De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural Madagascar
ABSTRACT As one of the most threatened mammalian taxa, lemurs of Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on conservation genomics to identify populations of particular concern. However, many o...
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Wiley
2025-01-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.70734 |
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| author | Lindsey Hauff Noa Elosmie Rasoanaivo Andriamahery Razafindrakoto Hajanirina Ravelonjanahary Patricia C. Wright Rindra Rakotoarivony Christina M. Bergey |
| author_facet | Lindsey Hauff Noa Elosmie Rasoanaivo Andriamahery Razafindrakoto Hajanirina Ravelonjanahary Patricia C. Wright Rindra Rakotoarivony Christina M. Bergey |
| author_sort | Lindsey Hauff |
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| description | ABSTRACT As one of the most threatened mammalian taxa, lemurs of Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on conservation genomics to identify populations of particular concern. However, many of these genomic approaches necessitate high‐quality genomes. While the advent of next‐generation sequencing technologies and the resulting reduction in associated costs have led to the proliferation of genomic data and high‐quality reference genomes, global discrepancies in genomic sequencing capabilities often result in biological samples from biodiverse host countries being exported to facilities in the Global North, creating inequalities in access and training within genomic research. Here, we present the first published reference genome for the endangered red‐fronted brown lemur (Eulemur rufifrons) from sequencing efforts conducted entirely within the host country using portable Oxford Nanopore sequencing. Using an archived E. rufifrons specimen, we conducted long‐read, nanopore sequencing at the Centre ValBio Research Station near Ranomafana National Park, in rural Madagascar, generating over 750 Gb of sequencing data from 10 MinION flow cells. Exclusively using this long‐read data, we assembled 2.157 gigabase, 2980‐contig nuclear assembly with an N50 of 101.6 Mb and a 17,108 bp mitogenome. The nuclear assembly had 30× average coverage and was comparable in completeness to other primate reference genomes, with a 96.1% BUSCO completeness score for primate‐specific genes. As the first published reference genome for E. rufifrons and the only annotated genome available for the speciose Eulemur genus, this resource will prove vital for conservation genomic studies while our efforts exhibit the potential of this protocol to address research inequalities and build genomic capacity. |
| format | Article |
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| institution | Kabale University |
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| language | English |
| publishDate | 2025-01-01 |
| publisher | Wiley |
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| series | Ecology and Evolution |
| spelling | doaj-art-9870eace22794d238fd7d4d416e85ee32025-01-29T05:08:41ZengWileyEcology and Evolution2045-77582025-01-01151n/an/a10.1002/ece3.70734De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural MadagascarLindsey Hauff0Noa Elosmie Rasoanaivo1Andriamahery Razafindrakoto2Hajanirina Ravelonjanahary3Patricia C. Wright4Rindra Rakotoarivony5Christina M. Bergey6Department of Ecology, Evolution, and Natural Resources Rutgers University New Brunswick New Jersey USADepartment of Zoology and Animal Biodiversity University of Antananarivo Antananarivo MadagascarCentre ValBio, Ranomafana National Park Ifanadiana MadagascarCentre ValBio, Ranomafana National Park Ifanadiana MadagascarCentre ValBio, Ranomafana National Park Ifanadiana MadagascarDepartment of Biological Anthropology and Sustainable Development University of Antananarivo Antananarivo MadagascarCenter for Human Evolutionary Studies Rutgers University New Brunswick New Jersey USAABSTRACT As one of the most threatened mammalian taxa, lemurs of Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on conservation genomics to identify populations of particular concern. However, many of these genomic approaches necessitate high‐quality genomes. While the advent of next‐generation sequencing technologies and the resulting reduction in associated costs have led to the proliferation of genomic data and high‐quality reference genomes, global discrepancies in genomic sequencing capabilities often result in biological samples from biodiverse host countries being exported to facilities in the Global North, creating inequalities in access and training within genomic research. Here, we present the first published reference genome for the endangered red‐fronted brown lemur (Eulemur rufifrons) from sequencing efforts conducted entirely within the host country using portable Oxford Nanopore sequencing. Using an archived E. rufifrons specimen, we conducted long‐read, nanopore sequencing at the Centre ValBio Research Station near Ranomafana National Park, in rural Madagascar, generating over 750 Gb of sequencing data from 10 MinION flow cells. Exclusively using this long‐read data, we assembled 2.157 gigabase, 2980‐contig nuclear assembly with an N50 of 101.6 Mb and a 17,108 bp mitogenome. The nuclear assembly had 30× average coverage and was comparable in completeness to other primate reference genomes, with a 96.1% BUSCO completeness score for primate‐specific genes. As the first published reference genome for E. rufifrons and the only annotated genome available for the speciose Eulemur genus, this resource will prove vital for conservation genomic studies while our efforts exhibit the potential of this protocol to address research inequalities and build genomic capacity.https://doi.org/10.1002/ece3.70734Centre ValBio Research Stationconservation genomicsgenome assemblyOxford Nanopore sequencingred‐fronted brown lemurreference genome |
| spellingShingle | Lindsey Hauff Noa Elosmie Rasoanaivo Andriamahery Razafindrakoto Hajanirina Ravelonjanahary Patricia C. Wright Rindra Rakotoarivony Christina M. Bergey De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural Madagascar Ecology and Evolution Centre ValBio Research Station conservation genomics genome assembly Oxford Nanopore sequencing red‐fronted brown lemur reference genome |
| title | De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural Madagascar |
| title_full | De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural Madagascar |
| title_fullStr | De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural Madagascar |
| title_full_unstemmed | De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural Madagascar |
| title_short | De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural Madagascar |
| title_sort | de novo genome assembly for an endangered lemur using portable nanopore sequencing in rural madagascar |
| topic | Centre ValBio Research Station conservation genomics genome assembly Oxford Nanopore sequencing red‐fronted brown lemur reference genome |
| url | https://doi.org/10.1002/ece3.70734 |
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