De novo construction of a transcriptome for the stink bug crop pest Chinavia impicticornis during late development

  1. Bruno C. Genevcius
  2. Tatiana T. Torres

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

Chinavia impicticornis is a neotropical stink bug of economic importance for various crops. Little is known about the development of the species, or the genetic mechanisms that may favor the establishment of populations in cultivated plants. Here, we conduct the first large-scale molecular study of C. impicticornis. Using tissues derived from the genitalia and the rest of the body for two immature stages of both males and females, we generated RNA-seq data, then assembled and functionally annotated a transcriptome. The de novo-assembled transcriptome contained around 400,000 contigs, with an average length of 688 bp. After pruning duplicated sequences and conducting a functional annotation, the final annotated transcriptome comprised 39,478 transcripts, of which 12,665 were assigned to Gene Ontology (GO) terms. These novel datasets will be invaluable for the discovery of molecular processes related to morphogenesis and immature biology. We hope to contribute to the growing body of research on stink bug evolution and development, as well as to the development of biorational pest management solutions.

Article activity feed

  1. GigaByte

    Now published in Gigabyte doi: 10.46471/gigabyte.11

    Bruno C. Genevcius Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, BrazilFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Bruno C. GenevciusFor correspondence: bgenevcius@gmail.comTatiana T. Torres Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, BrazilFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Tatiana T. Torres

    This work has been peer reviewed in GigaByte, which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

    **Reviewer 1. Peter Thorpe. ** Are all data available and do they match the descriptions in the paper?

    No. They are submitted but still private. These need to be released.

    Final Comments: SRA datasets need to be released.

    Recommendation: Minor Revision

    **Reviewer 2. Guillem Ylla. **

    Is the language of sufficient quality? While the text is mostly clear, I detected a few spelling mistakes (listed below) and there might be more that escaped my attention. I would recommend the authors to exhaustively check the MS. Line 53: “Stink bug” missing “bug”. Lines 39,58,69, and figures: Mixed usage of “Chinavia impicticornis” and “C. impicticornis”. After first appearance of the full name, authors should be consistent whether they keep using the full name or the abbreviation, but not mixing both.

    Are all data available and do they match the descriptions in the paper?
    No. The authors report multiple accession numbers from NCBI including a BioProject ID. But they are not open and I was unable to check if the data match the paper descriptions. The TSA accession seems that has not yet been created and the MS displays a placeholder (GIVF00000000) in its place.

    Are the data and metadata consistent with relevant minimum information or reporting standards? No. Missing items from the checklist. 1) "Any perl/python scripts created for analysis process ". In Line 94 “using a custom Perl script [16]”, the authors provide citation but not the code. 2) "Full (not summary) BUSCO results output files (text) ".

    Is the data acquisition clear, complete and methodologically sound?
    Yes. The end of the fifth nymphal instar dataset was obtained at “seven days after molting from fourth to fifth instar”. Could authors specify how many days is the 5th nymphal instar to have a better idea of how much longer is the 5th nymphal stage.

    Could the authors briefly describe the rationale o behind choosing 5th nymphal and instead of other nymphal stages? They explain why nymphal stages were used instead of adults, but not why the 5th nymphal instar.

    Is there sufficient detail in the methods and data-processing steps to allow reproduction?
    No. I would appreciate if the authors could share the code/commands for removing redundant reads and performing the assembly as supplementary materials or in GitHub (recommended).

    In the abstract, the authors describe 38,478 transcripts of which 12,665 had GO terms assigned. Is not clear where this number comes from. In line 120 is mentioned that “ 39,478 had successful matches in the NCBI”. Is there a type one of these two numbers (38,478 vs 39,478)? However, the MS says “we only kept contigs that matched to Arthropod species”, and this number is reported to be 33,871. I urge the authors to better explain the steps they followed and clarify where all these numbers come from.

    Is there sufficient data validation and statistical analyses of data quality?
    Yes. Using the whole insect body often includes contaminant RNAs from the gut microbiome, endosymbionts, viruses, and other microbiological specimens from the cuticles and environment. Since the authors do not filter out reads from possible contaminants before the assembly, I would appreciate it if they could perform a BUSCO analysis using the prokaryote database before and after the selection based on similarity to databases. This would allow estimating the number of contaminants in the original assembly and if they had successfully discarded after the selection.

    Lines 126-127 are not clear. There are 12,665 contigs that have 5,087 GO terms. I deduce that there are 12,665 contigs that have at least 1 GO term, and that they contain 5,087 distinct GO terms. Could authors make it more clear on the text?

    Is there sufficient information for others to reuse this dataset or integrate it with other data?
    Yes. I don’t think that a dataset consisting of 2-time points (early and late) of the same sarge (nymph 5) can be considered a “developmental transcriptome”. I would urge the authors to change the terminology and title.

    In the abstract, the authors claim that this is the “ first genome-scale study with”. Since the study is only transcriptomic, I find it misleading to define it as “genome-scale study”.

    1- I don’t think that a datasets consisting of 2 time points (early and late) of the same sarge (nymph 5) can be considered a “developmental transcriptome”. I would urge the authors to change the terminology and title.

    2- In the abstract, the authors claim that this is the “ first genome-scale study with”. Since the study is only transcriptomic, I find misleading to define it as “genome-scale study”.

    3- In table 1 and line 117 the authors claim that they generated the highest amount of RNA-seq reads for pentatomids to date. However, for the Halyomorpha halys there are multiple available RNA-seq datasets not mentioned, which taken together I suspect that they would accede the data generated for C. Impicticornis. I would suggest to reduce the tone of this statement of L117.

    4- Additionally, there are at least 3 available genomes for pentatomidaes species. I think that this information should at least be mentioned in the introduction.

    5- In line 61, could the authors define “almost nonexistent”, how many are there?

    Additionally, there are at least 3 available genomes for pentatomidaes species. I think that this information should at least be mentioned in the introduction.

    In line 61, could the authors define “almost nonexistent”, how many are there?

    Recommendation: Minor Revision

  2. Version published to 10.46471/gigabyte.11
  3. Version published to 10.1101/2020.12.04.412270v1 on bioRxiv