Achieving single-cell-resolution lineage tracing in zebrafish by continuous barcoding mutations during embryogenesis

Zhan Liu; Hui Zeng; Huimin Xiang; Shanjun Deng; Xionglei He

doi:10.1016/j.jgg.2024.04.004

Volume 51 Issue 9

Sep. 2024

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Article Navigation > Journal of Genetics and Genomics > 2024 > 51(9): 947-956

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Achieving single-cell-resolution lineage tracing in zebrafish by continuous barcoding mutations during embryogenesis

doi: 10.1016/j.jgg.2024.04.004

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China

Funds:

This work was supported by the National Key R&D Program of China (2021YFA1302500 and 2021YFA1302501) and the National Natural Science Foundation of China (32293190, 32293191, 31970570, and 32200492).

Received Date: 2024-03-03
Accepted Date: 2024-04-07
Rev Recd Date: 2024-04-03

Available Online: 2025-06-06

Publish Date: 2024-04-15

Abstract

Abstract

Unraveling the lineage relationships of all descendants from a zygote is fundamental to advancing our understanding of developmental and stem cell biology. However, existing cell barcoding technologies in zebrafish lack the resolution to capture the majority of cell divisions during embryogenesis. A recently developed method, a substitution mutation-aided lineage-tracing system (SMALT), successfully reconstructed high-resolution cell phylogenetic trees for Drosophila melanogaster. Here, we implement the SMALT system in zebrafish, recording a median of 14 substitution mutations on a one-kilobase-pair barcoding sequence for one-day post-fertilization embryos. Leveraging this system, we reconstruct four cell lineage trees for zebrafish fin cells, encompassing both original and regenerated fin. Each tree consists of hundreds of internal nodes with a median bootstrap support of 99%. Analysis of the obtained cell lineage trees reveals that regenerated fin cells mainly originate from cells in the same part of the fins. Through multiple times sampling germ cells from the same individual, we show the stability of the germ cell pool and the early separation of germ cell and somatic cell progenitors. Our system offers the potential for reconstructing high-quality cell phylogenies across diverse tissues, providing valuable insights into development and disease in zebrafish.
- Lineage tracing,
- Cellular barcoding,
- Zebrafish cell phylogeny,
- Fin regeneration,
- Germ cell lineage

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