A chromosome-scale assembly of the major African malaria vector Anopheles funestus
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Abstract
Background
Anopheles funestus is one of the 3 most consequential and widespread vectors of human malaria in tropical Africa. However, the lack of a high-quality reference genome has hindered the association of phenotypic traits with their genetic basis in this important mosquito.
Findings
Here we present a new high-quality A. funestus reference genome (AfunF3) assembled using 240× coverage of long-read single-molecule sequencing for contigging, combined with 100× coverage of short-read Hi-C data for chromosome scaffolding. The assembled contigs total 446 Mbp of sequence and contain substantial duplication due to alternative alleles present in the sequenced pool of mosquitos from the FUMOZ colony. Using alignment and depth-of-coverage information, these contigs were deduplicated to a 211 Mbp primary assembly, which is closer to the expected haploid genome size of 250 Mbp. This primary assembly consists of 1,053 contigs organized into 3 chromosome-scale scaffolds with an N50 contig size of 632 kbp and an N50 scaffold size of 93.811 Mbp, representing a 100-fold improvement in continuity versus the current reference assembly, AfunF1.
Conclusion
This highly contiguous and complete A. funestus reference genome assembly will serve as an improved basis for future studies of genomic variation and organization in this important disease vector.
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Now published in GigaScience doi: 10.1093/gigascience/giz063
Jay Ghurye 1Department of Computer Science, University of Maryland, College Park, MD2Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, MDFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSergey Koren 2Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, MDFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteScott T. Small 3Department of Biological Sciences, University of Notre Dame, South Bend, INFind this author on Google ScholarFind this author on PubMedSearch for this author on …
Now published in GigaScience doi: 10.1093/gigascience/giz063
Jay Ghurye 1Department of Computer Science, University of Maryland, College Park, MD2Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, MDFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSergey Koren 2Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, MDFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteScott T. Small 3Department of Biological Sciences, University of Notre Dame, South Bend, INFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSeth Redmond 4Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA5Department of Immunology and Infectious Disease, Harvard TH Chan School of Public Health, Boston, MAFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePaul Howell 6Centers for Disease Control, Atlanta, GAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdam M. Phillippy 2Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, MDFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNora J. Besansky 3Department of Biological Sciences, University of Notre Dame, South Bend, INFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz063 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101744 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101745
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