FAWMine: An integrated database and analysis platform for fall armyworm genomics

Abstract

Fall armyworm (Spodoptera frugiperda), a native insect species in the Americas, is rapidly becoming a major agricultural pest worldwide and is causing great damage to corn, rice, soybeans, and other crops. To control this pest, scientists have accumulated a great deal of high-throughput data of fall armyworm, and nine versions of its genomes and transcriptomes have been published. However, easily accessing and performing integrated analysis of these omics data sets is challenging. Here, we developed the Fall Armyworm Genome Database (FAWMine, http://159.226.67.243:8080/fawmine/) to maintain genome sequences, structural and functional annotations, transcriptomes, co-expression, protein interactions, homologs, pathways, and single-nucleotide variations. FAWMine provides a powerful framework that helps users to perform flexible and customized searching, present integrated data sets using diverse visualization methods, output results tables in a range of file formats, analyze candidate gene lists using multiple widgets, and query data available in other InterMine systems. Additionally, stand-alone JBrowse and BLAST services are also established, allowing the users to visualize RNA-Seq data and search genome and annotated gene sequences. Altogether, FAWMine is a useful tool for querying, visualizing, and analyzing compiled data sets rapidly and efficiently. FAWMine will be continually updated to function as a community resource for fall armyworm genomics and pest control research.

Identification of neuropeptides and neuropeptide receptor genes in Phauda flammans (Walker)

“…Novel neuropeptides could be supplemented via Genomics- and peptidomics -based discovery in the future 63 . Moreover, association of multiple omics, such as full-length transcriptome, proteome and metabolome might be needed 64 , which would contribute to the feeding and sexual behavior regulation researches in this diurnal moth P. flammans by outlining a chain with cascaded neuropeptide, neuropeptide receptor, pheromone metabolism and behavior.…”

Overseas immigration of fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), invading Korea and Japan in 2019

“…Smith), native to the tropical and subtropical regions of the Americas, is a serious invasive agricultural pest (Luginbill, 1928;Sparks, 1979). With its strong long-distance flight capability, fecundity and adaptability, FAW can spread rapidly and cause serious damage to crop production in suitable environments (Johnson, 1987;Early et al, 2018;Rwomushana et al, 2018;Yang et al, 2021).…”

“…Smith), native to the tropical and subtropical regions of the Americas, is a serious invasive agricultural pest (Luginbill, 1928 ; Sparks, 1979 ). With its strong long‐distance flight capability, fecundity and adaptability, FAW can spread rapidly and cause serious damage to crop production in suitable environments (Johnson, 1987 ; Early et al ., 2018 ; Rwomushana et al ., 2018 ; Yang et al ., 2021 ). Its caterpillars can feed on over 350 plant species, such as corn, sorghum, millet and barley (Montezano et al ., 2018 ), causing huge economic losses in crop production, particularly that of maize.…”

HumanMine: advanced data searching, analysis and cross-species comparison

“…InterMine was originally developed as FlyMine to address these issues for the Drosophila community. It has since been adopted by other model organism databases (MODs) including mouse (1), yeast (5), worm (http://intermine.wormbase.org), fish (3) and rat (2) and a growing number of databases covering other animals including, including Planaria (8), Hymenoptera (9), locusts (10) and armyworm (11). Plant species include Arabidopsis (6), Medicago (12), wheat (https://urgi.versailles.inra.fr/WheatMine), maize (11,13), and several from the legume family (14) (see registry.intermine.org).…”

“…It has since been adopted by other model organism databases (MODs) including mouse (1), yeast (5), worm (http://intermine.wormbase.org), fish (3) and rat (2) and a growing number of databases covering other animals including, including Planaria (8), Hymenoptera (9), locusts (10) and armyworm (11). Plant species include Arabidopsis (6), Medicago (12), wheat (https://urgi.versailles.inra.fr/WheatMine), maize (11,13), and several from the legume family (14) (see registry.intermine.org). InterMine is also used for drug development (TargetMine (15)) and by large scale projects and consortia (PhytoMine (16), modMine (17), AllianceMine (https://www.alliancegenome.org/alliancemine)).…”