RESUMO
The mRNA translation defines the composition of the cell proteome in all forms of life and diseases. In this process, precise selection of the mRNA translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for triplet decoding. We have gathered and curated all published TIS consensus context sequences. We also included the TIS consensus context from novel 538 fungal genomes available from NCBI's RefSeq database. To do so, we wrote ad hoc programs in PERL to find and extract the TIS for each annotated gene, plus ten bases upstream and three downstream. For each genome, the sequences around the TIS of each gene were obtained, and the consensus was further calculated according to the Cavener rules and by the LOGOS algorithm. We created AUGcontext DB, a portal with a comprehensive collection of TIS context sequences across eukaryotes in a range from -10 to + 6. The compilation covers species of 30 vertebrates, 17 invertebrates, 25 plants, 14 fungi, and 11 protists studied in silico; 23 experimental studies; data on biotechnology; and the discovery of 8 diseases associated with specific mutations. Additionally, TIS context sequences of cellular IRESs were included. AUGcontext DB belongs to the National Institute of Cancer (Instituto Nacional de Cancerología, INCan), Mexico, and is freely available at http://108.161.138.77:8096/. Our catalogue allows us to do comparative studies between species, may help improve the diagnosis of certain diseases, and will be key to maximize the production of recombinant proteins.
Assuntos
Códon de Iniciação , Eucariotos , RNA Mensageiro , Eucariotos/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Animais , Humanos , Fases de Leitura Aberta , Software , Iniciação Traducional da Cadeia Peptídica , Biossíntese de Proteínas , Biologia Computacional/métodos , Bases de Dados GenéticasRESUMO
Polar marine macroalgae thrive in extreme conditions, often displaying geographic isolation and high degree of endemism. The "phycosphere" refers to the zone around the algae inhabited by microrganisms. Our study used DNA metabarcoding to survey the eukaryotic communities associated with seven seaweed species obtained at King George Island (South Shetland Islands, maritime Antarctic), including two Rhodophyta, two Chlorophyta and three Phaeophyceae. The ITS2 region was used as a barcode and our analysis yielded 77 eukaryotic ASVs spanning five Kingdoms (Fungi, Metazoa, Chromista, Protozoa, and Viridiplantae) and ten phyla (Ascomycota, Basidiomycota, Cercozoa, Ciliophora, Ochrophyta, Amebozoa, Chlorophyta, Rhodophyta, Bryophyta and Cnidaria). Additionally, we identified 14 potential new occurrence records for Antarctica. Ciliates and green algae were the most species-rich groups. The most abundant assigned associated species was Monostroma angicava (Chrorophyta). Within the macroalgal, the Chlorophyceans Ulothrix sp. hosted the greatest number of taxa, followed by Monostroma hariotii. Our data suggested that Antarctic macroalgae host a rich diversity of associated organisms and the biodiversity associated with the phycosphere remains underestimated.
Assuntos
Biodiversidade , Código de Barras de DNA Taxonômico , Alga Marinha , Regiões Antárticas , Alga Marinha/classificação , Alga Marinha/genética , Eucariotos/classificação , Eucariotos/genéticaRESUMO
Marine protists are key components of biogeochemical cycles and microbial food webs, which respond quickly to environmental factors. In the Gulf of Mexico (GoM), the Loop Current intensifies in summer and supplies the gulf with warm and oligotrophic waters. However, the cyclonic eddies within the GoM create favorable conditions for biological productivity by bringing nutrient-rich water to the subsurface layer. In this study, we investigated the response of the protist community to the regional physicochemical conditions, its spatial and temporal variability, the influence of mesoscale structures, and its ecological roles in the mixed layer (ML) and deep chlorophyll maximum (DCM). This is the first study to conduct a V9-18S rRNA gene survey for this community in the Mexican Exclusive Economic Zone of the GoM. The regional distribution, temporal changes, and mesoscale structures significantly affected the structure of the protist community in the ML. In contrast, only mesoscale structures significantly affected the protist community in the DCM. Different protist assemblages were also present between the ML and DCM, with the Alveolata representing â¼60% of the community in both layers, followed by haptophytes and MAST (Marine Stramenopiles) in the ML; pelagophytes and radiolarians were the more prevalent taxa in the DCM. Finally, co-occurrence analyses revealed that competition, parasitism, and predation were the potential interactions shaping these communities at both depths.
