Cargando…
Large scale changes in the transcriptome of Eisenia fetida during regeneration
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 w...
Autores principales: | , , , , , , , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6160089/ https://www.ncbi.nlm.nih.gov/pubmed/30260966 http://dx.doi.org/10.1371/journal.pone.0204234 |
_version_ | 1783358696663810048 |
---|---|
author | Bhambri, Aksheev Dhaunta, Neeraj Patel, Surendra Singh Hardikar, Mitali Bhatt, Abhishek Srikakulam, Nagesh Shridhar, Shruti Vellarikkal, Shamsudheen Pandey, Rajesh Jayarajan, Rijith Verma, Ankit Kumar, Vikram Gautam, Pradeep Khanna, Yukti Khan, Jameel Ahmed Fromm, Bastian Peterson, Kevin J. Scaria, Vinod Sivasubbu, Sridhar Pillai, Beena |
author_facet | Bhambri, Aksheev Dhaunta, Neeraj Patel, Surendra Singh Hardikar, Mitali Bhatt, Abhishek Srikakulam, Nagesh Shridhar, Shruti Vellarikkal, Shamsudheen Pandey, Rajesh Jayarajan, Rijith Verma, Ankit Kumar, Vikram Gautam, Pradeep Khanna, Yukti Khan, Jameel Ahmed Fromm, Bastian Peterson, Kevin J. Scaria, Vinod Sivasubbu, Sridhar Pillai, Beena |
author_sort | Bhambri, Aksheev |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6160089 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-61600892018-10-19 Large scale changes in the transcriptome of Eisenia fetida during regeneration Bhambri, Aksheev Dhaunta, Neeraj Patel, Surendra Singh Hardikar, Mitali Bhatt, Abhishek Srikakulam, Nagesh Shridhar, Shruti Vellarikkal, Shamsudheen Pandey, Rajesh Jayarajan, Rijith Verma, Ankit Kumar, Vikram Gautam, Pradeep Khanna, Yukti Khan, Jameel Ahmed Fromm, Bastian Peterson, Kevin J. Scaria, Vinod Sivasubbu, Sridhar Pillai, Beena PLoS One Research Article 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. Public Library of Science 2018-09-27 /pmc/articles/PMC6160089/ /pubmed/30260966 http://dx.doi.org/10.1371/journal.pone.0204234 Text en © 2018 Bhambri et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Bhambri, Aksheev Dhaunta, Neeraj Patel, Surendra Singh Hardikar, Mitali Bhatt, Abhishek Srikakulam, Nagesh Shridhar, Shruti Vellarikkal, Shamsudheen Pandey, Rajesh Jayarajan, Rijith Verma, Ankit Kumar, Vikram Gautam, Pradeep Khanna, Yukti Khan, Jameel Ahmed Fromm, Bastian Peterson, Kevin J. Scaria, Vinod Sivasubbu, Sridhar Pillai, Beena Large scale changes in the transcriptome of Eisenia fetida during regeneration |
title | Large scale changes in the transcriptome of Eisenia fetida during regeneration |
title_full | Large scale changes in the transcriptome of Eisenia fetida during regeneration |
title_fullStr | Large scale changes in the transcriptome of Eisenia fetida during regeneration |
title_full_unstemmed | Large scale changes in the transcriptome of Eisenia fetida during regeneration |
title_short | Large scale changes in the transcriptome of Eisenia fetida during regeneration |
title_sort | large scale changes in the transcriptome of eisenia fetida during regeneration |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6160089/ https://www.ncbi.nlm.nih.gov/pubmed/30260966 http://dx.doi.org/10.1371/journal.pone.0204234 |
work_keys_str_mv | AT bhambriaksheev largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT dhauntaneeraj largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT patelsurendrasingh largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT hardikarmitali largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT bhattabhishek largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT srikakulamnagesh largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT shridharshruti largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT vellarikkalshamsudheen largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT pandeyrajesh largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT jayarajanrijith largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT vermaankit largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT kumarvikram largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT gautampradeep largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT khannayukti largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT khanjameelahmed largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT frommbastian largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT petersonkevinj largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT scariavinod largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT sivasubbusridhar largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration AT pillaibeena largescalechangesinthetranscriptomeofeiseniafetidaduringregeneration |