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

Yong Shao, Xiao-Bo Wang, Jin-Jin Zhang, Ming-Li Li, Shou-Song Wu, Xi-Yao Ma, Xue Wang, Hui-Fang Zhao, Yuan Li, Helen He Zhu, David M. Irwin, Wang De-Peng, Guo-Jie Zhang (), Jue Ruan () and Dong-Dong Wu ()
Additional contact information
Yong Shao: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Xiao-Bo Wang: Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences
Jin-Jin Zhang: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Ming-Li Li: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Shou-Song Wu: Guanglong Earthworm Breeding Institute
Xi-Yao Ma: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Xue Wang: State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University
Hui-Fang Zhao: State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University
Yuan Li: Nextomics Biosciences Institute
Helen He Zhu: State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University
David M. Irwin: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Wang De-Peng: Nextomics Biosciences Institute
Guo-Jie Zhang: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Jue Ruan: Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences
Dong-Dong Wu: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences

Nature Communications, 2020, vol. 11, issue 1, 1-15

Abstract: 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 RNA-sequencing provides insight into the regenerative process at a cellular level and finds that the largest proportion of cells present during regeneration are stem cells.

Date: 2020
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DOI: 10.1038/s41467-020-16454-8

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