Assuntos
Estações do Ano , Água do Mar , Golfo do México , Água do Mar/microbiologia , Água do Mar/parasitologia , RNA Ribossômico 18S/genética , Eucariotos/genética , Eucariotos/classificação , Eucariotos/isolamento & purificação , Clorofila , Biodiversidade , MéxicoRESUMO
A key trait of Eukarya is the independent evolution of complex multicellularity in animals, land plants, fungi, brown algae, and red algae. This phenotype is characterized by the initial exaptation of cell-cell adhesion genes followed by the emergence of mechanisms for cell-cell communication, together with the expansion of transcription factor gene families responsible for cell and tissue identity. The number of cell types is commonly used as a quantitative proxy for biological complexity in comparative genomics studies. While expansions of individual gene families have been associated with variations in the number of cell types within individual complex multicellular lineages, the molecular and functional roles responsible for the independent evolution of complex multicellular across Eukarya remain poorly understood. We employed a phylogeny-aware strategy to conduct a genomic-scale search for associations between the number of cell types and the abundance of genomic components across a phylogenetically diverse set of 81 eukaryotic species, including species from all complex multicellular lineages. Our annotation schemas represent 2 complimentary aspects of genomic information: homology, represented by conserved sequences, and function, represented by Gene Ontology terms. We found many gene families sharing common biological themes that define complex multicellular to be independently expanded in 2 or more complex multicellular lineages, such as components of the extracellular matrix, cell-cell communication mechanisms, and developmental pathways. Additionally, we describe many previously unknown associations of biological themes and biological complexity, such as expansions of genes playing roles in wound response, immunity, cell migration, regulatory processes, and response to natural rhythms. Together, our findings unveil a set of functional and molecular convergences independently expanded in complex multicellular lineages likely due to the common selective pressures in their lifestyles.
Assuntos
Filogenia , Eucariotos/genética , Evolução Biológica , Animais , Genômica/métodos , Evolução MolecularRESUMO
BACKGROUND: The backbone of the eukaryotic tree of life contains taxa only found in molecular surveys, of which we still have a limited understanding. Such is the case of Picozoa, an enigmatic lineage of heterotrophic picoeukaryotes within the supergroup Archaeplastida, which has emerged as a significant component of marine microbial planktonic communities. To enhance our understanding of the diversity, distribution, and ecology of Picozoa, we conduct a comprehensive assessment at different levels, from assemblages to taxa, employing phylogenetic analysis, species distribution modeling, and ecological niche characterization. RESULTS: Picozoa was among the ten most abundant eukaryotic groups, found almost exclusively in marine environments. The phylum was represented by 179 Picozoa's OTU (pOTUs) placed in five phylogenetic clades. Picozoa community structure had a clear latitudinal pattern, with polar assemblages tending to cluster separately from non-polar ones. Based on the abundance and occupancy pattern, the pOTUs were classified into four categories: Low-abundant, Widespread, Polar, and Non-polar. We calculated the ecological niche of each of these categories. Notably, pOTUs sharing similar ecological niches were not closely related species, indicating a phylogenetic overdispersion in Picozoa communities. This could be attributed to competitive exclusion and the strong influence of the seasonal amplitude of variations in environmental factors, such as temperature, shaping physiological and ecological traits. CONCLUSIONS: Overall, this work advances our understanding of uncharted protists' evolutionary dynamics and ecological strategies. Our results highlight the importance of understanding the species-level ecology of marine heteroflagellates like Picozoa. The observed phylogenetic overdispersion challenges the concept of phylogenetic niche conservatism in protist communities, suggesting that closely related species do not necessarily share similar ecological niches. Video Abstract.
