Centro de Investigación en Genómica y Bioinformática (CGB)Contiene la producción documental del CGBhttps://repositorio.umayor.cl/xmlui/handle/sibum/80042024-03-29T01:40:04Z2024-03-29T01:40:04ZMulti-trait and multi-environment genomic prediction for flowering traits in maize: a deep learning approachMora-Poblete, FreddyMaldonado, Carlos [Univ Mayor, Fac Ciencias, Ctr Genomica & Bioinformat, Chile]Henrique, LumaUhdre, RenanScapim, Carlos AlbertoMangolim, Claudete Aparecidahttps://repositorio.umayor.cl/xmlui/handle/sibum/95292024-03-27T23:17:58Z2023-08-01T00:00:00ZMulti-trait and multi-environment genomic prediction for flowering traits in maize: a deep learning approach
Mora-Poblete, Freddy; Maldonado, Carlos [Univ Mayor, Fac Ciencias, Ctr Genomica & Bioinformat, Chile]; Henrique, Luma; Uhdre, Renan; Scapim, Carlos Alberto; Mangolim, Claudete Aparecida
Maize (Zea mays L.), the third most widely cultivated cereal crop in the world, plays a critical role in global food security. To improve the efficiency of selecting superior genotypes in breeding programs, researchers have aimed to identify key genomic regions that impact agronomic traits. In this study, the performance of multi-trait, multi-environment deep learning models was compared to that of Bayesian models (Markov Chain Monte Carlo generalized linear mixed models (MCMCglmm), Bayesian Genomic Genotype-Environment Interaction (BGGE), and Bayesian Multi-Trait and Multi-Environment (BMTME)) in terms of the prediction accuracy of flowering-related traits (Anthesis-Silking Interval: ASI, Female Flowering: FF, and Male Flowering: MF). A tropical maize panel of 258 inbred lines from Brazil was evaluated in three sites (Cambira-2018, Sabaudia-2018, and Iguatemi-2020 and 2021) using approximately 290,000 single nucleotide polymorphisms (SNPs). The results demonstrated a 14.4% increase in prediction accuracy when employing multi-trait models compared to the use of a single trait in a single environment approach. The accuracy of predictions also improved by 6.4% when using a single trait in a multi-environment scheme compared to using multi-trait analysis. Additionally, deep learning models consistently outperformed Bayesian models in both single and multiple trait and environment approaches. A complementary genome-wide association study identified associations with 26 candidate genes related to flowering time traits, and 31 marker-trait associations were identified, accounting for 37%, 37%, and 22% of the phenotypic variation of ASI, FF and MF, respectively. In conclusion, our findings suggest that deep learning models have the potential to significantly improve the accuracy of predictions, regardless of the approach used and provide support for the efficacy of this method in genomic selection for flowering-related traits in tropical maize.
2023-08-01T00:00:00ZEditorial: Physiological, biochemical and molecular approaches in response to abiotic stresses in plantsCamargo Mendes, GiselleMueller, CarolineMiyasaka Almeida, Andrea [Univ Mayor, Ctr Genom & Bioinformat, Chile]https://repositorio.umayor.cl/xmlui/handle/sibum/95282024-03-27T23:07:28Z2023-04-21T00:00:00ZEditorial: Physiological, biochemical and molecular approaches in response to abiotic stresses in plants
Camargo Mendes, Giselle; Mueller, Caroline; Miyasaka Almeida, Andrea [Univ Mayor, Ctr Genom & Bioinformat, Chile]
Sin resumen.
