Version 1
: Received: 13 June 2024 / Approved: 16 June 2024 / Online: 18 June 2024 (04:32:53 CEST)
How to cite:
Estrada, R.; Romero, Y.; Figueroa, D.; Quilcate, C.; Casanova, D.; Vasquez, H. V.; Alvarado, W.; Maicelo, J. L.; Arbizu, C. I. Draft Genome Sequence and SSR Data Mining of “Pumpo” (Bos taurus), a Top Bull From a Peruvian Genetic Nucleus. Preprints2024, 2024061085. https://doi.org/10.20944/preprints202406.1085.v1
Estrada, R.; Romero, Y.; Figueroa, D.; Quilcate, C.; Casanova, D.; Vasquez, H. V.; Alvarado, W.; Maicelo, J. L.; Arbizu, C. I. Draft Genome Sequence and SSR Data Mining of “Pumpo” (Bos taurus), a Top Bull From a Peruvian Genetic Nucleus. Preprints 2024, 2024061085. https://doi.org/10.20944/preprints202406.1085.v1
Estrada, R.; Romero, Y.; Figueroa, D.; Quilcate, C.; Casanova, D.; Vasquez, H. V.; Alvarado, W.; Maicelo, J. L.; Arbizu, C. I. Draft Genome Sequence and SSR Data Mining of “Pumpo” (Bos taurus), a Top Bull From a Peruvian Genetic Nucleus. Preprints2024, 2024061085. https://doi.org/10.20944/preprints202406.1085.v1
APA Style
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” (<em>Bos taurus</em>), a Top Bull From a Peruvian Genetic Nucleus. Preprints. https://doi.org/10.20944/preprints202406.1085.v1
Chicago/Turabian Style
Estrada, R., Jorge L. Maicelo and Carlos I. Arbizu. 2024 "Draft Genome Sequence and SSR Data Mining of “Pumpo” (<em>Bos taurus</em>), a Top Bull From a Peruvian Genetic Nucleus" Preprints. https://doi.org/10.20944/preprints202406.1085.v1
Abstract
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.
Keywords
Draft-Genome; Pumpo; BUSCO; Genome Assembly; SSR Analysis
Subject
Biology and Life Sciences, Animal Science, Veterinary Science and Zoology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
,
,
