The endoderm cell trajectory of urochordate Styela clava reveals the dual developmental origin and evolution of digestive tract
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Curated by eLife
eLife Assessment
This potentially important paper questions the evolutionary origin of the tunicate endoderm, using single-cell sequencing on a developmental series of the ascidian Styela clava that covers metamorphosis and gut development. The authors base their conclusions on a comparison with the development of mouse gut endoderm, where they point out similarities in the origin of tissues, perhaps representing a case of "deep homology". This work has the potential to make a significant contribution to the field of chordate evolution, but in its current form, the evidence it presents is incomplete and is limited by a problematic discussion of evolutionary implications and by major issues regarding the clarity and cogency of data presentation.
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Abstract
The digestive system exhibits extensive diversity in developmental mechanisms and morphology across metazoans, yet the evolutionary origins underlying its organ differentiation remain unclear. Here, single-cell RNA sequencing was employed to investigate endodermal cell lineage specification during metamorphosis in the urochordate Styela clava, a newly established model for chordate evolution. By profiling 26,099 cells across five stages, we identified 21 major cell clusters and reconstructed the endodermal differentiation trajectories. Our analysis reveals two larval endodermal progenitor populations with distinct differentiation potentials. Pseudotime and RNA velocity analyses indicate that these progenitors give rise to stomach and intestinal lineages, respectively. Cross-species comparisons reveal putative homologous relationships between ascidian endodermal lineages and mouse definitive and visceral endodermal lineages, suggesting dual origins of digestive tract in chordates. We also identified conserved TGF-β and FGF regulatory programs in digestive organ patterning and highlight earlier fate restriction of stomach and intestinal progenitors in ascidians compared to vertebrates. These findings provide insights into how chordate digestive organs evolved from ancestral endodermal patterning programs.
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Author response:
We sincerely thank the Reviewing Editor, Senior Editor, and both reviewers for their careful and constructive assessment of our manuscript. We are encouraged that the reviewers recognize the value of our dataset and its potential contribution. We greatly appreciate the thoughtful comments and have carefully considered the reviews. We plan to revise the manuscript accordingly.
First, we will revise and refine the cross-species comparative analysis, with particular attention to clarifying the basis of the comparisons between ascidian and mouse endodermal lineages. In particular, we will adopt a more cautious and precise comparative framework, clarify the scope and limitations of the mouse comparison, and broaden the context by incorporating additional vertebrate and invertebrate deuterostome systems where relevant.
Second,…
Author response:
We sincerely thank the Reviewing Editor, Senior Editor, and both reviewers for their careful and constructive assessment of our manuscript. We are encouraged that the reviewers recognize the value of our dataset and its potential contribution. We greatly appreciate the thoughtful comments and have carefully considered the reviews. We plan to revise the manuscript accordingly.
First, we will revise and refine the cross-species comparative analysis, with particular attention to clarifying the basis of the comparisons between ascidian and mouse endodermal lineages. In particular, we will adopt a more cautious and precise comparative framework, clarify the scope and limitations of the mouse comparison, and broaden the context by incorporating additional vertebrate and invertebrate deuterostome systems where relevant.
Second, we will strengthen the gene-level interpretation of the identified endodermal populations and clarify the molecular basis for the similarities and differences. In particular, we will more clearly identify the key marker genes defining each population, better explain their relationship to previously described developmental sources.
Third, we will improve the clarity of the Results presentation, including the description of the two major endodermal progenitor populations and their subcategories, as well as the organization of the text, figures, and figure legends.
Fourth, we will substantially rewrite the Discussion, especially the sections dealing with evolutionary implications, to ensure that our interpretations are presented in a more cautious manner.
These revisions are intended to address the reviewers’ concerns regarding both the evolutionary framing and the presentation of the data. We believe that these revisions, which will include both rewriting and additional analyses, will improve the clarity and rigor of the manuscript. We look forward to submitting a revised version.
We thank the editors and reviewers again for their time and expertise.
