A chromosome-scale assembly of the major African malaria vector Anopheles funestus

Jay Ghurye, Sergey Koren, Scott T. Small, Seth Redmond, Paul Howell, Adam M. Phillippy, Nora J. Besansky

Research output: Contribution to journalArticleResearchpeer-review

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.

Original languageEnglish
Article numbergiz063
Number of pages8
JournalGigaScience
Volume8
Issue number6
DOIs
Publication statusPublished - 1 Jun 2019
Externally publishedYes

Keywords

  • Anopheles mosquito
  • DNA sequencing
  • genome assembly
  • Hi-C chromosome conformation capture
  • malaria

Cite this

Ghurye, J., Koren, S., Small, S. T., Redmond, S., Howell, P., Phillippy, A. M., & Besansky, N. J. (2019). A chromosome-scale assembly of the major African malaria vector Anopheles funestus. GigaScience, 8(6), [giz063]. https://doi.org/10.1093/gigascience/giz063
Ghurye, Jay ; Koren, Sergey ; Small, Scott T. ; Redmond, Seth ; Howell, Paul ; Phillippy, Adam M. ; Besansky, Nora J. / A chromosome-scale assembly of the major African malaria vector Anopheles funestus. In: GigaScience. 2019 ; Vol. 8, No. 6.
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Ghurye, J, Koren, S, Small, ST, Redmond, S, Howell, P, Phillippy, AM & Besansky, NJ 2019, 'A chromosome-scale assembly of the major African malaria vector Anopheles funestus', GigaScience, vol. 8, no. 6, giz063. https://doi.org/10.1093/gigascience/giz063

A chromosome-scale assembly of the major African malaria vector Anopheles funestus. / Ghurye, Jay; Koren, Sergey; Small, Scott T.; Redmond, Seth; Howell, Paul; Phillippy, Adam M.; Besansky, Nora J.

In: GigaScience, Vol. 8, No. 6, giz063, 01.06.2019.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Ghurye, Jay

AU - Koren, Sergey

AU - Small, Scott T.

AU - Redmond, Seth

AU - Howell, Paul

AU - Phillippy, Adam M.

AU - Besansky, Nora J.

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N2 - 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.

AB - 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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