Improved high quality sand fly assemblies enabled by ultra low input long read sequencing

Abstract

Phlebotomine sand flies are the vectors of leishmaniasis, a neglected tropical disease. High-quality reference genomes are an important tool for understanding the biology and eco-evolutionary dynamics underpinning disease epidemiology. Previous leishmaniasis vector reference sequences were limited by sequencing technologies available at the time and inadequate for high-resolution genomic inquiry. Here, we present updated reference assemblies of two sand flies, Phlebotomus papatasi and Lutzomyia longipalpis. These chromosome-level assemblies were generated using an ultra-low input library protocol, PacBio HiFi long reads, and Hi-C technology. The new P. papatasi reference has a final assembly span of 351.6 Mb and contig and scaffold N50s of 926 kb and 111.8 Mb, respectively. The new Lu. longipalpis reference has a final assembly span of 147.8 Mb and contig and scaffold N50s of 1.09 Mb and 40.6 Mb, respectively. Benchmarking Universal Single-Copy Orthologue (BUSCO) assessments indicated 94.5% and 95.6% complete single copy insecta orthologs for P. papatasi and Lu. longipalpis. These improved assemblies will serve as an invaluable resource for future genomic work on phlebotomine sandflies.

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Huang, M., Kingan, S., Shoue, D., Nguyen, O., Froenicke, L., Galvin, B., Lambert, C., Khan, R., Maheshwari, C., Weisz, D., Maslen, G., Davison, H., Aiden, E. L., Korlach, J., Dudchenko, O., McDowell, M. A., & Richards, S. (2024). Improved high quality sand fly assemblies enabled by ultra low input long read sequencing. Scientific Data, 11(1), 918. https://doi.org/10.1038/s41597-024-03628-y

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