Assuntos
Eucariotos , Filogenia , Eucariotos/classificação , Eucariotos/genética , Biodiversidade , Organismos Aquáticos/classificação , Ecossistema , Água do Mar/parasitologiaRESUMO
Protists can endure challenging environments sustaining key ecosystem processes of the microbial food webs even under aridic or hypersaline conditions. We studied the diversity of protists at different latitudes of the Atacama Desert by massive sequencing of the hypervariable region V9 of the 18S rRNA gene from soils and microbial mats collected in the Andes. The main protist groups in soils detected in active stage through cDNA were cercozoans, ciliates, and kinetoplastids, while the diversity of protists was higher including diatoms and amoebae in the microbial mat detected solely through DNA. Co-occurrence networks from soils indicated similar assemblages dominated by amplicon sequence variants (ASVs) identified as Rhogostoma, Euplotes, and Neobodo. Microbial mat networks, on the other hand, were structured by ASVs classified as raphid-pennate diatoms and amoebae from the genera Hartmannella and Vannella, mostly negatively correlated to flagellates and microalgae. Additionally, our phylogenetic inferences of ASVs classified as Euplotes, Neobodo, and Rhogostoma were supported by sequence data of strains isolated during this study. Our results represent the first snapshot of the diversity patterns of culturable and unculturable protists and putative keystone taxa detected at remote habitats from the Atacama Desert.
Assuntos
Biodiversidade , Clima Desértico , Líquens , Chile , Líquens/genética , RNA Ribossômico 18S/genética , Eucariotos/genética , Eucariotos/classificação , Código de Barras de DNA Taxonômico , Filogenia , Solo/parasitologiaRESUMO
The hadopelagic environment remains highly understudied due to the inherent difficulties in sampling at these depths. The use of sediment environmental DNA (eDNA) can overcome some of these restrictions as settled and preserved DNA represent an archive of the biological communities. We use sediment eDNA to assess changes in the community within one of the world's most productive open-ocean ecosystems: the Atacama Trench. The ecosystems around the Atacama Trench have been intensively fished and are affected by climate oscillations, but the understanding of potential impacts on the marine community is limited. We sampled five sites using sediment cores at water depths from 2400 to ~8000 m. The chronologies of the sedimentary record were determined using 210Pbex. Environmental DNA was extracted from core slices and metabarcoding was used to identify the eukaryote community using two separate primer pairs for different sections of the 18S rRNA gene (V9 and V7) effectively targeting pelagic taxa. The reconstructed communities were similar among markers and mainly composed of chordates and members of the Chromista kingdom. Alpha diversity was estimated for all sites in intervals of 15 years (from 1842 to 2018), showing a severe drop in biodiversity from 1970 to 1985 that aligns with one of the strongest known El Niño events and extensive fishing efforts during the time. We find a direct impact of sea surface temperature on the community composition over time. Fish and cnidarian read abundance was examined separately to determine whether fishing had a direct impact, but no direct relation was found. These results demonstrate that sediment eDNA can be a valuable emerging tool providing insight in historical perspectives on ecosystem developments. This study constitutes an important step toward an improved understanding of the importance of environmental and anthropogenic drivers in affecting open and deep ocean communities.
Assuntos
Biodiversidade , DNA Ambiental , Ecossistema , Sedimentos Geológicos , RNA Ribossômico 18S , Sedimentos Geológicos/análise , DNA Ambiental/análise , RNA Ribossômico 18S/genética , Chile , Animais , Código de Barras de DNA Taxonômico , Eucariotos/genética , Organismos Aquáticos/genéticaRESUMO
This study addresses the environmental problem of PET plastic through in silico bioprospecting for the identification and experimental validation of novel PET degrading eukaryotes through the in silico bioprospectingI of PETases, employing a methodology that combines Hidden Markov Models (HMMs), clustering techniques, molecular docking, and dynamic simulations. A total of 424 putative PETase sequences were identified from 219 eukaryotic organisms, highlighting six sequences with low affinity energies. The Aspergillus luchuensis sequence showed the lowest Gibbs free energy and exhibited stability at different temperatures in molecular dynamics assays. Experimental validation, through a plate clearance assay and HPLC, confirmed PETase activity in three wild-type fungal strains, with A. luchuensis showing the highest efficiency. The results obtained demonstrate the effectiveness of combining computational and experimental approaches as proof of concept to discover and validate eukaryotes with PET-degrading capabilities opening new perspectives for the sustainable management of this type of waste and contributing to its environmental mitigation.
