Examinando por Materia "Genomes"

Mostrando 1 - 10 de 10

The complete mitochondrial genome of a Peruvian creole cattle (Bos taurus) and its phylogenetic analysis
(Wageningen Academic Publishers, 2023-02-09) Arbizu Berrocal, Carlos Irvin; Ferro Mauricio, Rubén Darío; Chávez Galarza, Julio César; Vásquez Pérez, Héctor Vladimir; Maicelo Quintana, Jorge Luis; Poemape Tuesta, Carlos Augusto; Gonzáles, J.; Quilcate Pairazamán, Carlos Enrique; Corredor Arizapana, Flor Anita
The population of Peruvian creole cattle (PCC) is decreasing mainly due to the introduction of more productive breeds in recent years. We report the complete mitochondrial genome sequence of a PCC bull for the first time. This genome was 16,339 bp in length with the base composition 31.43% A, 28.64% T, 26.81% C, and 13.12% G. It contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. Among the 37 genes, 28 were positioned on the H-strand and 9 were positioned on the L-strand. The most frequently used codons were CUA (Leucine), AUA (Isoleucine), AUU (Isoleucine), AUC (Isoleucine) and ACA (Threonine). Maximum likelihood analysis clearly demonstrated that PCC are strongly related to a native African breed, giving insights into the maternal ancestry of PCC. The annotated mitochondrial genome of PCC would serve as an important genetic data set for further breeding work and conservation strategies.
Draft genome sequence and SSR data mining of “pumpo” (Bos taurus), a top bull from a peruvian genetic nucleus
(MDPI, 2024-06-18) 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
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.
Draft genome sequence data of Fusarium verticillioides strain REC01, a phytopathogen isolated from a Peruvian maize
(Elsevier, 2024-09-23) Estrada Cañari, Richard; Aragón, Liliana; Pérez Porras, Wendy E.; Romero Avila, Yolanda; Martínez Vidal, Gabriel; García, Karina; Cruz Luis, Juancarlos; Arbizu Berrocal, Carlos I.
Fusarium verticillioides represents a major phytopathogenic threat to maize crops worldwide. In this study, we present genomic sequence data of a phytopathogen isolated from a maize stem that shows obvious signs of vascular rot. Using rigorous microbiological identification techniques, we correlated the disease symptoms observed in an affected maize region with the presence of the pathogen. Subsequently, the pathogen was cultured in a suitable fungal growth medium and extensive morphological characterization was performed. In addition, a pathogenicity test was carried out in a DCA model with three treatments and seven repetitions. De novo assembly from Illumina Novaseq 60 0 0 sequencing yielded 456 contigs, which together constitute a 42.8 Mb genome assembly with a GC % content of 48.26. Subsequent comparative analyses were performed with other Fusarium genomes available in the NCBI database.
Draft genome sequence of Fusarium oxysporum f. sp. cubense tropical race 4 from Peru, obtained by nanopore and illumina hybrid assembly
(American Society for Microbiology, 2022-08-08) Leiva, Ana M.; Rouard, Mathieu; Lopez-Alvarez, Diana; Cenci, Alberto; Breton, Catherine; Acuña Payano, Rosalyn Katherine; Rojas Llanque, Juan Carlos; Dita, Miguel; Cuellar, Wilmer J.
Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is the causal agent of Fusarium wilt, a major threat to the banana industry worldwide. Here, we report the genome of a Foc TR4 strain from Peru, sequenced using a combination of Illumina and Oxford Nanopore Technologies.
Draft genome sequence resource of Erwinia sp. Strain INIA01, a phytopathogen isolated from a diseased stalk of peruvian maize
(Microbiology resource announcements, 2023-04-13) Estrada Cañari, Richard; Saldaña Serrano, Carla Lizet; Pérez Porras, Wendy Elizabeth; Arteaga, Linda; Martínez Vidal, Gabriel; Injante Silva, Pedro Hugo; Duran Gomez, Moises Rodrigo; Salazar Coronal, Wilian; Cosme de la Cruz, Roberto Carlos; Poemape Tuesta, Carlos Augusto; Arbizu Berrocal, Carlos Irvin
Here, we report the complete genome sequence of Erwinia sp. strain INIA01, a bacterium isolated from lesions of Zea mays from northern Peru. This genome possesses two circular replicons, a 4.2-Mb chromosome, and a 438-kb plasmid.
First draft genome assembly of the Peruvian creole cattle breed (Bos taurus) and its comparative genomics among the Bovinae subfamily
(MDPI, 2022-08-18) 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
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.
