Draft genome sequence and SSR data mining of “pumpo” (Bos taurus), a top bull from a peruvian genetic nucleus
Pumpo is a Simmental breed and an essential livestock resource in the nucleus genetic cattle of Peru. This study provides a draft genome sequence of a top bull using a de novo assembly approach on the Illumina Novaseq X platform, yielding 208 GB of raw sequencing data with 150 bp paired‐end reads. T...
| Main Authors: | , , , , , , , , |
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| Format: | Artículo preliminar |
| Language: | Inglés |
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MDPI
2024
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| Subjects: | |
| Online Access: | https://hdl.handle.net/20.500.12955/2531 https://doi.org/10.20944/preprints202406.1085.v1 |
| _version_ | 1855490531797237760 |
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| author | Estrada Cañari, Richard Romero Avila, Yolanda Figueroa Venegas, Deyanira Antonella Quilcate Pairazaman, Carlos Enrique Casanova Nuñez Melgar, David Pavel Vásquez Pérez, Hector Vladimir Alvarado Chuqui, Wigoberto Maicelo Quintana, Jorge Luis Arbizu Berrocal, Carlos Irvin |
| author_browse | Alvarado Chuqui, Wigoberto Arbizu Berrocal, Carlos Irvin Casanova Nuñez Melgar, David Pavel Estrada Cañari, Richard Figueroa Venegas, Deyanira Antonella Maicelo Quintana, Jorge Luis Quilcate Pairazaman, Carlos Enrique Romero Avila, Yolanda Vásquez Pérez, Hector Vladimir |
| author_facet | Estrada Cañari, Richard Romero Avila, Yolanda Figueroa Venegas, Deyanira Antonella Quilcate Pairazaman, Carlos Enrique Casanova Nuñez Melgar, David Pavel Vásquez Pérez, Hector Vladimir Alvarado Chuqui, Wigoberto Maicelo Quintana, Jorge Luis Arbizu Berrocal, Carlos Irvin |
| author_sort | Estrada Cañari, Richard |
| collection | Repositorio INIA |
| description | Pumpo is a Simmental breed and an essential livestock resource in the nucleus genetic cattle of Peru. This study provides a draft genome sequence of a top bull using a de novo assembly approach on the Illumina Novaseq X platform, yielding 208 GB of raw sequencing data with 150 bp paired‐end reads. The final genome assembly resulted in a size of 2.06 Gb with an N50 contig length of 108 Mb and a completeness of 95.7% according to BUSCO analysis. A total of 973,925 simple sequence repeats (SSRs) were identified, with a predominance of mononucleotide repeats. The genome showed low heterozygosity (0.568%) and moderate repeatability (11.5%), aligning with other Bos taurus genomes. Reference‐guided scaffolding improved the assembly quality significantly, producing an N50 scaffold value of 108 Mb. The SSR analysis of the Pumpo genome identified 973,925 SSRs with a frequency of 2,808 SSRs per kilobase, predominantly mononucleotide repeats, and 85,453 found in compound formations. Obtaining knowledge of the genome of a breeding Simmental bull is essential to optimize breeding programs and improve productivity. |
| format | Artículo preliminar |
| id | INIA2531 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | INIA25312025-05-26T01:02:43Z Draft genome sequence and SSR data mining of “pumpo” (Bos taurus), a top bull from a peruvian genetic nucleus Estrada Cañari, Richard Romero Avila, Yolanda Figueroa Venegas, Deyanira Antonella Quilcate Pairazaman, Carlos Enrique Casanova Nuñez Melgar, David Pavel Vásquez Pérez, Hector Vladimir Alvarado Chuqui, Wigoberto Maicelo Quintana, Jorge Luis Arbizu Berrocal, Carlos Irvin Draft-Genome Pumpo Bos taurus BUSCO Genome Assembly SSR Analysis https://purl.org/pe-repo/ocde/ford#4.02.01 Genomes Genomas Bos taurus Genome annotation Anotación del genoma Microsatellites Microsatélites Pumpo is a Simmental