The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Jay Ghurye - One of the best experts on this subject based on the ideXlab platform.
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a chromosome scale assembly of the major african malaria vector anopheles funestus
GigaScience, 2019Co-Authors: Jay Ghurye, Seth Redmond, Paul I Howell, Sergey Koren, Adam M Phillippy, Scott T. Small, Nora J. BesanskyAbstract: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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a chromosome scale assembly of the major african malaria vector anopheles funestus
bioRxiv, 2018Co-Authors: Jay Ghurye, Seth Redmond, Paul I Howell, Sergey Koren, Adam M Phillippy, Scott T. Small, Nora J. BesanskyAbstract:Abstract Background Anopheles funestus is one of the three 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 An. funestus reference genome (AfunF3) assembled using 240x coverage of long-read single-molecule sequencing for Contigging, combined with 100x 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 An. funestus reference genome assembly will serve as an improved basis for future studies of genomic variation and organization in this important disease vector.
Nora J. Besansky - One of the best experts on this subject based on the ideXlab platform.
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a chromosome scale assembly of the major african malaria vector anopheles funestus
GigaScience, 2019Co-Authors: Jay Ghurye, Seth Redmond, Paul I Howell, Sergey Koren, Adam M Phillippy, Scott T. Small, Nora J. BesanskyAbstract: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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a chromosome scale assembly of the major african malaria vector anopheles funestus
bioRxiv, 2018Co-Authors: Jay Ghurye, Seth Redmond, Paul I Howell, Sergey Koren, Adam M Phillippy, Scott T. Small, Nora J. BesanskyAbstract:Abstract Background Anopheles funestus is one of the three 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 An. funestus reference genome (AfunF3) assembled using 240x coverage of long-read single-molecule sequencing for Contigging, combined with 100x 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 An. funestus reference genome assembly will serve as an improved basis for future studies of genomic variation and organization in this important disease vector.
Seth Redmond - One of the best experts on this subject based on the ideXlab platform.
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a chromosome scale assembly of the major african malaria vector anopheles funestus
GigaScience, 2019Co-Authors: Jay Ghurye, Seth Redmond, Paul I Howell, Sergey Koren, Adam M Phillippy, Scott T. Small, Nora J. BesanskyAbstract: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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a chromosome scale assembly of the major african malaria vector anopheles funestus
bioRxiv, 2018Co-Authors: Jay Ghurye, Seth Redmond, Paul I Howell, Sergey Koren, Adam M Phillippy, Scott T. Small, Nora J. BesanskyAbstract:Abstract Background Anopheles funestus is one of the three 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 An. funestus reference genome (AfunF3) assembled using 240x coverage of long-read single-molecule sequencing for Contigging, combined with 100x 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 An. funestus reference genome assembly will serve as an improved basis for future studies of genomic variation and organization in this important disease vector.
Brian P Lazzaro - One of the best experts on this subject based on the ideXlab platform.
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de novo transcriptome sequencing in anopheles funestus using illumina rna seq technology
PLOS ONE, 2010Co-Authors: Jacob E Crawford, Wamdaogo M Guelbeogo, Antoine Sanou, Alphonse Traore, Kenneth D Vernick, Nfale Sagnon, Brian P LazzaroAbstract:Background: Anopheles funestus is one of the primary vectors of human malaria, which causes a million deaths each year in sub-Saharan Africa. Few scientific resources are available to facilitate studies of this mosquito species and relatively little is known about its basic biology and evolution, making development and implementation of novel disease control efforts more difficult. The An. funestus genome has not been sequenced, so in order to facilitate genome-scale experimental biology, we have sequenced the adult female transcriptome of An. funestus from a newly founded colony in Burkina Faso, West Africa, using the Illumina GAIIx next generation sequencing platform. Methodology/Principal Findings: We assembled short Illumina reads de novo using a novel approach involving iterative de novo assemblies and ‘‘target-based’’ Contig clustering. We then selected a conservative set of 15,527 Contigs through comparisons to four Dipteran transcriptomes as well as multiple functional and conserved protein domain databases. Comparison to the Anopheles gambiae immune system identified 339 Contigs as putative immune genes, thus identifying a large portion of the immune system that can form the basis for subsequent studies of this important malaria vector. We identified 5,434 1:1 orthologues between An. funestus and An. gambiae and found that among these 1:1 orthologues, the protein sequence of those with putative immune function were significantly more diverged than the transcriptome as a whole. Short read alignments to the Contig set revealed almost 367,000 genetic polymorphisms segregating in the An. funestus colony and demonstrated the utility of the assembled transcriptome for use in RNA-seq based measurements of gene expression. Conclusions/Significance: We developed a pipeline that makes de novo transcriptome sequencing possible in virtually any organism at a very reasonable cost ($6,300 in sequencing costs in our case). We anticipate that our approach could be used to develop genomic resources in a diversity of systems for which full genome sequence is currently unavailable. Our An. funestus Contig set and analytical results provide a valuable resource for future studies in this non-model, but epidemiologically critical, vector insect.
Kenneth D Vernick - One of the best experts on this subject based on the ideXlab platform.
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de novo transcriptome sequencing in anopheles funestus using illumina rna seq technology
PLOS ONE, 2010Co-Authors: Jacob E Crawford, Wamdaogo M Guelbeogo, Antoine Sanou, Alphonse Traore, Kenneth D Vernick, Nfale Sagnon, Brian P LazzaroAbstract:Background: Anopheles funestus is one of the primary vectors of human malaria, which causes a million deaths each year in sub-Saharan Africa. Few scientific resources are available to facilitate studies of this mosquito species and relatively little is known about its basic biology and evolution, making development and implementation of novel disease control efforts more difficult. The An. funestus genome has not been sequenced, so in order to facilitate genome-scale experimental biology, we have sequenced the adult female transcriptome of An. funestus from a newly founded colony in Burkina Faso, West Africa, using the Illumina GAIIx next generation sequencing platform. Methodology/Principal Findings: We assembled short Illumina reads de novo using a novel approach involving iterative de novo assemblies and ‘‘target-based’’ Contig clustering. We then selected a conservative set of 15,527 Contigs through comparisons to four Dipteran transcriptomes as well as multiple functional and conserved protein domain databases. Comparison to the Anopheles gambiae immune system identified 339 Contigs as putative immune genes, thus identifying a large portion of the immune system that can form the basis for subsequent studies of this important malaria vector. We identified 5,434 1:1 orthologues between An. funestus and An. gambiae and found that among these 1:1 orthologues, the protein sequence of those with putative immune function were significantly more diverged than the transcriptome as a whole. Short read alignments to the Contig set revealed almost 367,000 genetic polymorphisms segregating in the An. funestus colony and demonstrated the utility of the assembled transcriptome for use in RNA-seq based measurements of gene expression. Conclusions/Significance: We developed a pipeline that makes de novo transcriptome sequencing possible in virtually any organism at a very reasonable cost ($6,300 in sequencing costs in our case). We anticipate that our approach could be used to develop genomic resources in a diversity of systems for which full genome sequence is currently unavailable. Our An. funestus Contig set and analytical results provide a valuable resource for future studies in this non-model, but epidemiologically critical, vector insect.