Phylogenomic Analysis of the Plastid Genome of the Peruvian Purple Maize Zea mays subsp. mays cv. ‘INIA 601’
(MDPI, 2022-10-15) Montenegro Cabrera, Juan Daniel; Julca Chavez, Irene Consuelo; Chumbe Nolasco, Lenin Dimitriv; Rodríguez Pérez, Lila Maciel; Sevilla Panizo, Ricardo; Medina Hoyos, Alicia Elizabeth; Gutiérrez Reynoso, Dina Lida; Guerrero Abad, Juan Carlos; Amasifuen Guerra, Carlos Alberto; García Serquén, Aura Liz
Peru is an important center of diversity for maize; its different cultivars have been adapted to distinct altitudes and water availability and possess an array of kernel colors (red, blue, and purple), which are highly appreciated by local populations. Specifically, Peruvian purple maize is a collection of native landraces selected and maintained by indigenous cultures due to its intense purple color in the seed, bract, and cob. This color is produced by anthocyanin pigments, which have gained interest due to their potential use in the food, agriculture, and pharmaceutical industry. It is generally accepted that the Peruvian purple maize originated from a single ancestral landrace ‘Kculli’, but it is not well understood. To study the origin of the Peruvian purple maize, we assembled the plastid genomes of the new cultivar ‘INIA 601’ with a high concentration of anthocyanins, comparing them with 27 cultivars/landraces of South America, 9 Z. mays subsp. parviglumis, and 5 partial genomes of Z. mays subsp. mexicana. Using these genomes, plus four other maize genomes and two outgroups from the NCBI database, we reconstructed the phylogenetic relationship of Z. mays. Our results suggest a polyphyletic origin of purple maize in South America and agree with a complex scenario of domestication with recurrent gene flow from wild relatives. Additionally, we identify 18 plastid positions that can be used as high-confidence genetic markers for further studies. Altogether, these plastid genomes constitute a valuable resource to study the evolution and domestication of Z. mays in South America.
Reference-Guided Draft Genome Assembly, Annotation and SSR Mining Data of the Peruvian Creole Cattle (Bos taurus)
(MDPI, 2022-11-09) 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
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.
Revealing the complete chloroplast genome of an Andean horticultural crop, sweet cucumber (Solanum muricatum), and its comparison with other Solanaceae species
(MDPI, 2022-09-01) Saldaña Serrano, Carla Lizet; Chávez Galarza, Julio César; De la Cruz, Germán; Jhoncon, Jorge H.; Guerrero Abad, Juan Carlos; Vásquez Pérez, Héctor Vladimir; Maicelo Quintana, Jorge Luis; Arbizu Berrocal, Carlos Irvin
Sweet cucumber (Solanum muricatum) sect. Basarthrum is a neglected horticultural crop native to the Andean region. It is naturally distributed very close to other two Solanum crops of high importance, potatoes, and tomatoes. To date, molecular tools for this crop remain undetermined. In this study, the complete sweet cucumber chloroplast (cp) genome was obtained and compared with seven Solanaceae species. The cp genome of S. muricatum was 155,681 bp in length and included a large single copy (LSC) region of 86,182 bp and a small single-copy (SSC) region of 18,360 bp, separated by a pair of inverted repeats (IR) regions of 25,568 bp. The cp genome possessed 87 protein-coding genes (CDS), 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes, and one pseudogene. Furthermore, 48 perfect microsatellites were identified. These repeats were mainly located in the noncoding regions. Whole cp genome comparative analysis revealed that the SSC and LSC regions showed more divergence than IR regions. Similar to previous studies, our phylogenetic analysis showed that S. muricatum is a sister species to members of sections Petota + Lycopersicum + Etuberosum. We expect that this first sweet cucumber chloroplast genome will provide potential molecular markers and genomic resources to shed light on the genetic diversity and population studies of S. muricatum, which will allow us to identify varieties and ecotypes. Finally, the features and the structural differentiation will provide us with information about the genes of interest, generating tools for the most precise selection of the best individuals of sweet cucumber, in less time and with fewer resources.
The Passion Fruit Genome
(Springer Nature, 2022-11-04) Carneiro Vieira, Maria Lucia; Portugal Costa, Zirlane; Mello Varani, Alessandro; Sader, Mariela Analia; Cauz-Santos, Luiz Augusto; Augusto Giopatto, Helena; Egoávil del Reátegui, Alina Carmen; Bergès, Hélène; Barros Monteiro-Vitorello, Claudia; Carnier Dornelas, Marcelo; Pedrosa-Harand, Andrea
The genus Passiflora comprises a large group of plants popularly known as passion fruits, much appreciated for their exotic flowers and edible fruits. The genus has long attracted considerable attention due to its economic value, broad geographic distribution and remarkable species diversity, which are found in tropical and subtropical regions of the Neotropics. Despite their biological attributes and economic importance, the species are largely neglected when it comes to conducting genomic studies. However, in 2021, a chromosome-scale genome assembly was published for a purple passion fruit cultivar (Passiflora edulis) and a genome sequence resource of the wild species, P. organensis, was assembled by adopting short- and long-read technologies. In contrast to P. edulis (1,327 Mbp), P. organensis has a small genome (259 Mbp). In this chapter we summarize some interesting results that emerged from the analysis of the Passiflora sequences, including satellite DNAs and transposable element characterization in the context of cytogenetics and evolution of the genus, organellar genome organization, and the MADS-box gene family that is known to have important biological roles in Passiflora, especially with regard to reproductive development. Although understudied, over the last decades, work on breeding passion fruit varieties has been conducted in some private and public institutions with a view to releasing cultivars of P. edulis, the main cultivated species worldwide. Therefore, studies related to genetics and breeding are also summarized.