breed and an essential livestock resource in the nucleus genetic cattle of Peru. This study provides a draft genome sequence of a top bull using a de novo assembly approach on the Illumina Novaseq X platform, yielding 208 GB of raw sequencing data with 150 bp paired‐end reads. The final genome assembly resulted in a size of 2.06 Gb with an N50 contig length of 108 Mb and a completeness of 95.7% according to BUSCO analysis. A total of 973,925 simple sequence repeats (SSRs) were identified, with a predominance of mononucleotide repeats. The genome showed low heterozygosity (0.568%) and moderate repeatability (11.5%), aligning with other Bos taurus genomes. Reference‐guided scaffolding improved the assembly quality significantly, producing an N50 scaffold value of 108 Mb. The SSR analysis of the Pumpo genome identified 973,925 SSRs with a frequency of 2,808 SSRs per kilobase, predominantly mononucleotide repeats, and 85,453 found in compound formations. Obtaining knowledge of the genome of a breeding Simmental bull is essential to optimize breeding programs and improve productivity. This research was funded by the following research project: “Mejoramiento de la disponibilidad de material genético de ganado bovino con alto valor a nivel nacional 7 departamentos” of the Ministry of Agrarian Development and Irrigation (MIDAGRI) of the Peruvian Government, with grant number CUI 2432072. 2024-07-03T03:39:24Z 2024-07-03T03:39:24Z 2024-06-18 info:eu-repo/semantics/workingPaper Estrada, R.; Romero, Y.; Figueroa, D.; Quilcate, C.; Casanova, D.; Vasquez, H. V.; Alvarado, W.; Maicelo, J. L.; & Arbizu, C. I. (2024). Draft genome sequence and SSR data mining of “pumpo” (Bos taurus), a top bull from a peruvian genetic nucleus. Preprints, 2024061085. doi: 10.20944/preprints202406.1085.v1 2310-287X https://hdl.handle.net/20.500.12955/2531 https://doi.org/10.20944/preprints202406.1085.v1 eng urn:issn: 2310-287X 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 | Draft-Genome Pumpo Bos taurus BUSCO Genome Assembly SSR Analysis https://purl.org/pe-repo/ocde/ford#4.02.01 Genomes Genomas Bos taurus Genome annotation Anotación del genoma Microsatellites Microsatélites Estrada Cañari, Richard Romero Avila, Yolanda Figueroa Venegas, Deyanira Antonella Quilcate Pairazaman, Carlos Enrique Casanova Nuñez Melgar, David Pavel Vásquez Pérez, Hector Vladimir Alvarado Chuqui, Wigoberto Maicelo Quintana, Jorge Luis Arbizu Berrocal, Carlos Irvin Draft genome sequence and SSR data mining of “pumpo” (Bos taurus), a top bull from a peruvian genetic nucleus |
| title | Draft genome sequence and SSR data mining of “pumpo” (Bos taurus), a top bull from a peruvian genetic nucleus |
| title_full | Draft genome sequence and SSR data mining of “pumpo” (Bos taurus), a top bull from a peruvian genetic nucleus |
| title_fullStr | Draft genome sequence and SSR data mining of “pumpo” (Bos taurus), a top bull from a peruvian genetic nucleus |
| title_full_unstemmed | Draft genome sequence and SSR data mining of “pumpo” (Bos taurus), a top bull from a peruvian genetic nucleus |
| title_short | Draft genome sequence and SSR data mining of “pumpo” (Bos taurus), a top bull from a peruvian genetic nucleus |
| title_sort | draft genome sequence and ssr data mining of pumpo bos taurus a top bull from a peruvian genetic nucleus |
| topic | Draft-Genome Pumpo Bos taurus BUSCO Genome Assembly SSR Analysis https://purl.org/pe-repo/ocde/ford#4.02.01 Genomes Genomas Bos taurus Genome annotation Anotación del genoma Microsatellites Microsatélites |
| url | https://hdl.handle.net/20.500.12955/2531 https://doi.org/10.20944/preprints202406.1085.v1 |
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