First draft genome assembly of the Peruvian creole cattle breed (Bos taurus) and its comparative genomics among the Bovinae subfamily
The Peruvian creole cattle (PCC) is a neglected breed, and is an essential livestock resource in the Andean region of Peru. To develop a modern breeding program and conservation strategies for the PCC, a better understanding of the genetics of this breed is needed. We sequenced the whole genome of t...
| Autores principales: | , , , , , , , , |
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| Formato: | Artículo preliminar |
| Lenguaje: | Inglés |
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MDPI
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/20.500.12955/2271 https://doi.org/10.20944/preprints202208.0349.v1 |
| _version_ | 1855490628843995136 |
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| author | Estrada Cañari, Richard Corredor Arizapana, Flor Anita Figueroa Venegas, Deyanira Antonella Salazar Coronel, Wilian Quilcate Pairazamán, Carlos Enrique Vásquez Pérez, Héctor Vladimir Maicelo Quintana, Jorge Luis Gonzales, Jhony Arbizu Berrocal, Carlos Irvin |
| author_browse | Arbizu Berrocal, Carlos Irvin Corredor Arizapana, Flor Anita Estrada Cañari, Richard Figueroa Venegas, Deyanira Antonella Gonzales, Jhony Maicelo Quintana, Jorge Luis Quilcate Pairazamán, Carlos Enrique Salazar Coronel, Wilian Vásquez Pérez, Héctor Vladimir |
| author_facet | Estrada Cañari, Richard Corredor Arizapana, Flor Anita Figueroa Venegas, Deyanira Antonella Salazar Coronel, Wilian Quilcate Pairazamán, Carlos Enrique Vásquez Pérez, Héctor Vladimir Maicelo Quintana, Jorge Luis Gonzales, Jhony Arbizu Berrocal, Carlos Irvin |
| author_sort | Estrada Cañari, Richard |
| collection | Repositorio INIA |
| description | The Peruvian creole cattle (PCC) is a neglected breed, and is an essential livestock resource in the Andean region of Peru. To develop a modern breeding program and conservation strategies for the PCC, a better understanding of the genetics of this breed is needed. We sequenced the whole genome of the PCC using a paired-end 150 strategy on the Illumina HiSeq 2500 platform, obtaining 320 GB of sequencing data. The obtained genome size of the PCC was 2.77 Gb with a contig N50 of 108Mb and 92.59% complete BUSCOs. Also, we identified 40.22% of repetitive DNA of the genome assembly, of which retroelements occupy 32.39% of the total genome. A total of 19,803 protein-coding genes were annotated in the PCC genome. We downloaded proteomes and genomes of the Bovinae subfamily, and conducted a comparative analysis with our draft genome. Phylogenomic analysis showed that PCC is related to Bos indicus. Also, we identified 7,746 family genes shared among the Bovinae subfamily. This first PCC genome is expected to contribute to a better understanding of its genetics to adapt to the tough conditions of the Andean ecosystem, and evolution. |
| format | Artículo preliminar |
| id | INIA2271 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | INIA22712024-01-26T21:41:51Z First draft genome assembly of the Peruvian creole cattle breed (Bos taurus) and its comparative genomics among the Bovinae subfamily Estrada Cañari, Richard Corredor Arizapana, Flor Anita Figueroa Venegas, Deyanira Antonella Salazar Coronel, Wilian Quilcate Pairazamán, Carlos Enrique Vásquez Pérez, Héctor Vladimir Maicelo Quintana, Jorge Luis Gonzales, Jhony Arbizu Berrocal, Carlos Irvin NGS Andean Neglected breed Genome https://purl.org/pe-repo/ocde/ford#4.02.01 Genomes Genomas Bos Taurus The Peruvian creole cattle (PCC) is a neglected breed, and is an essential livestock resource in the Andean region of Peru. To develop a modern breeding program and conservation strategies for the PCC, a better understanding of the genetics of this breed is needed. We sequenced the whole genome of the PCC using a paired-end 150 strategy on the Illumina HiSeq 2500 platform, obtaining 320 GB of sequencing data. The obtained genome size of the PCC was 2.77 Gb with a contig N50 of 108Mb and 92.59% complete BUSCOs. Also, we identified 40.22% of repetitive DNA of the genome assembly, of which retroelements occupy 32.39% of the total genome. A total of 19,803 protein-coding genes were annotated in the PCC genome. We downloaded proteomes and genomes of the Bovinae subfamily, and conducted a comparative analysis with our draft genome. Phylogenomic analysis showed that PCC is related to Bos indicus. Also, we identified 7,746 family genes shared among the Bovinae subfamily. This first PCC genome is expected to contribute to a better understanding of its genetics to adapt to the tough conditions of the Andean ecosystem, and evolution. 2023-08-31T17:33:41Z 2023-08-31T17:33:41Z 2022-08-18 info:eu-repo/semantics/workingPaper Estrada, R.; Corredor, F. A.; Figueroa, D.; Salazar, W.; Quilcate, C.; Vásquez, H. V.; ... & Arbizu, C. I. (2022). First draft genome assembly of the Peruvian creole cattle breed (Bos taurus) and its comparative genomics among the Bovinae subfamily. Preprints, doi: 10.20944/preprints202208.0349.v1 https://hdl.handle.net/20.500.12955/2271 https://doi.org/10.20944/preprints202208.0349.v1 eng Preprints info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ application/pdf application/pdf MDPI CH Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | NGS Andean Neglected breed Genome https://purl.org/pe-repo/ocde/ford#4.02.01 Genomes Genomas Bos Taurus Estrada Cañari, Richard Corredor Arizapana, Flor Anita Figueroa Venegas, Deyanira Antonella Salazar Coronel, Wilian Quilcate Pairazamán, Carlos Enrique Vásquez Pérez, Héctor Vladimir Maicelo Quintana, Jorge Luis Gonzales, Jhony Arbizu Berrocal, Carlos Irvin First draft genome assembly of the Peruvian creole cattle breed (Bos taurus) and its comparative genomics among the Bovinae subfamily |
| title | First draft genome assembly of the Peruvian creole cattle breed (Bos taurus) and its comparative genomics among the Bovinae subfamily |
| title_full | First draft genome assembly of the Peruvian creole cattle breed (Bos taurus) and its comparative genomics among the Bovinae subfamily |
| title_fullStr | First draft genome assembly of the Peruvian creole cattle breed (Bos taurus) and its comparative genomics among the Bovinae subfamily |
| title_full_unstemmed | First draft genome assembly of the Peruvian creole cattle breed (Bos taurus) and its comparative genomics among the Bovinae subfamily |
| title_short | First draft genome assembly of the Peruvian creole cattle breed (Bos taurus) and its comparative genomics among the Bovinae subfamily |
| title_sort | first draft genome assembly of the peruvian creole cattle breed bos taurus and its comparative genomics among the bovinae subfamily |
| topic | NGS Andean Neglected breed Genome https://purl.org/pe-repo/ocde/ford#4.02.01 Genomes Genomas Bos Taurus |
| url | https://hdl.handle.net/20.500.12955/2271 https://doi.org/10.20944/preprints202208.0349.v1 |
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