Assuntos
Biodegradação Ambiental , Bioprospecção , Eucariotos , Simulação por Computador , Aspergillus/enzimologiaRESUMO
Heterotrophic protists are vital in Earth's ecosystems, influencing carbon and nutrient cycles and occupying key positions in food webs as microbial predators. Fossils and molecular data suggest the emergence of predatory microeukaryotes and the transition to a eukaryote-rich marine environment by 800 million years ago (Ma). Neoproterozoic vase-shaped microfossils (VSMs) linked to Arcellinida testate amoebae represent the oldest evidence of heterotrophic microeukaryotes. This study explores the phylogenetic relationship and divergence times of modern Arcellinida and related taxa using a relaxed molecular clock approach. We estimate the origin of nodes leading to extant members of the Arcellinida Order to have happened during the latest Mesoproterozoic and Neoproterozoic (1054 to 661 Ma), while the divergence of extant infraorders postdates the Silurian. Our results demonstrate that at least one major heterotrophic eukaryote lineage originated during the Neoproterozoic. A putative radiation of eukaryotic groups (e.g., Arcellinida) during the early-Neoproterozoic sustained by favorable ecological and environmental conditions may have contributed to eukaryotic life endurance during the Cryogenian severe ice ages. Moreover, we infer that Arcellinida most likely already inhabited terrestrial habitats during the Neoproterozoic, coexisting with terrestrial Fungi and green algae, before land plant radiation. The most recent extant Arcellinida groups diverged during the Silurian Period, alongside other taxa within Fungi and flowering plants. These findings shed light on heterotrophic microeukaryotes' evolutionary history and ecological significance in Earth's ecosystems, using testate amoebae as a proxy.
Assuntos
Ecossistema , Fósseis , Processos Heterotróficos , Filogenia , Biodiversidade , Evolução Biológica , Amebozoários/genética , Amebozoários/classificação , Amoeba/genética , Amoeba/classificação , Amoeba/fisiologia , Eucariotos/genética , Eucariotos/classificaçãoRESUMO
In this Inaugural Article the author briefly revises its scientific career and how he starts to work with parasitic protozoa. Emphasis is given to his contribution to topics such as a) the structural organization of the surface of protozoa using freeze-fracture and deep-etching; b) the cytoskeleton of protozoa, especially structures such as the subpellicular microtubules of trypanosomatids, the conoid of Toxoplasma gondii, microtubules and inner membrane complex of this protozoan, and the costa of Tritrichomonas foetus; c) the flagellulm of trypanosomatids, that in addition to the axoneme contains a complex network of filaments that constitute the paraflagellar rod; d) special organelles such as the acidocalcisome, hydrogenosome, and glycosome; and e) the highly polarized endocytic pathway found in epimastigote forms of Trypanosoma cruzi.
Assuntos
Eucariotos , Microtúbulos , Masculino , Humanos , Citoesqueleto , Microscopia Eletrônica de Varredura , AxonemaRESUMO
Deep learning models (DLMs) have gained importance in predicting, detecting, translating, and classifying a diversity of inputs. In bioinformatics, DLMs have been used to predict protein structures, transcription factor-binding sites, and promoters. In this work, we propose a hybrid model to identify transcription factors (TFs) among prokaryotic and eukaryotic protein sequences, named Deep Regulation (DeepReg) model. Two architectures were used in the DL model: a convolutional neural network (CNN), and a bidirectional long-short-term memory (BiLSTM). DeepReg reached a precision of 0.99, a recall of 0.97, and an F1-score of 0.98. The quality of our predictions, the bias-variance trade-off approach, and the characterization of new TF predictions were evaluated and compared against those produced by DeepTFactor, as well as against experimental data from three model organisms. Predictions based on our DLM tended to exhibit less variance and bias than those from DeepTFactor, thus increasing reliability and decreasing overfitting.
