The genome annotation and comparative genomics analysis of Spodoptera frugiperda.
The fall armyworm Spodoptera frugiperda was first found in China in January, 2019, and has rapidly spread to 20 provinces within half a year. This insect has caused the great economic losses and social concerns all over the world. Genome data is important for studying the molecular mechanisms of many important traits such as long-distance migration, invasive and insecticide resistance of this notorious insect pest. Nowadays, five versions of S. frugiperda genome assembles have been reported, but some genome annotation information was still unavailable. In addition, only the genome assembly obtained from Sf9 cell has a high scaffold N50 of 601.1 Kb. 28.1% of the Sf9 cell-line genome is identified as repeat sequences. We assessed its genome space using the software Core Eukaryotic Genes Mapping Approach (CEGMA) and Benchmarking Universal Single-Copy Orthologs (BUSCO), showing that 93.6% CEGMA genes and 90.8% BUSCO genes are successfully recovered. To provide gene information of S. frugiperda, we annotated the genome of the Sf9 cell line using the pipeline of Optimized Maker-based Insect Genome Annotation (OMIGA), yielding 25 699 protein-coding genes which can be obtained from http://www.insect-genome.com/FAW/. Among which, 15 623 genes have GO terms and 9 213 genes have homology in the KEGG database. Phylogenetic analysis shows S. frugiperda diverges from the common ancestor of S. frugiperda and Spodoptera litura approximately 12.84 million years ago. In addition, we identified 2 490 single-copy genes, 891 Lepidoptera specific genes, 2 360 S. frugiperda-specific duplication genes and 4 180 species-specific genes in the S. frugiperda genome. GO enrichment analyses show that S. frugiperda-specific duplication genes are significantly overrepresented for DNA integration and DNA metabolic process, and species-specific genes are mostly related to enzyme activity, photoreceptor and carbohydrate metabolism. KEGG enrichment analyses show that species species-specific genes are highly related to amino acids metabolism, carbohydrate metabolism and Wnt signaling pathway. Our data provide the genomic information of S. frugiperda, which should be great helpful for further understanding its biological characteristics and developing novel control methods.