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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
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FAWMine: An integrated database and analysis platform for fall armyworm genomics.

Pengcheng Yang1,2, Depin Wang3, Wei Guo2,4

  • 1Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.

Insect Science
|January 29, 2021
PubMed
Summary

The Fall Armyworm Genome Database (FAWMine) offers integrated access to extensive omics data for the invasive fall armyworm (Spodoptera frugiperda). This resource aids researchers in analyzing genomic and transcriptomic data for effective pest control strategies.

Keywords:
InterMinedata warehouseinvasive speciespopulation resequencing; transcriptome

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Area of Science:

  • Agricultural Entomology
  • Bioinformatics
  • Genomics

Background:

  • The fall armyworm (Spodoptera frugiperda) is a significant global agricultural pest, causing widespread crop damage.
  • Numerous genomic and transcriptomic datasets exist for this pest, but integrated analysis is challenging.

Purpose of the Study:

  • To develop a centralized, accessible platform for fall armyworm omics data.
  • To facilitate integrated analysis of genomic, transcriptomic, and other high-throughput data for pest control research.

Main Methods:

  • Development of the Fall Armyworm Genome Database (FAWMine).
  • Integration of genome sequences, annotations, transcriptomes, co-expression data, protein interactions, homologs, pathways, and single-nucleotide variations.
  • Implementation of search, visualization, data export, and analysis tools, including stand-alone JBrowse and BLAST services.

Main Results:

  • FAWMine provides a comprehensive framework for querying and analyzing diverse fall armyworm datasets.
  • Users can perform flexible searches, visualize integrated data, export results, and analyze candidate genes.
  • Integrated JBrowse and BLAST services enable RNA-Seq data visualization and sequence searching.

Conclusions:

  • FAWMine serves as a valuable, continually updated resource for researchers studying fall armyworm genomics.
  • The database enhances the efficiency of data querying, visualization, and analysis for pest control research.