Assuntos
Aprendizado Profundo , Fatores de Transcrição , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Biologia Computacional/métodos , Células Procarióticas/metabolismo , Redes Neurais de Computação , Eucariotos/genética , Genoma , Células Eucarióticas/metabolismo , Sítios de LigaçãoRESUMO
Protists encompass a vast widely distributed group of organisms, surpassing the diversity observed in metazoans. Their diverse ecological niches and life forms are intriguing characteristics that render them valuable subjects for in-depth cell biology studies. Throughout history, viruses have played a pivotal role in elucidating complex cellular processes, particularly in the context of cellular responses to viral infections. In this comprehensive review, we provide an overview of the cellular alterations that are triggered in specific hosts following different viral infections and explore intricate biological interactions observed in experimental conditions using different host-pathogen groups.
Assuntos
Viroses , Vírus , Humanos , Eucariotos , EcossistemaRESUMO
mRNA translation is a fundamental process for life. Selection of the translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for mRNA decoding. Studies in vertebrate mRNAs discovered that a purine at -3 and a G at +4 (where A of the AUG initiator codon is numbered + 1), promote TIS recognition. However, the TIS context in other eukaryotes has been poorly experimentally analyzed. We analyzed in vitro the influence of the -3, -2, -1 and + 4 positions of the TIS context in rabbit, Drosophila, wheat, and yeast. We observed that -3A conferred the best translational efficiency across these species. However, we found variability at the + 4 position for optimal translation. In addition, the Kozak motif that was defined from mammalian cells was only weakly predictive for wheat and essentially non-predictive for yeast. We discovered eight conserved sequences that significantly disfavored translation. Due to the big differences in translational efficiency observed among weak TIS context sequences, we define a novel category that we termed 'barren AUG context sequences (BACS)', which represent sequences disfavoring translation. Analysis of mRNA-ribosomal complexes structures provided insights into the function of BACS. The gene ontology of the BACS-containing mRNAs is presented.
Assuntos
Códon de Iniciação , Sequência Conservada , Biossíntese de Proteínas , Animais , Coelhos , Códon de Iniciação/genética , Mamíferos/genética , Iniciação Traducional da Cadeia Peptídica , RNA Mensageiro/metabolismo , Leveduras , Eucariotos/genética , Eucariotos/metabolismoRESUMO
Tiny ocean plankton (picoplankton) are fundamental for the functioning of the biosphere, but the ecological mechanisms shaping their biogeography were partially understood. Comprehending whether these microorganisms are structured by niche versus neutral processes is relevant in the context of global change. We investigate the ecological processes (selection, dispersal, and drift) structuring global-ocean picoplanktonic communities inhabiting the epipelagic (0 to 200 meters), mesopelagic (200 to 1000 meters), and bathypelagic (1000 to 4000 meters) zones. We found that selection decreased, while dispersal limitation increased with depth, possibly due to differences in habitat heterogeneity and dispersal barriers such as water masses and bottom topography. Picoplankton ß-diversity positively correlated with environmental heterogeneity and water mass variability, but this relationship tended to be weaker for eukaryotes than for prokaryotes. Community patterns were more pronounced in the Mediterranean Sea, probably because of its cross-basin environmental heterogeneity and deep-water isolation. We conclude that different combinations of ecological mechanisms shape the biogeography of the ocean microbiome across depths.
Assuntos
Microbiota , Plâncton , Eucariotos , Água , Oceanos e MaresRESUMO
Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.
