Browsing by Author "Shoue, Douglas"

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    Improved high quality sand fly assemblies enabled by ultra low input long read sequencing
    (Springer Nature, 2024) Huang, Michelle; Kingan, Sarah; Shoue, Douglas; Nguyen, Oanh; Froenicke, Lutz; Galvin, Brendan; Lambert, Christine; Khan, Ruqayya; Maheshwari, Chirag; Weisz, David; Maslen, Gareth; Davison, Helen; Aiden, Erez Lieberman; Korlach, Jonas; Dudchenko, Olga; McDowell, Mary Ann; Richards, Stephen; Center for Theoretical Biological Physics
    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.