Reference-Guided Draft Genome Assembly, Annotation and SSR Mining Data of the Peruvian Creole Cattle (Bos taurus)
The Peruvian creole cattle (PCC) is a neglected breed and 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 P...
| Autores principales: | , , , , , , , , |
|---|---|
| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
MDPI
2022
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/20.500.12955/2054 https://doi.org/10.3390/data7110155 |
| _version_ | 1855490214686883840 |
|---|---|
| author | Estrada Cañari, Richard Corredor Arizapana, Flor Anita Figueroa, Deyanira 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, Deyanira 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, Deyanira 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 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 de novo assembly approach with a paired-end 150 strategy on the Illumina HiSeq 2500 platform, obtaining 320 GB of sequencing data. A reference scaffolding was used to improve the draft genome. The obtained genome size of the PCC was 2.81 Gb with a contig N50 of 108 Mb and 92.59% complete BUSCOs. This genome size is similar to the genome references of Bos taurus and B. indicus. In addition, 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. For SSR data mining, we detected similar statistics in comparison with other breeds. The PCC genome will contribute to a better understanding of the genetics of this species and its adaptation to tough conditions in the Andean ecosystem. |
| format | Artículo |
| id | INIA2054 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | INIA20542023-08-23T22:23:32Z Reference-Guided Draft Genome Assembly, Annotation and SSR Mining Data of the Peruvian Creole Cattle (Bos taurus) Estrada Cañari, Richard Corredor Arizapana, Flor Anita Figueroa, Deyanira Salazar Coronel, Wilian Quilcate Pairazamán, Carlos Enrique Vásquez Pérez, Héctor Vladimir Maicelo Quintana, Jorge Luis Gonzales, Jhony Arbizu Berrocal, Carlos Irvin NGS Neglected breed Genome Reference scaffolding Microsatellites https://purl.org/pe-repo/ocde/ford#4.03.01 High-throughput sequencing Breeds (animals) Genomes Microsatellites The Peruvian creole cattle (PCC) is a neglected breed and 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 de novo assembly approach with a paired-end 150 strategy on the Illumina HiSeq 2500 platform, obtaining 320 GB of sequencing data. A reference scaffolding was used to improve the draft genome. The obtained genome size of the PCC was 2.81 Gb with a contig N50 of 108 Mb and 92.59% complete BUSCOs. This genome size is similar to the genome references of Bos taurus and B. indicus. In addition, 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. For SSR data mining, we detected similar statistics in comparison with other breeds. The PCC genome will contribute to a better understanding of the genetics of this species and its adaptation to tough conditions in the Andean ecosystem. 2022-12-30T16:07:17Z 2022-12-30T16:07:17Z 2022-11-09 info:eu-repo/semantics/article Estrada, R.; Corredor, F.; Figueroa, D.; Salazar, W.; Quilcate, C.; Vásquez, H.; Maicelo, J.; Gonzales, J. & Arbizu, C. (2022). Reference-Guided Draft Genome Assembly, Annotation and SSR Mining Data of the Peruvian Creole Cattle (Bos taurus). Data 2022, 7, 155. doi: 10.3390/data7110155 https://hdl.handle.net/20.500.12955/2054 https://doi.org/10.3390/data7110155 eng Data info:eu-repo/semantics/openAccess Attribution-NonCommercial-NoDerivs 3.0 United States http://creativecommons.org/licenses/by-nc-nd/3.0/us/ application/pdf application/pdf MDPI CH Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | NGS Neglected breed Genome Reference scaffolding Microsatellites https://purl.org/pe-repo/ocde/ford#4.03.01 High-throughput sequencing Breeds (animals) Genomes Microsatellites Estrada Cañari, Richard Corredor Arizapana, Flor Anita Figueroa, Deyanira Salazar Coronel, Wilian Quilcate Pairazamán, Carlos Enrique Vásquez Pérez, Héctor Vladimir Maicelo Quintana, Jorge Luis Gonzales, Jhony Arbizu Berrocal, Carlos Irvin Reference-Guided Draft Genome Assembly, Annotation and SSR Mining Data of the Peruvian Creole Cattle (Bos taurus) |
| title | Reference-Guided Draft Genome Assembly, Annotation and SSR Mining Data of the Peruvian Creole Cattle (Bos taurus) |
| title_full | Reference-Guided Draft Genome Assembly, Annotation and SSR Mining Data of the Peruvian Creole Cattle (Bos taurus) |
| title_fullStr | Reference-Guided Draft Genome Assembly, Annotation and SSR Mining Data of the Peruvian Creole Cattle (Bos taurus) |
| title_full_unstemmed | Reference-Guided Draft Genome Assembly, Annotation and SSR Mining Data of the Peruvian Creole Cattle (Bos taurus) |
| title_short | Reference-Guided Draft Genome Assembly, Annotation and SSR Mining Data of the Peruvian Creole Cattle (Bos taurus) |
| title_sort | reference guided draft genome assembly annotation and ssr mining data of the peruvian creole cattle bos taurus |
| topic | NGS Neglected breed Genome Reference scaffolding Microsatellites https://purl.org/pe-repo/ocde/ford#4.03.01 High-throughput sequencing Breeds (animals) Genomes Microsatellites |
| url | https://hdl.handle.net/20.500.12955/2054 https://doi.org/10.3390/data7110155 |
| work_keys_str_mv | AT estradacanaririchard referenceguideddraftgenomeassemblyannotationandssrminingdataoftheperuviancreolecattlebostaurus AT corredorarizapanafloranita referenceguideddraftgenomeassemblyannotationandssrminingdataoftheperuviancreolecattlebostaurus AT figueroadeyanira referenceguideddraftgenomeassemblyannotationandssrminingdataoftheperuviancreolecattlebostaurus AT salazarcoronelwilian referenceguideddraftgenomeassemblyannotationandssrminingdataoftheperuviancreolecattlebostaurus AT quilcatepairazamancarlosenrique referenceguideddraftgenomeassemblyannotationandssrminingdataoftheperuviancreolecattlebostaurus AT vasquezperezhectorvladimir referenceguideddraftgenomeassemblyannotationandssrminingdataoftheperuviancreolecattlebostaurus AT maiceloquintanajorgeluis referenceguideddraftgenomeassemblyannotationandssrminingdataoftheperuviancreolecattlebostaurus AT gonzalesjhony referenceguideddraftgenomeassemblyannotationandssrminingdataoftheperuviancreolecattlebostaurus AT arbizuberrocalcarlosirvin referenceguideddraftgenomeassemblyannotationandssrminingdataoftheperuviancreolecattlebostaurus |