Manuscript title (or id)
Characterization of Long Non-Coding RNAs in the Eastern Oyster (Crassostrea virginica): Sex-Biased Expression, Sequence Conservation, and Co-expression Networks Under Ocean Acidification
Link to the draft you reviewed
https://docs.google.com/document/d/1Nx1GdJ2igvxWMo5VWHY2fL_H_Ws_ek-dFwd70-nQTrk/edit?tab=t.0#heading=h.auc0rhvni8uo
Section(s) reviewed
What's working well
Discussion is looking great! Maybe a couple of small tables in results
Suggestions for improvement
RESULTS
The first Results paragraph could more explicitly summarize the overall approach (the guide calls this a pivotal paragraph for readers who skip Methods) — right now it jumps straight into length statistics.
The main weakness is that the Results are text-heavy where figures and tables would carry the load far better (see next section). Specific spots:
-
The cross-species BLAST counts (2,389; 807; 42; 40; 0) and the BRH reductions (9 pairs; 1 pair; 0) are a small table waiting to happen — precise values across several species is the textbook "use a table" case.
-
The DE results (2,370 lncRNAs by sex; 1 female / 5 male; 36,242 mRNAs; etc.) would be clearer as a small summary table, and the PCA you describe - if easy to add as supplement, would do.
Smaller points: tense is consistently past (good). Watch a couple of interpretation leaks — e.g., "This pattern indicates that the lncRNA in Cluster A may serve as a central regulatory candidate" edges toward Discussion territory; in Results, state the structure ("Cluster A comprised one lncRNA connected to 67 mRNAs") and save "may serve as a regulatory candidate" for the Discussion.
The numbering skip (2.0, 2.1, 2.3 — no 2.2) should be fixed.
FIGURES AND TABLES
Two caption refinements per the guide: Figure 1's title should state the conclusion, not just the subject. Instead of "lncRNA-mRNA co-expression network in Crassostrea virginica," try "A single lncRNA hub dominates the C. virginica co-expression network, linked to translation- and ribosome-associated mRNAs."
DISCUSSION
This is well-constructed and does the three jobs the guide asks of a Discussion: it answers the question, interprets each key result against prior literature, and positions the contribution. The opening paragraph answers the research question in plain language without statistics — exactly right for a pivotal first paragraph. The shape mirrors the Introduction, broadening from specific findings to "a foundation for advancing from lncRNA discovery to functional inference." Future directions are specific and useful (time-course RNA-seq, knockdown, chromatin accessibility) rather than the forbidden "more research is needed."
Strengths to keep: the limitations are handled with "but-yes" framing ("The limited differential expression... does not preclude regulatory roles...") and, importantly, the section does not end on limitations — it ends on the broader contribution. That is the correct structure.
Refinements:
-
The first paragraph is long and somewhat re-summarizes results. Tighten it; the guide wants this paragraph short and answer-focused.
-
A couple of claims could use a citation right beside them — e.g., the comparison to cancer co-expression studies is cited (Liu & Zhao, 2016; Wu et al. 2016), good, but check that interpretive claims about ribosome/translation modules in other systems are anchored where made.
-
Grammar/agreement to fix: "This evidence indicate" -> "indicates"; "these results indicate" constructions are fine but proofread for subject-verb agreement throughout, which slips a few times.
Questions for the author (optional)
No response
Overall assessment
⚓ Ready to sail — minor polish only
Manuscript title (or id)
Characterization of Long Non-Coding RNAs in the Eastern Oyster (Crassostrea virginica): Sex-Biased Expression, Sequence Conservation, and Co-expression Networks Under Ocean Acidification
Link to the draft you reviewed
https://docs.google.com/document/d/1Nx1GdJ2igvxWMo5VWHY2fL_H_Ws_ek-dFwd70-nQTrk/edit?tab=t.0#heading=h.auc0rhvni8uo
Section(s) reviewed
What's working well
Discussion is looking great! Maybe a couple of small tables in results
Suggestions for improvement
RESULTS
The first Results paragraph could more explicitly summarize the overall approach (the guide calls this a pivotal paragraph for readers who skip Methods) — right now it jumps straight into length statistics.
The main weakness is that the Results are text-heavy where figures and tables would carry the load far better (see next section). Specific spots:
The cross-species BLAST counts (2,389; 807; 42; 40; 0) and the BRH reductions (9 pairs; 1 pair; 0) are a small table waiting to happen — precise values across several species is the textbook "use a table" case.
The DE results (2,370 lncRNAs by sex; 1 female / 5 male; 36,242 mRNAs; etc.) would be clearer as a small summary table, and the PCA you describe - if easy to add as supplement, would do.
Smaller points: tense is consistently past (good). Watch a couple of interpretation leaks — e.g., "This pattern indicates that the lncRNA in Cluster A may serve as a central regulatory candidate" edges toward Discussion territory; in Results, state the structure ("Cluster A comprised one lncRNA connected to 67 mRNAs") and save "may serve as a regulatory candidate" for the Discussion.
The numbering skip (2.0, 2.1, 2.3 — no 2.2) should be fixed.
FIGURES AND TABLES
Two caption refinements per the guide: Figure 1's title should state the conclusion, not just the subject. Instead of "lncRNA-mRNA co-expression network in Crassostrea virginica," try "A single lncRNA hub dominates the C. virginica co-expression network, linked to translation- and ribosome-associated mRNAs."
DISCUSSION
This is well-constructed and does the three jobs the guide asks of a Discussion: it answers the question, interprets each key result against prior literature, and positions the contribution. The opening paragraph answers the research question in plain language without statistics — exactly right for a pivotal first paragraph. The shape mirrors the Introduction, broadening from specific findings to "a foundation for advancing from lncRNA discovery to functional inference." Future directions are specific and useful (time-course RNA-seq, knockdown, chromatin accessibility) rather than the forbidden "more research is needed."
Strengths to keep: the limitations are handled with "but-yes" framing ("The limited differential expression... does not preclude regulatory roles...") and, importantly, the section does not end on limitations — it ends on the broader contribution. That is the correct structure.
Refinements:
The first paragraph is long and somewhat re-summarizes results. Tighten it; the guide wants this paragraph short and answer-focused.
A couple of claims could use a citation right beside them — e.g., the comparison to cancer co-expression studies is cited (Liu & Zhao, 2016; Wu et al. 2016), good, but check that interpretive claims about ribosome/translation modules in other systems are anchored where made.
Grammar/agreement to fix: "This evidence indicate" -> "indicates"; "these results indicate" constructions are fine but proofread for subject-verb agreement throughout, which slips a few times.
Questions for the author (optional)
No response
Overall assessment
⚓ Ready to sail — minor polish only