15days post amputation), intermediate (20days post amputation) and late (30 days post amputation) by RNAseq based de novo assembly and comparison of transcriptomes. We also generated a draft genome sequence of this terrestrial red worm using short reads and mate-pair reads. An in-depth analysis of the miRNome of the worm showed that many miRNA gene families have undergone extensive duplications. Sox4, a master regulator of TGF-beta mediated epithelial-mesenchymal transition was induced in the newly regenerated tissue. Genes for several proteins such as sialidases and neurotrophins were identified amongst the differentially expressed transcripts. The regeneration of the ventral nerve cord was also accompanied by the induction of nerve growth factor and neurofilament genes. We identified 315 novel differentially expressed transcripts in the transcriptome, that have no homolog in any other species. Surprisingly, 82% of these novel differentially expressed transcripts showed poor potential for coding proteins, suggesting that novel ncRNAs may play a critical role in regeneration of earthworm.

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

“…Phenotypic and transcriptomic changes during regeneration. Some studies have documented transcriptomic and some phenotypic changes of posterior regeneration in the earthworms 15,19 , but very few researches are focused on the anterior regeneration 13 , particularly for E. andrei. Therefore, in the present study, we focused on the anterior regeneration in the earthworm E. andrei.…”

“…The evolution of genome sequence only tells a part of the story of regeneration 15,16 ; integrating the transcriptional regulation of genes will help to investigate the mechanisms underlying regeneration of earthworms 11,15,57 . For example, the changes of gene expression in a series of long time scale post-amputation (i.e., 15d, 20d and 30d) have been investigated in E. fetida regeneration 15 . However, the molecular regulation during early phases of anterior regeneration still remains largely unclear in the earthworm.…”

“…In Annelida, only three whole genomes, a marine polychaete (Capitella teleta), a freshwater leech (Helobdella robusta) and Eisenia fetida, have been sequenced [14][15][16] . To date, our knowledge and understanding of regeneration in earthworms has been limited by this lack of high-quality genomes, which have severely hindered our exploration of the genetic mechanisms underlying regeneration in earthworms.…”

High-quality genome assembly of Metaphire vulgaris

“…And the annotation study were conducted by Paul et al (2018), although the quality of the assembled genome sequences was not of a sufficient quality for downstream analyses (N50 = 1.85 Kb). Bhambri et al (2018) sequenced a different strain of E. fetida and conducted genome-wide analyses and transcriptome studies. This study also failed to produce a genome assembly sufficient for accurate gene annotation (N50 = 9.31 Kb).…”

The genomes of invasive coral Tubastraea spp. (Dendrophylliidae) as tool for the development of biotechnological solutions

“…A Hemerythrin-like protein was found expressed only in the regeneration process, suggesting that it is a "regeneration-specific" gene. A few studies have found genes related to differentiation and regeneration in hydra and salamander [6][7][8][9] that were up-regulated in the sea anemone N. vectensis during the regeneration process.…”