Annotation of putative circadian rhythm-associated genes in Diaphorina citri (Hemiptera: Liviidae)
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Abstract
The circadian rhythm involves multiple genes that generate an internal molecular clock, allowing organisms to anticipate environmental conditions produced by the Earth’s rotation on its axis. Here, we present the results of the manual curation of 27 genes that are associated with circadian rhythm in the genome of Diaphorina citri, the Asian citrus psyllid. This insect is the vector for the bacterial pathogen Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus greening disease (Huanglongbing). This disease severely affects citrus industries and has drastically decreased crop yields worldwide. Based on cry1 and cry2 identified in the psyllid genome, D. citri likely possesses a circadian model similar to the lepidopteran butterfly, Danaus plexippus. Manual annotation will improve the quality of circadian rhythm gene models, allowing the future development of molecular therapeutics, such as RNA interference or antisense technologies, to target these genes to disrupt the psyllid biology.
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Abstract
This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.48), and has published the reviews under the same license. These are as follows.
**Reviewer 1. Mary Ann Tuli **
Are all data available and do they match the descriptions in the paper?
No. The author states, "The gene models will also be part of an updated OGS version 3 for D. citri". I am wondering when this updated version will be available. In addition the author states, "the data is also available through NCBI (BioProject: PRJNA29447". It would be good to include the GenBank accession numbers of the 27 D. citri genes.
Is there sufficient information for others to reuse this dataset or integrate it with other data?
Yes. It does meet reuse criteria, but will be more reusable once the data is available from the Citrus …
Abstract
This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.48), and has published the reviews under the same license. These are as follows.
**Reviewer 1. Mary Ann Tuli **
Are all data available and do they match the descriptions in the paper?
No. The author states, "The gene models will also be part of an updated OGS version 3 for D. citri". I am wondering when this updated version will be available. In addition the author states, "the data is also available through NCBI (BioProject: PRJNA29447". It would be good to include the GenBank accession numbers of the 27 D. citri genes.
Is there sufficient information for others to reuse this dataset or integrate it with other data?
Yes. It does meet reuse criteria, but will be more reusable once the data is available from the Citrus Greening website.
**Reviewer 2. Ruihan Li **
Are all data available and do they match the descriptions in the paper?
No. No new sequencing data were generated in this paper. The author only modified the previous gene sets. Citation of raw data from the evidence supporting annotation mentioned in table2 should also be given.
Is there sufficient detail in the methods and data-processing steps to allow reproduction?
No. The method section of this paper seems too brief and should be supplemented in detail.
Additional Comments:
The author of “Annotation of Putative Circadian Rhythm-Associated Genes in Diaphorina citri (Hemiptera : Liviidae)” manually annotated 27 genes related to circadian rhythm in the genome of Diaphorina citri. This study summarized the circadian model in D. citri which may help people to protect citrus from the citrus greening disease. But I have some comments that would need to be taken into consideration. General comments: The method section of this paper seems too brief and should be supplemented in detail according to these studied rhythm genes. No new sequencing data were generated in this paper. The author only modified the previous gene sets. Citation of raw data from the evidence supporting annotation mentioned in table2 should also be given. Specific comments: Page 2: “…will allow future molecular therapeutics…” the molecular therapeutics for what? The object should be specified. Page 3: The author only said "Based on the critical importance of the genes identified" in the section of Introduction, but did not introduce the circadian physiological habits of this insect, which like whether they stay in a tree all the time. Another problem is that the gene functions in table1 seem to be mostly related to development, reproduction and even death, but not directly related to circadian rhythms. The relationship between these genes with rhythms needs to be supplemented. Table 1: Details of these references should be placed at the end of the article instead of in the table. Functional descriptions of these genes should be supplemented. Page 6, “…, but also makes the D. melanogaster model different from non-dipterans due to their possession of cry2.” The D. Melanogaster model and the Drosophila Model are mentioned several times in this paragraph. Do they express the same meaning? Please use the same expression to avoid misunderstanding. Table 2：“X” and “space” should be explained in the table notes. In addition, the analysis methods of “MCOT, ISO-SEQ, RNA-Seq and Ortholog” in the "Evidence Supporting Annotation" are not described in this article. Are these results collected from an existing online database or generated from new analysis that author done in this study? The section of Method is surprisingly simple. The necessary steps should be supplemented clearly. Figure2: If the author quote someone else's picture, please cite the sources of these references. Figure 3 is meaningless and suggested to be removed. Page12: How were “genome assembly errors” discovered? Did the author compare transcriptome data with genome data? Please supplement the method clearly. RNA-Seq experimental analysis is mentioned in the conclusion, but there is no relevant experiment in this paper. Why included this sentence in the conclusion? -
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