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eLife Assessment
This potentially important paper questions the evolutionary origin of the tunicate endoderm, using single-cell sequencing on a developmental series of the ascidian Styela clava that covers metamorphosis and gut development. The authors base their conclusions on a comparison with the development of mouse gut endoderm, where they point out similarities in the origin of tissues, perhaps representing a case of "deep homology". This work has the potential to make a significant contribution to the field of chordate evolution, but in its current form, the evidence it presents is incomplete and is limited by a problematic discussion of evolutionary implications and by major issues regarding the clarity and cogency of data presentation.
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Reviewer #1 (Public review):
Summary:
The authors employ state-of-the-art single-cell sequencing technologies to map the gene expression profiles of the developing digestive tract in the ascidian Styela clava, a member of the invertebrate sister group to vertebrates. This data has the potential to provide a new perspective on the relationships between the guts of an invertebrate like this ascidian relative to vertebrate systems. Key findings include the elaboration of our understanding that the Styela gut arises from two distinct cellular origins, with this being comparable to the dual embryogenic origin of vertebrate guts (at least, as exemplified by the mouse digestive tract arising from both definitive and visceral endoderm).
Strengths:
The resolution that can be achieved from the series of developmental stages analysed by the …
Reviewer #1 (Public review):
Summary:
The authors employ state-of-the-art single-cell sequencing technologies to map the gene expression profiles of the developing digestive tract in the ascidian Styela clava, a member of the invertebrate sister group to vertebrates. This data has the potential to provide a new perspective on the relationships between the guts of an invertebrate like this ascidian relative to vertebrate systems. Key findings include the elaboration of our understanding that the Styela gut arises from two distinct cellular origins, with this being comparable to the dual embryogenic origin of vertebrate guts (at least, as exemplified by the mouse digestive tract arising from both definitive and visceral endoderm).
Strengths:
The resolution that can be achieved from the series of developmental stages analysed by the authors through the metamorphosis and early gut specification and development is vital to the strength of this new dataset. This new scRNAseq data is likely to provide a useful foundation for future work that delves into the functions of various genes within regions of the ascidian gut.
Weaknesses:
The main weakness of the manuscript as it currently stands is the lack of clarity about the genetic comparisons between ascidian and mouse, and what the precise genetic underpinnings are for any statements of similarity.
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Reviewer #2 (Public review):
This manuscript explores endodermal lineage specification during metamorphosis in Styela clava. As biphasic lifestyle organisms, the endoderm exists as a rudiment in the non-feeding larvae that differentiates throughout metamorphosis to build the digestive components of the adult body plan. The authors of this manuscript use scRNA sequencing of individuals throughout the metamorphic process, as well as maturing juveniles, to follow the trajectories of the endodermal precursors. They identify two distinct populations that give rise to the stomach and intestinal lineages, and they suggest that there are homologous relationships between tunicate & vertebrate dual-origin endodermal lineages. Additionally, the authors highlight the role of conserved FGF signal-dependent programs in digestive organ patterning and …
Reviewer #2 (Public review):
This manuscript explores endodermal lineage specification during metamorphosis in Styela clava. As biphasic lifestyle organisms, the endoderm exists as a rudiment in the non-feeding larvae that differentiates throughout metamorphosis to build the digestive components of the adult body plan. The authors of this manuscript use scRNA sequencing of individuals throughout the metamorphic process, as well as maturing juveniles, to follow the trajectories of the endodermal precursors. They identify two distinct populations that give rise to the stomach and intestinal lineages, and they suggest that there are homologous relationships between tunicate & vertebrate dual-origin endodermal lineages. Additionally, the authors highlight the role of conserved FGF signal-dependent programs in digestive organ patterning and suggest that endodermal fate restriction occurs earlier in Styela in comparison with the mouse gut.
Overall, the paper is the first in-depth look at tunicate endodermal fate from a single-cell sequencing perspective and provides a robust framework for understanding the evolutionary origins of the deuterostome/chordate gut. The data is substantial and of great interest. However, we find their discussion of evolutionary implications to be highly problematic, and there are also numerous major issues regarding the clarity and cogency of their data presentation. Thus, we consider that substantial revision is required to provide a more accurate analysis of this data and its evolutionary implications. This revision would not require further experimentation.
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