First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey ( Ateles fusciceps fusciceps ), a critically endangered species, using Oxford Nanopore Technologies
The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered [International union for conservation of nature (IUCN)]. It faces multiple threats, the most significant one bein...
| Main Authors: | , , , , , , |
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| Format: | Journal article |
| Language: | English |
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Genetics Society of America
2024
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| _version_ | 1826313116364832768 |
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| author | Pozo, G Albuja-Quintana, M Larreátegui, L Gutiérrez, B Fuentes, N Alfonso-Cortés, F Torres, MDL |
| author_facet | Pozo, G Albuja-Quintana, M Larreátegui, L Gutiérrez, B Fuentes, N Alfonso-Cortés, F Torres, MDL |
| author_sort | Pozo, G |
| collection | OXFORD |
| description | The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered [International union for conservation of nature (IUCN)]. It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are keys for the management of endangered species, but this requires a reference genome, which until now was unavailable for A. f. fusciceps. The present study reports the first whole-genome sequence and assembly of A. f. fusciceps generated using Oxford Nanopore long reads. DNA was extracted from a subadult male, and libraries were prepared for sequencing following the Ligation Sequencing Kit SQK-LSK112 workflow. Sequencing was performed using a MinION Mk1C sequencer. The sequencing reads were processed to generate a genome assembly. Two different assemblers were used to obtain draft genomes using raw reads, of which the Flye assembly was found to be superior. The final assembly has a total length of 2.63 Gb and contains 3,861 contigs, with an N50 of 7,560,531 bp. The assembly was analyzed for annotation completeness based on primate ortholog prediction using a high-resolution database, and was found to be 84.3% complete, with a low number of duplicated genes indicating a precise assembly. The annotation of the assembly predicted 31,417 protein-coding genes, comparable with other mammal assemblies. A reference genome for this critically endangered species will allow researchers to gain insight into the genetics of its populations and thus aid conservation and management efforts of this vulnerable species. |
| first_indexed | 2024-09-25T04:07:56Z |
| format | Journal article |
| id | oxford-uuid:d35ebb09-2b2a-4e8b-9844-9dced0e4d9d4 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-09-25T04:07:56Z |
| publishDate | 2024 |
| publisher | Genetics Society of America |
| record_format | dspace |
| spelling | oxford-uuid:d35ebb09-2b2a-4e8b-9844-9dced0e4d9d42024-05-30T10:14:23ZFirst whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey ( Ateles fusciceps fusciceps ), a critically endangered species, using Oxford Nanopore TechnologiesJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:d35ebb09-2b2a-4e8b-9844-9dced0e4d9d4EnglishJisc Publications RouterGenetics Society of America2024Pozo, GAlbuja-Quintana, MLarreátegui, LGutiérrez, BFuentes, NAlfonso-Cortés, FTorres, MDLThe Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered [International union for conservation of nature (IUCN)]. It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are keys for the management of endangered species, but this requires a reference genome, which until now was unavailable for A. f. fusciceps. The present study reports the first whole-genome sequence and assembly of A. f. fusciceps generated using Oxford Nanopore long reads. DNA was extracted from a subadult male, and libraries were prepared for sequencing following the Ligation Sequencing Kit SQK-LSK112 workflow. Sequencing was performed using a MinION Mk1C sequencer. The sequencing reads were processed to generate a genome assembly. Two different assemblers were used to obtain draft genomes using raw reads, of which the Flye assembly was found to be superior. The final assembly has a total length of 2.63 Gb and contains 3,861 contigs, with an N50 of 7,560,531 bp. The assembly was analyzed for annotation completeness based on primate ortholog prediction using a high-resolution database, and was found to be 84.3% complete, with a low number of duplicated genes indicating a precise assembly. The annotation of the assembly predicted 31,417 protein-coding genes, comparable with other mammal assemblies. A reference genome for this critically endangered species will allow researchers to gain insight into the genetics of its populations and thus aid conservation and management efforts of this vulnerable species. |
| spellingShingle | Pozo, G Albuja-Quintana, M Larreátegui, L Gutiérrez, B Fuentes, N Alfonso-Cortés, F Torres, MDL First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey ( Ateles fusciceps fusciceps ), a critically endangered species, using Oxford Nanopore Technologies |
| title | First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey ( Ateles fusciceps fusciceps ), a critically endangered species, using Oxford Nanopore Technologies |
| title_full | First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey ( Ateles fusciceps fusciceps ), a critically endangered species, using Oxford Nanopore Technologies |
| title_fullStr | First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey ( Ateles fusciceps fusciceps ), a critically endangered species, using Oxford Nanopore Technologies |
| title_full_unstemmed | First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey ( Ateles fusciceps fusciceps ), a critically endangered species, using Oxford Nanopore Technologies |
| title_short | First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey ( Ateles fusciceps fusciceps ), a critically endangered species, using Oxford Nanopore Technologies |
| title_sort | first whole genome sequence and assembly of the ecuadorian brown headed spider monkey ateles fusciceps fusciceps a critically endangered species using oxford nanopore technologies |
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