Assuntos
Eucariotos , Microbiota , Animais , Eucariotos/genética , RNA Ribossômico 16S/genética , Microbiota/genética , Metagenoma , Peixes/genética , Organismos Aquáticos/genética , Mamíferos/genéticaRESUMO
In eukaryotic organisms the ensemble of 5' splice site sequences reflects the balance between natural nucleotide variability and minimal molecular constraints necessary to ensure splicing fidelity. This compromise shapes the underlying statistical patterns in the composition of donor splice site sequences. The scope of this study was to mine conserved and divergent signals in the composition of 5' splice site sequences. Because 5' donor sequences are a major cue for proper recognition of splice sites, we reasoned that statistical regularities in their composition could reflect the biological functionality and evolutionary history associated with splicing mechanisms. Results: We considered a regularized maximum entropy modeling framework to mine for non-trivial two-site correlations in donor sequence datasets corresponding to 30 different eukaryotes. For each analyzed species, we identified minimal sets of two-site coupling patterns that were able to replicate, at a given regularization level, the observed one-site and two-site frequencies in donor sequences. By performing a systematic and comparative analysis of 5'splice sites we showed that lineage information could be traced from joint di-nucleotide probabilities. We were able to identify characteristic two-site coupling patterns for plants and animals, and propose that they may echo differences in splicing regulation previously reported between these groups.
Assuntos
Sítios de Splice de RNA , Splicing de RNA , Animais , Sítios de Splice de RNA/genética , Sequência de Bases , Splicing de RNA/genética , Plantas/genética , Fungos/genética , Eucariotos , Nucleotídeos , ÍntronsRESUMO
BACKGROUND AND AIMS: At the West Antarctic Peninsula, snow algae blooms are composed of complex microbial communities dominated by green microalgae and bacteria. During their progression, the assembly of these microbial communities occurs under harsh environmental conditions and variable nutrient content due to fast snow melting. To date, it is still unclear what are the ecological mechanisms governing the composition and abundance of microorganisms during the formation of snow algae blooms. In this study, we aim to examine the main ecological mechanisms governing the assembly of snow algae blooms from early stages to colorful stages blooms. METHODS: The composition of the microbial communities within snow algae blooms was recorded in the West Antarctic Peninsula (Isabel Riquelme Islet) during a 35-day period using 16S rRNA and 18S rRNA metabarcoding. In addition, the contribution of different ecological processes to the assembly of the microbial community was quantified using phylogenetic bin-based null model analysis. RESULTS: Our results showed that alpha diversity indices of the eukaryotic communities displayed a higher variation during the formation of the algae bloom compared with the bacterial community. Additionally, in a macronutrients rich environment, the content of nitrate, ammonium, phosphate, and organic carbon did not play a major role in structuring the community. The quantification of ecological processes showed that the bacterial community assembly was governed by selective processes such as homogenous selection. In contrast, stochastic processes such as dispersal limitation and drift, and to a lesser extent, homogenous selection, regulate the eukaryotic community. CONCLUSIONS: Overall, our study highlights the differences in the microbial assembly between bacteria and eukaryotes in snow algae blooms and proposes a model to integrate both assembly processes. Video Abstract.
Assuntos
Eucariotos , Microbiota , Regiões Antárticas , Filogenia , RNA Ribossômico 16S/genética , Microbiota/genéticaRESUMO
Analysis of eukaryotic genomes requires the detection and classification of transposable elements (TEs), a crucial but complex and time-consuming task. To improve the performance of tools that accomplish these tasks, Machine Learning approaches (ML) that leverage computer resources, such as GPUs (Graphical Processing Unit) and multiple CPU (Central Processing Unit) cores, have been adopted. However, until now, the use of ML techniques has mostly been limited to classification of TEs. Herein, a detection-classification strategy (named YORO) based on convolutional neural networks is adapted from computer vision (YOLO) to genomics. This approach enables the detection of genomic objects through the prediction of the position, length, and classification in large DNA sequences such as fully sequenced genomes. As a proof of concept, the internal protein-coding domains of LTR-retrotransposons are used to train the proposed neural network. Precision, recall, accuracy, F1-score, execution times and time ratios, as well as several graphical representations were used as metrics to measure performance. These promising results open the door for a new generation of Deep Learning tools for genomics. YORO architecture is available at https://github.com/simonorozcoarias/YORO.