Assembly of highly contiguous diploid genome for the agricultural pest Tuta absoluta

Tuta absoluta represents one of the largest threats to tomato production worldwide. While initially contained to South America throughout the 20th century, T. absoluta were detected in Spain in 2006 before rapidly spreading throughout Europe and Asia over the next decade. To facilitate study of pesticide resistance, adaptation, and control strategies, researchers require a high quality, highly contiguous, and well-annotated genome assembly. The currently published genome assembly was generated using short-read technology for the purpose of developing molecular markers and studying population genetics; however, due to the genome’s large size, heterozygosity, and repetitiveness, the assembly was highly fragmented, making it unsuitable for annotation or functional genomic studies. To address this, we extracted DNA from a single T. absoluta individual for sequencing with long-read PacBio HiFi technology to avoid assembly issues expected due to high genetic diversity and repetitiveness. We have now successfully created a diploid assembly that contains 98% of complete Lepidopteran BUSCO groups and 99% of initial raw reads, with an N50 of 13.3Mb. The genome is 3% heterozygous, and is 60% composed of repeat elements, explaining the fragmented nature of the previous assemblies. By annotating this assembly with previously published RNAseq, protein, and repeat-element datasets, we expect this resource to advance efforts in understanding and developing control strategies for this invasive moth.