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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 papatasiandLutzomyia longipalpis. These chromosome-level assemblies were generated using an ultra-low input library protocol, PacBio HiFi long reads, and Hi-C technology. The newP. papatasireference has a final assembly span of 351.6 Mb and contig and scaffold N50s of 926 kb and 111.8 Mb, respectively. The newLu. longipalpisreference 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 forP. papatasiandLu. longipalpis. These improved assemblies will serve as an invaluable resource for future genomic work on phlebotomine sandflies.
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This content will become publicly available on December 1, 2026
Universal orthologs infer deep phylogenies and improve genome quality assessments
Abstract BackgroundUniversal single-copy orthologs are the most conserved components of genomes. Although they are routinely used for studying evolutionary histories and assessing new assemblies, current methods do not incorporate information from available genomic data. ResultsHere, we first determine the influence of evolutionary history on universal gene content and find that across 11,098 genomes of plants, fungi, and animals comprising 2606 taxonomic groups, 215 groups significantly vary from their respective lineages in terms of BUSCO (Benchmarking Universal Single Copy Orthologs) completeness. Additionally, 169 groups display an elevated complement of duplicated orthologs, likely from ancestral whole genome duplication events. Secondly, we investigate the extent of taxonomic congruence in broad BUSCO-derived phylogenies. For 275 suitable families out of 543 tested, sites evolving at higher rates produce at most 23.84% more taxonomically concordant, and at least 46.15% less terminally variable phylogenies compared to lower-rate sites. We find that BUSCO concatenated and coalescent trees have comparable accuracy and conclude that higher rate sites from concatenated alignments produce the most congruent and least variable phylogenies. Finally, we show that undetected, yet pervasive BUSCO gene loss events lead to misrepresentations of assembly quality. To overcome this, we filter a Curated set of BUSCOs (CUSCOs) that provide up to 6.99% fewer false positives compared to the standard search and introduce novel methods for comparing assemblies using gene synteny. ConclusionsOverall, we highlight the importance of considering evolutionary histories during assembly evaluations and release the phyca software toolkit that reconstructs consistent phylogenies and offers more precise assembly assessments.
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- Award ID(s):
- 2022055
- PAR ID:
- 10632967
- Publisher / Repository:
- BMC Biology
- Date Published:
- Journal Name:
- BMC Biology
- Volume:
- 23
- Issue:
- 1
- ISSN:
- 1741-7007
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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