Cell landscape of larval and adult Xenopus laevis at single-cell resolution

Abstract

The rapid development of high-throughput single-cell RNA sequencing technology offers a good opportunity to dissect cell heterogeneity of animals. A large number of organism-wide single-cell atlases have been constructed for vertebrates such as Homo sapiens, Macaca fascicularis, Mus musculus and Danio rerio. However, an intermediate taxon that links mammals to vertebrates of more ancient origin is still lacking. Here, we construct the first Xenopus cell landscape to date, including larval and adult organs. Common cell lineage-specific transcription factors have been identified in vertebrates, including fish, amphibians and mammals. The comparison of larval and adult erythrocytes identifies stage-specific hemoglobin subtypes, as well as a common type of cluster containing both larval and adult hemoglobin, mainly at NF59. In addition, cell lineages originating from all three layers exhibits both antigen processing and presentation during metamorphosis, indicating a common regulatory mechanism during metamorphosis. Overall, our study provides a large-scale resource for research on Xenopus metamorphosis and adult organs.

Construction of a cross-species cell landscape at single-cell level

“…Besides MCDAA, ZCDL and DCL, there were several cell landscapes also performed by Microwell-seq, such as human ( 16 ), axolotl ( 69 ), Xenopus ( 70 ) and earthworm ( 26 ). Combining these cell landscapes with other single cell atlases from published works, including monkey ( 71 ), rat ( 32 ), sea squirt ( 24 ), C.elegans ( 22 ), planarian ( 72 ), Nematostella ( 23 ), hydra ( 73 ) and sponge ( 74 ), we constructed an integrated online portal, Cell Landscape (Figure 4A ), which provided a foundation for a large-scale single-cell atlas and served as a powerful tool to investigate their biological importance.…”

Germline stem cells in human

“…Single-cell transcriptome shows that the germline of Xenopus is evolutionarily closer to that of zebrafish than to humans and mice. 45 In some model organisms, including Xenopus , 46 – 58 zebrafish, 59 – 69 and chicken, 70 – 82 their PGCs are specified via the maternally inherited germ plasm, including vasa and nanos, during the first several cleavages. In contrast, in mammals, the PGCs are specified by induction during early embryo development.…”

Lineage Landscape: a comprehensive database that records lineage commitment across species

“…The single-cell transcriptomics module collects transcriptomics data during lineage differentiation or development at the single-cell level. It systematically documents cell type-specific changes in gene expression across multiple organs and species, including humans ( 17 , 32 , 33 ), mice ( 1 , 34–36 ), frogs ( 22 ), zebrafishes ( 23 ) and so on. This module also provides a collection of high-resolution, comprehensive reference maps of different cell types/subtypes.…”

“…Considering the increasing number of lineage differentiation-related studies from a broad spectrum of developmental stages and species, aggregating such data into a database has become imperative for the field ( 22–24 ). To this end, we present Lineage Landscape, a novel lineage differentiation database that allows convenient access to multiple high-throughput omics data collected from different species and developmental stages.…”