2023-04-21T00:00:00ZPhylogenomic analysis of the Porphyromonas gingivalis-Porphyromonas gulae duo: approaches to the origin of periodontitisMorales-Olavarria, Mauricio [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]Nuñez-Belmar, Josefa [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]González, Damariz [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]Vicencio, EmilianoRivas-Pardo, Jaime Andrés [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]Cortez, CristianCárdenas, Juan P. [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]https://repositorio.umayor.cl/xmlui/handle/sibum/95272024-03-27T22:47:16Z2023-07-19T00:00:00ZPhylogenomic analysis of the Porphyromonas gingivalis-Porphyromonas gulae duo: approaches to the origin of periodontitis
Morales-Olavarria, Mauricio [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]; Nuñez-Belmar, Josefa [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]; González, Damariz [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]; Vicencio, Emiliano; Rivas-Pardo, Jaime Andrés [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]; Cortez, Cristian; Cárdenas, Juan P. [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]
Porphyromonas gingivalis is an oral human pathogen associated with the onset and progression of periodontitis, a chronic immune-inflammatory disease characterized by the destruction of the teeth-supporting tissue. P. gingivalis belongs to the genus Porphyromonas, which is characterized by being composed of Gram-negative, asaccharolytic, non-spore-forming, non-motile, obligatory anaerobic species, inhabiting niches such as the oral cavity, urogenital tract, gastrointestinal tract and infected wound from different mammals including humans. Among the Porphyromonas genus, P. gingivalis stands out for its specificity in colonizing the human oral cavity and its keystone pathogen role in periodontitis pathogenesis. To understand the evolutionary process behind P. gingivalis in the context of the Pophyoromonas genus, in this study, we performed a comparative genomics study with publicly available Porphyromonas genomes, focused on four main objectives: (A) to confirm the phylogenetic position of P. gingivalis in the Porphyromonas genus by phylogenomic analysis; (B) the definition and comparison of the pangenomes of P. gingivalis and its relative P. gulae; and (C) the evaluation of the gene family gain/loss events during the divergence of P. gingivalis and P. gulae; (D) the evaluation of the evolutionary pressure (represented by the calculation of Tajima-D values and dN/dS ratios) comparing gene families of P. gingivalis and P. gulae. Our analysis found 84 high-quality assemblies representing P. gingivalis and 14 P. gulae strains (from a total of 233 Porphyromonas genomes). Phylogenomic analysis confirmed that P. gingivalis and P. gulae are highly related lineages, close to P. loveana. Both organisms harbored open pangenomes, with a strong core-to-accessory ratio for housekeeping genes and a negative ratio for unknown function genes. Our analyses also characterized the gene set differentiating P. gulae from P. gingivalis, mainly associated with unknown functions. Relevant virulence factors, such as the FimA, Mfa1, and the hemagglutinins, are conserved in P. gulae, P. gingivalis, and P. loveana, suggesting that the origin of those factors occurred previous to the P. gulae - P. gingivalis divergence. These results suggest an unexpected evolutionary relationship between the P. gulae - P. gingivalis duo and P. loveana, showing more clues about the origin of the role of those organisms in periodontitis.
2023-07-19T00:00:00ZInsights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gutGonzález, Damariz [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]Morales-Olavarria, Mauricio [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]Vidal-Veuthey, Boris [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]Cárdenas, Juan P. [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]https://repositorio.umayor.cl/xmlui/handle/sibum/95262024-03-27T22:36:05Z2023-09-14T00:00:00ZInsights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut
González, Damariz [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]; Morales-Olavarria, Mauricio [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]; Vidal-Veuthey, Boris [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]; Cárdenas, Juan P. [Univ Mayor, Fac Ciencias Ingn & Tecnol, Ctr Genom & Bioinformat, Chile]
Akkermansia, a relevant mucin degrader from the vertebrate gut microbiota, is a member of the deeply branched Verrucomicrobiota, as well as the only known member of this phylum to be described as inhabitants of the gut. Only a few Akkermansia species have been officially described so far, although there is genomic evidence addressing the existence of more species-level variants for this genus. This niche specialization makes Akkermansia an interesting model for studying the evolution of microorganisms to their adaptation to the gastrointestinal tract environment, including which kind of functions were gained when the Akkermansia genus originated or how the evolutionary pressure functions over those genes. In order to gain more insight into Akkermansia adaptations to the gastrointestinal tract niche, we performed a phylogenomic analysis of 367 high-quality Akkermansia isolates and metagenome-assembled genomes, in addition to other members of Verrucomicrobiota. This work was focused on three aspects: the definition of Akkermansia genomic species clusters and the calculation and functional characterization of the pangenome for the most represented species; the evolutionary relationship between Akkermansia and their closest relatives from Verrucomicrobiota, defining the gene families which were gained or lost during the emergence of the last Akkermansia common ancestor (LAkkCA) and; the evaluation of the evolutionary pressure metrics for each relevant gene family of main Akkermansia species. This analysis found 25 Akkermansia genomic species clusters distributed in two main clades, divergent from their non-Akkermansia relatives. Pangenome analyses suggest that Akkermansia species have open pangenomes, and the gene gain/loss model indicates that genes associated with mucin degradation (both glycoside hydrolases and peptidases), (micro)aerobic metabolism, surface interaction, and adhesion were part of LAkkCA. Specifically, mucin degradation is a very ancestral innovation involved in the origin of Akkermansia. Horizontal gene transfer detection suggests that Akkermansia could receive genes mostly from unknown sources or from other Gram-negative gut bacteria. Evolutionary metrics suggest that Akkemansia species evolved differently, and even some conserved genes suffered different evolutionary pressures among clades. These results suggest a complex evolutionary landscape of the genus and indicate that mucin degradation could be an essential feature in Akkermansia evolution as a symbiotic species.
2023-09-14T00:00:00Z