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

Michelle Huang; Sarah Kingan; Douglas Shoue; Oanh Nguyen; Lutz Froenicke; Brendan Galvin; Christine Lambert; Ruqayya Khan; Chirag Maheshwari; David Weisz; Gareth Maslen; Helen Davison; Erez Lieberman Aiden; Jonas Korlach; Olga Dudchenko; Mary Ann McDowell; Stephen Richards

doi:10.1038/s41597-024-03628-y

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

Sci Data. 2024 Aug 24;11(1):918. doi: 10.1038/s41597-024-03628-y.

Authors

Michelle Huang¹, Sarah Kingan², Douglas Shoue¹, Oanh Nguyen³, Lutz Froenicke³, Brendan Galvin², Christine Lambert², Ruqayya Khan^{4

5}, Chirag Maheshwari^{4

5}, David Weisz^{4

5}, Gareth Maslen⁶, Helen Davison⁷, Erez Lieberman Aiden^{4

5

8

9}, Jonas Korlach², Olga Dudchenko^{4

5

8}, Mary Ann McDowell^{10

11}, Stephen Richards¹²

Affiliations

¹ Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
² Pacific Biosciences, Menlo Park, CA, USA.
³ DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, USA.
⁴ The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, 77030, USA.
⁵ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
⁶ Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
⁷ Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
⁸ Center for Theoretical and Biological Physics, Rice University, Houston, TX, 77030, USA.
⁹ Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
¹⁰ Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA. [email protected].
¹¹ Eck Institute for Global Health, University of Notre dame, Notre Dame, IN, USA. [email protected].
¹² Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA. [email protected].

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.

Publication types

Dataset

MeSH terms

Animals
Genome, Insect*
High-Throughput Nucleotide Sequencing
Insect Vectors / genetics
Phlebotomus / classification
Phlebotomus / genetics
Psychodidae* / genetics
Sequence Analysis, DNA

Abstract

Publication types

MeSH terms

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