Examinando por Materia "High-throughput sequencing"

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Complete mitogenome of “pumpo” (Bos taurus), a top bull from a Peruvian genetic nucleus, and its phylogenetic analysis
(MDPI, 2024-05-28) Estrada Cañari, Richard; Figueroa Venegas, Deyanira Antonella; Romero Avila, Yolanda; Alvarez García, Wuesley Yusmein; Rojas Cruz, Diorman; Alvarado, Wigoberto; Maicelo, Jorge L.; Quilcate Pairazamán, Carlos Enrique; Arbizu Berrocal, Carlos Irvin
The mitochondrial genome of Pumpo (Bos taurus), a prominent breed contributing to livestock farming, was sequenced using the Illumina HiSeq 2500 platform. Assembly and annotation of the mitochondrial genome were achieved through a multifaceted approach employing bioinformatics tools such as Trim Galore, SPAdes, and Geseq, followed by meticulous manual inspection. Additionally, analyses covering tRNA secondary structure and codon usage bias were conducted for comprehensive characterization. The 16,341 base pair mitochondrial genome comprises 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Phylogenetic analysis places Pumpo within a clade predominantly composed of European cattle, reflecting its prevalence in Europe. This comprehensive study underscores the importance of mitochondrial genome analysis in understanding cattle evolution and highlights the potential of genetic improvement programs in livestock farming, thus contributing to enhanced livestock practices.
Genetic diversity and population structure of a Peruvian cattle herd using SNP data
(Frontiers Media S.A., 2023-03-10) Corredor Arizapana, Flor Anita; Figueroa Venegas, Deyanira Antonella; Estrada Cañari, Richard; Salazar Coronel, Wilian; Quilcate Pairazamán, Carlos Enrique; Vásquez Pérez, Héctor Vladimir; Gonzales Malca, Jhony Alberto; Maicelo Quintana, Jorge Luis; Medina Morales, Percy Edilberto; Arbizu Berrocal, Carlos Irvin
New-generation sequencing technologies, among them SNP chips for massive genotyping, are useful for the effective management of genetic resources. To date, molecular studies in Peruvian cattle are still scarce. For the first time, the genetic diversity and population structure of a reproductive nucleus cattle herd of four commercial breeds from a Peruvian institution were determined. This nucleus comprises Brahman (N = 9), Braunvieh (N = 9), Gyr (N = 5), and Simmental (N = 15) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N = 9), were incorporated. Female individuals were genotyped with the GGPBovine100K and ma les with the BovineHD. Quality control, and the proportion of polymorphic SNPs, minor allele frequency, expected heterozygosity, observed heterozygosity, and inbreeding coefficient were estimated for the five breeds. Admixture, principal component analysis (PCA), and discriminant analysis of principal components (DAPC) were performed. Also, a dendrogram was constructed using the Neighbor-Joining clustering algorithm. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 51.42% in Gyr to 97.58% in AFB. Also, AFB showed the highest expected heterozygosity estimate (0.41 ± 0.01), while Brahman the lowest (0.33 ± 0.01). Besides, Braunvieh possessed the highest observed heterozygosity (0.43 ± 0.01), while Brahman the lowest (0.37 ± 0.02), indicating that Brahman was less diverse. According to the molecular variance analysis, 75.71% of the variance occurs within individuals, whereas 24.29% occurs among populations. The pairwise genetic differentiation estimates (FST) between breeds showed values that ranged from 0.08 (Braunvieh vs. AFB) to 0.37 (Brahman vs. Braunvieh). Similarly, pairwise Reynold’s distance ranged from 0.09 (Braunvieh vs. AFB) to 0.46 (Brahman vs. Braunvieh). The dendrogram, similar to the PCA, identified two groups, showing a clear separation between Bos indicus (Brahman and Gyr) and B. taurus breeds (Braunvieh, Simmental, and AFB). Simmental and Braunvieh grouped closely with the AFB cattle. Similar results were obtained for the population structure analysis with K = 2. The results from this study would contribute to the appropriate management, avoiding loss of genetic variability in these breeds and for future improvements in this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.
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 phylogeography of potato virus X shows the fingerprints of its human vector
(MDPI, 2021-09-09) Fuentes, Segundo; Gibbs, Adrian J.; Hajizadeh, Mohammad; Perez, Ana; Adams, Ian Patrick; Fribourg, Cesar E.; Kreuze, Jan; Fox, Adrian; Boonham, Neil; Jones, Roger A. C.
Potato virus X (PVX) occurs worldwide and causes an important potato disease. Complete PVX genomes were obtained from 326 new isolates from Peru, which is within the potato crop′s main domestication center, 10 from historical PVX isolates from the Andes (Bolivia, Peru) or Europe (UK), and three from Africa (Burundi). Concatenated open reading frames (ORFs) from these genomes plus 49 published genomic sequences were analyzed. Only 18 of them were recombinants, 17 of them Peruvian. A phylogeny of the non-recombinant sequences found two major (I, II) and five minor (I-1, I-2, II-1, II-2, II-3) phylogroups, which included 12 statistically supported clusters. Analysis of 488 coat protein (CP) gene sequences, including 128 published previously, gave a completely congruent phylogeny. Among the minor phylogroups, I-2 and II-3 only contained Andean isolates, I-1 and II-2 were of both Andean and other isolates, but all of the three II-1 isolates were European. I-1, I-2, II-1 and II-2 all contained biologically typed isolates. Population genetic and dating analyses indicated that PVX emerged after potato’s domestication 9000 years ago and was transported to Europe after the 15th century. Major clusters A–D probably resulted from expansions that occurred soon after the potato late-blight pandemic of the mid-19th century. Genetic comparisons of the PVX populations of different Peruvian Departments found similarities between those linked by local transport of seed potato tubers for summer rain-watered highland crops, and those linked to winter-irrigated crops in nearby coastal Departments. Comparisons also showed that, although the Andean PVX population was diverse and evolving neutrally, its spread to Europe and then elsewhere involved population expansion. PVX forms a basal Potexvirus genus lineage but its immediate progenitor is unknown. Establishing whether PVX′s entirely Andean phylogroups I-2 and II-3 and its Andean recombinants threaten potato production elsewhere requires future biological studies.