Life-cycle-related gene expression patterns in the brown algae

Reviewer #1 (Public review):

Summary:

The authors have examined gene expression between life cycle stages in a range of brown macroalgae to examine whether there are conserved aspects of biological features.

Strengths:

The manuscript incorporates large gene expression datasets from 10 different species and therefore enables a comprehensive assessment of the degree of conservation of different aspects of gene expression and underlying biology.

The findings represent an important step forward in our understanding of the core aspects of cell biology that differ between life cycle phases and provide a substantial resource for further detailed studies in this area. Convincing evidence is provided for the conservation of life-cycle-specific gene expression between species, particularly in core housekeeping gene modules.

Weaknesses:

I found a few weaknesses in the methodology and experimental design. I think the manuscript could have been clearer when linking the findings to the biology of the brown algae.

Reviewer #2 (Public review):

Summary:

The manuscript by Ratchinski et al presents a comprehensive analysis of developmental and life history gene expression patterns in brown algal species. The manuscript shows that the degree of generation bias or generation-specific gene expression correlates with the degree of dimorphism. It also reports conservation of life cycle features within generations and marked changes in gene expression patterns in Ectocarpus in the transition between gamete and early sporophyte. The manuscript also reports considerable conservation of gene expression modules between two representative species, particularly in genes associated with conserved functional characteristics.

Strengths:

The manuscript represents a considerable "tour de force" dataset and analytical effort. While the data presented is largely descriptive, it is likely to provide a very useful resource for studies of brown algal development and for comparative studies with other developmental and life cycle systems.

Weaknesses:

Notwithstanding the well-known issues associated with inferring function from transcriptomics-only studies, no major weaknesses were identified by this reviewer.