Examinando por Materia "Bioinformatics"

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Alterations in the gut microbial composition and diversity associated with diarrhea in neonatal Peruvian alpacas
(Elsevier, 2024-05-09) Zapata Coacalla, Celso; Estrada Cañari, Richard; Oros Butron, Oscar; Sánchez Herencia, Diana; Maicelo Quintana, Jorge L.; Arbizu Berrocal, Carlos I.; Coila Añasco, Pedro
Diarrhea in alpacas is a clinically significant condition and the primary cause of morbidity in neonatal Peruvian alpacas. This study aimed to correlate early diarrhea in crias of alpaca with changes in the microbiota community. A total of 19 alpacas (aged 1–2 months) were collected, including nine with a health condition and ten healthy ones. Fecal samples were obtained under sterile conditions and their DNA was extracted. Sequencing of the V3-V4 region of the 16S rRNA gene was conducted in the Illumina platform, followed by bioinformatics analysis. Reduced microbial diversity was evident in alpacas afflicted with diarrhea, delineating contrasting microbial compositions in comparison to their healthy counterparts. The study characterized the predominant bacterial classes and phyla within the gut microbiota, with Firmicutes, Verrucomicrobiota, and Bacteroidota collectively constituting approximately 80% of the total bacterial population. Substantial disparities in these microbial compositions were observed between the two groups, a variance that appeared to be influenced by both age and the health status of the alpacas. The bacterial class Verrucomicrobiae exhibited a significant presence within the group of alpacas suffering from illness. Furthermore, specific pathogenic species such as Clostridium spiroforme, Blautia, and Bacteroides fragilis were detected in significantly higher proportions among the afflicted alpacas. The functional diversity across the two groups was also found to be markedly different, a distinction that is graphically represented in a heat map illustrating the fifty principal differential KEGGs. This study provides valuable insights into the role of gut microbiota in alpaca health and may have implications for veterinary care and management.
Assessment of the genetic diversity and population structure of the peruvian andean legume, tarwi (Lupinus mutabilis), with high quality SNPs
(MDPI, 2023-03-16) Huaringa Joaquin, Amelia Wite; Saldaña Serrano, Carla Lizet; Saravia Navarro, David; García Bendezú, Sady; Rodriguez Grados, Pedro Manuel; Salazar Coronel, Wilian; Camarena Mayta, Felix; Injante Silva, Pedro Hugo; Arbizu Berrocal, Carlos Irvin
Lupinus mutabilis Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the genetic parameters of plants with reliable and modern methods such as genotyping by sequencing (GBS). Here, for the first time, we used single nucleotide polymorphism (SNP) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, like the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59%) and indicated that variability within populations is 92.41%. Population divergence (Fst) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative Fis for both populations, demonstrating that, like other Lupinus species, tarwi also depends on cross-pollination. SNP markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.
Genetic diversity and population structure of the Peruvian Andean legume, tarwi (Lupinus mutabilis), with high quality SNPs
(MDPI, 2023-01-19) Huaringa Joaquin, Amelia; Saldaña Serrano, Carla Lizet; Saravia Navarro, David; García Bendezú, Sady; Rodriguez Grados, Pedro; Salazar Coronel, Wilian; Camarena, Felix; Injante Silva, Pedro Hugo; Arbizu Berrocal, Carlos Irvin
Lupinus mutabilis Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the genetic parameters of plants with reliable and modern methods such as genotyping by sequencing (GBS). Here, for the first time, we used single nucleotide polymorphism (SNP) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, like the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59%) and indicated that variability within populations is 92.41%. Population divergence (Fst) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative Fis for both populations, demonstrating that, like other Lupinus species, tarwi also depends on cross-pollination. SNP markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.