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

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

Journal

Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192

Informations de publication

Date de publication:
24 Aug 2024
Historique:
received: 29 02 2024
accepted: 09 07 2024
medline: 26 8 2024
pubmed: 26 8 2024
entrez: 24 8 2024
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s41597-024-03628-y PMID: 39181902
pubmed: 39181902
doi: 10.1038/s41597-024-03628-y
pii: 10.1038/s41597-024-03628-y
doi:

Types de publication

Journal Article Dataset

Langues

eng

Sous-ensembles de citation

IM

Pagination

918

Subventions

Organisme : U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)
ID : 5R03AI153899-02
Organisme : U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)
ID : 5R03AI153899-02

Informations de copyright

© 2024. The Author(s).

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Auteurs

Michelle Huang (M)

Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.

Sarah Kingan (S)

Pacific Biosciences, Menlo Park, CA, USA.

Douglas Shoue (D)

Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.

Oanh Nguyen (O)

DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, USA.

Lutz Froenicke (L)

DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, USA.

Brendan Galvin (B)

Pacific Biosciences, Menlo Park, CA, USA.

Christine Lambert (C)

Pacific Biosciences, Menlo Park, CA, USA.

Ruqayya Khan (R)

The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, 77030, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.

Chirag Maheshwari (C)

The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, 77030, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.

David Weisz (D)

The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, 77030, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.

Gareth Maslen (G)

Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.

Helen Davison (H)

Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
ORCID: 0000-0002-4302-5756

Erez Lieberman Aiden (EL)

The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, 77030, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Center for Theoretical and Biological Physics, Rice University, Houston, TX, 77030, USA.
Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.

Jonas Korlach (J)

Pacific Biosciences, Menlo Park, CA, USA.

Olga Dudchenko (O)

The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, 77030, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Center for Theoretical and Biological Physics, Rice University, Houston, TX, 77030, USA.

Mary Ann McDowell (MA)

Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA. mcdowell.11@nd.edu.
Eck Institute for Global Health, University of Notre dame, Notre Dame, IN, USA. mcdowell.11@nd.edu.

Stephen Richards (S)

Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA. stephenr@bcm.edu.
ORCID: 0000-0001-8959-5466

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Improved high quality sand fly assemblies...
questionsmedicales.fr › Eucaryotes › Animaux › Invertébrés › Arthropodes › Insectes › Pterygota › Neoptera › Holometabola › Diptera › Psychodidae › Improved high quality sand fly assemblies...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome d'insecte › Improved high quality sand fly assemblies...
questionsmedicales.fr › Eucaryotes › Animaux › Invertébrés › Arthropodes › Insectes › Pterygota › Neoptera › Holometabola › Diptera › Psychodidae › Phlebotomus › Improved high quality sand fly assemblies...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Chaîne d'infection › Vecteurs de maladies › Vecteurs arthropodes › Vecteurs insectes › Improved high quality sand fly assemblies...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Improved high quality sand fly assemblies...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Improved high quality sand fly assemblies...