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Manduca sexta Official Gene Set v2.2

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posted on 2024-02-16, 18:18 authored by Michael KanostMichael Kanost, Gary Blissard, Stephen Richards, Susan Brown, Alexie Papanicolaou, Nicolae Herndon, Haobo Jiang
<p><em>Manduca sexta</em>, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. <em>M. sexta</em> larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine.</p> <p>This dataset presents the <em>Manduca sexta</em> Official Gene Set (OGS) v2.2. It is derived from Official Gene Sets OGSv2.0 and OGSv2.1. OGSv2.0 was modified to meet NCBI-GenBank quality review, resulting in OGSv2.1. This was deposited in NCBI GenBank (accession number AIXA00000000). OGS2.1 was lifted over to assembly JHU_Msex_v1.0/GCF_014839805.1 using the LiftOff (<a href="https://doi.org/10.1093/bioinformatics/btaa1016">https://doi.org/10.1093/bioinformatics/btaa1016</a>) and Genometools (<a href="http://genometools.org/">http://genometools.org/</a>) software, resulting in OGSv2.2. OGSv2.2 has quality issues due to the liftover - the i5k Workspace@NAL recommends NCBI Annotation Release 102 for general analysis, instead. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Manduca sexta Official Gene Set v2.2.</p> <p>File Name: OGSv2.2.tar.gz</p><p>Resource Description: The attached tar.gz archive (OGSv2.2.tar.gz) contains the following files:</p> <p>mansex_OGSv2.2.gff. Gff3 file of all gene predictions of Manduca sexta genome annotations OGSv2.2 readme.txt. A readme describing the OGS generation process. </p></li></ul><p></p>

Funding

National Institutes of Health: GM041247

Defense Advanced Research Projects Agency

History

Related Materials

  1. 1.
    DOI - Is supplement to Kanost, M. R., Arrese, E. L., Cao, X., Chen, Y.-R., Chellapilla, S., Goldsmith, M. R., Grosse-Wilde, E., Heckel, D. G., Herndon, N., Jiang, H., Papanicolaou, A., Qu, J., Soulages, J. L., Vogel, H., Walters, J., Waterhouse, R. M., Ahn, S.-J., Almeida, F. C., An, C., … Blissard, G. W. (2016). Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. Insect Biochemistry and Molecular Biology, 76, 118–147. https://doi.org/10.1016/j.ibmb.2016.07.005
  2. 2.
    URL - Is supplemented by Genome assembly JHU_Msex_v1.0 (GCF_014839805.1_)
  3. 3.
    URL - Is supplemented by I5k Workspace@NAL Manduca sexta page
  4. 4.
    URL - Is supplemented by IsVersonOf: Manduca sexta Official Gene Set v2.0
  5. 5.
    DOI - Is supplemented by Cao, X., & Jiang, H. (2015). Integrated modeling of protein-coding genes in the Manduca sexta genome using RNA-Seq data from the biochemical model insect. Insect Biochemistry and Molecular Biology, 62, 2–10. https://doi.org/10.1016/j.ibmb.2015.01.007
  6. 6.
    DOI - Is supplemented by Zhang, X., Zheng, Y., Cao, X., Ren, R., Yu, X.-Q., & Jiang, H. (2015). Identification and profiling of Manduca sexta microRNAs and their possible roles in regulating specific transcripts in fat body, hemocytes, and midgut. Insect Biochemistry and Molecular Biology, 62, 11–22. https://doi.org/10.1016/j.ibmb.2014.08.006
  7. 7.
    DOI - Is supplemented by He, Y., Cao, X., Li, K., Hu, Y., Chen, Y., Blissard, G., Kanost, M. R., & Jiang, H. (2015). A genome-wide analysis of antimicrobial effector genes and their transcription patterns in Manduca sexta. Insect Biochemistry and Molecular Biology, 62, 23–37. https://doi.org/10.1016/j.ibmb.2015.01.015
  8. 8.
    DOI - Is supplemented by Zhang, X., He, Y., Cao, X., Gunaratna, R. T., Chen, Y., Blissard, G., Kanost, M. R., & Jiang, H. (2015). Phylogenetic analysis and expression profiling of the pattern recognition receptors: Insights into molecular recognition of invading pathogens in Manduca sexta. Insect Biochemistry and Molecular Biology, 62, 38–50. https://doi.org/10.1016/j.ibmb.2015.02.001
  9. 9.
    DOI - Is supplemented by Cao, X., He, Y., Hu, Y., Zhang, X., Wang, Y., Zou, Z., Chen, Y., Blissard, G. W., Kanost, M. R., & Jiang, H. (2015). Sequence conservation, phylogenetic relationships, and expression profiles of nondigestive serine proteases and serine protease homologs in Manduca sexta. Insect Biochemistry and Molecular Biology, 62, 51–63. https://doi.org/10.1016/j.ibmb.2014.10.006
  10. 10.
    DOI - Is supplemented by Cao, X., He, Y., Hu, Y., Wang, Y., Chen, Y.-R., Bryant, B., Clem, R. J., Schwartz, L. M., Blissard, G., & Jiang, H. (2015). The immune signaling pathways of Manduca sexta. Insect Biochemistry and Molecular Biology, 62, 64–74. https://doi.org/10.1016/j.ibmb.2015.03.006

Data contact name

Kanost, Michael

Data contact email

kanost@ksu.edu

Publisher

Ag Data Commons

Intended use

This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.

Temporal Extent Start Date

2018-09-01

Temporal Extent End Date

2018-09-30

Theme

  • Not specified

Geographic Coverage

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ISO Topic Category

  • biota

Ag Data Commons Group

  • Insects - i5K

National Agricultural Library Thesaurus terms

genomics; genes; prediction; genome assembly; sequence analysis; genome; Manduca sexta; insects; models; insect biochemistry; immunity; insect larvae; allelochemicals; nicotine; tissues; gene expression regulation; apoptosis; vacuoles; exoskeleton; egg shell; muscles; vision; ion channels; signal transduction; neuropeptides; neurotransmitters; lipid metabolism

Primary article PubAg Handle

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Kanost, Michael R.; Blissard, Gary; Richards, Stephen; Brown, Susan; Papanicolaou, Alexie; Herndon, Nicolae; Jiang, Haobo (2021). Manduca sexta Official Gene Set v2.2. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1522540

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    Categories

    Keywords

    genome assemblysequence analysisgenome annotationManduca sexta

    Licence

    CC BY-SA 4.0

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