Browsing by Author "Díaz, Sebastián"

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    DNA sequencing in the classroom: complete genome sequence of two earwig (Dermaptera; Insecta) species
    (2023) Kobayashi, Sanae; Maldonado, Jonathan E.; Gaete, Alexis; Araya, Ingrid; Aguado-Norese, Constanza; Cumplido, Nicolás; Díaz, Sebastián; Espinoza, Alonso; Fernández, Edelmira; Gajardo, Felipe; González-Ordenes, Felipe; Hauyon, Khantati; Maldonado, Piedad; Maldonado, Rodrigo; Pochet, Isabel; Riveros, Aníbal; Sandoval, Paula; Sepúlveda-González, Ailynne; Stuardo, Camila; Tapia-Reyes, Patricio; Thornton, Carolina; Undurraga, Soledad; Varas, Macarena; Valdivieso, Camilo; Gutiérrez Ilabaca, Rodrigo Antonio; Orellana, Ariel; Montecino, Martín; Maass, Alejandro; González, Mauricio; Allende, Miguel L.; Hodar, Christian; Irles, Paula
    Background Despite representing the largest fraction of animal life, the number of insect species whose genome has been sequenced is barely in the hundreds. The order Dermaptera (the earwigs) suffers from a lack of genomic information despite its unique position as one of the basally derived insect groups and its importance in agroecosystems. As part of a national educational and outreach program in genomics, a plan was formulated to engage the participation of high school students in a genome sequencing project. Students from twelve schools across Chile were instructed to capture earwig specimens in their geographical area, to identify them and to provide material for genome sequencing to be carried out by themselves in their schools. Results The school students collected specimens from two cosmopolitan earwig species: Euborellia annulipes (Fam. Anisolabididae) and Forficula auricularia (Fam. Forficulidae). Genomic DNA was extracted and, with the help of scientific teams that traveled to the schools, was sequenced using nanopore sequencers. The sequence data obtained for both species was assembled and annotated. We obtained genome sizes of 1.18 Gb (F. auricularia) and 0.94 Gb (E. annulipes) with the number of predicted protein coding genes being 31,800 and 40,000, respectively. Our analysis showed that we were able to capture a high percentage (≥ 93%) of conserved proteins indicating genomes that are useful for comparative and functional analysis. We were also able to characterize structural elements such as repetitive sequences and non-coding RNA genes. Finally, functional categories of genes that are overrepresented in each species suggest important differences in the process underlying the formation of germ cells, and modes of reproduction between them, features that are one of the distinguishing biological properties that characterize these two distant families of Dermaptera. Conclusions This work represents an unprecedented instance where the scientific and lay community have come together to collaborate in a genome sequencing project. The versatility and accessibility of nanopore sequencers was key to the success of the initiative. We were able to obtain full genome sequences of two important and widely distributed species of insects which had not been analyzed at this level previously. The data made available by the project should illuminate future studies on the Dermaptera.
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    Urban Fabric Patterns on Urban Wetland
    (2021) Rojas Quezada, Carolina Alejandra; Díaz, Sebastián; Munizaga, Juan; Trapani, Ferdinando; Mohareb, Nabil; Rosso, Federica; Kolokotsa, Denia; Maruthaveeran, Sreetheran; Ghoneem, Mahmoud; CEDEUS (Chile)
    The Author(s), under exclusive license to Springer Nature Switzerland AG.Latin American cities have experienced rapid urbanization and with it the social and environmental challenges caused by urban sprawl. Over the last decades, this increase has led to strong wetland area loss and fragmentation. It has negatively impacted its ecological value and biodiversity, and ignored their ecosystems services. This study analyzes wetland urbanization patterns in the Metropolitan area of Concepción (South of Chile). It proposes a characterization of the urban fabrics using the urbanization variables of density of population and dwellings, distances to roads and city center, and % covered by roads and green areas surrounding the wetland, in order to evaluate which urban variable explains the increase in urbanization, reducing recreation services for the well-being of residents from the different urban fabrics. In Chilean cities, urban wetlands are typically built on with dwellings that are not friendly with the natural environment. The urbanization intensity is modeled with a linear regression ordinary least squares (OLS), and predictions or a model of the dependent variable in terms of its relationships to a set of explanatory urban variables is generated. The built-up area (BA) is the dependent variable, and the variables of densities, distances, green spaces, and roads are independent. A discussion about the effect of spatial urbanization on urban wetlands is achieved, and the urbanization intensity is determined. The study adds to the discussion about spatial patterns and urban processes in urban landscapes; the results are inputs for natural planning and designing for people who intend to use urban wetlands in cities as nature-based solutions