Reference-Guided Draft Genome Assembly, Annotation and SSR Mining Data of the Peruvian Creole Cattle ( Bos taurus )

Richard Estrada, Flor-Anita Corredor, Deyanira Figueroa, Wilian Salazar, Carlos Quilcate, Héctor V. Vásquez, Jorge L. Maicelo, Jhony Gonzales and Carlos I. Arbizu ()
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Richard Estrada: Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
Flor-Anita Corredor: Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
Deyanira Figueroa: Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
Wilian Salazar: Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
Carlos Quilcate: Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
Héctor V. Vásquez: Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
Jorge L. Maicelo: Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
Jhony Gonzales: Laboratorio de Biología Molecular, Universidad Nacional de Frontera, Av. San Hilarión 101, Sullana 20103, Peru
Carlos I. Arbizu: Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru

Data, 2022, vol. 7, issue 11, 1-12

Abstract: 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.

Keywords: NGS; neglected breed; genome; reference scaffolding; microsatellites (search for similar items in EconPapers)
JEL-codes: C8 C80 C81 C82 C83 (search for similar items in EconPapers)
Date: 2022
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