Ragini Kihlman, Ilkka Launonen, Mikko J Sillanpää, Patrik Waldmann
{"title":"Sub-sampling graph neural networks for genomic prediction of quantitative phenotypes","authors":"Ragini Kihlman, Ilkka Launonen, Mikko J Sillanpää, Patrik Waldmann","doi":"10.1093/g3journal/jkae216","DOIUrl":"https://doi.org/10.1093/g3journal/jkae216","url":null,"abstract":"In genomics, use of deep learning (DL) is rapidly growing and DL has successfully demonstrated its ability to uncover complex relationships in large biological and biomedical data sets. With the development of high-throughput sequencing techniques, genomic markers can now be allocated to large sections of a genome. By analysing allele sharing between individuals, one may calculate realized genomic relationships from single nucleotide polymorphisms (SNPs) data rather than relying on known pedigree relationships under polygenic model. The traditional approaches in genome-wide prediction (GWP) of quantitative phenotypes utilise genomic relationships in fixed global covariance modelling, possibly with some non-linear kernel mapping (for example Gaussian processes). On the other hand, the DL approaches proposed so far for GWP fail to take into account the non-Euclidean graph structure of relationships between individuals over several generations. In this paper, we propose one global convolutional neural network (GCN) and one local sub-sampling architecture (GCN-RS) that are specifically designed to perform regression analysis based on genomic relationship information. A GCN is tailored to non-Euclidean spaces and consists of several layers of graph convolutions. The GCN-RS architecture is designed to further improve the GCN’s performance by sub-sampling the graph to reduce the dimensionality of the input data. Through these graph convolutional layers, the GCN maps input genomic markers to their quantitative phenotype values. The graphs are constructed using an iterative nearest neighbour approach. Comparisons show that the GCN-RS outperforms the popular Genomic Best Linear Unbiased Predictor (GBLUP) method on one simulated and three real data sets from wheat, mice and pig with a predictive improvement of 4.4% to 49.4% in terms of test mean squared error (MSE). This indicates that GCN-RS is a promising tool for genomic predictions in plants and animals. Furthermore, GCN-RS is computationally efficient, making it a viable option for large-scale applications.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142199777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Daniel Matúš, Willem Berend Post, Victoria Elisabeth Groß, Alexander Bernd Knierim, Christina Katharina Kuhn, Franziska Fiedler, Darian Benno Tietgen, Johanna Lena Schön, Torsten Schöneberg, Simone Prömel
{"title":"The N terminus-only (trans) function of the Adhesion GPCR Latrophilin-1 controls multiple processes in reproduction of C. elegans.","authors":"Daniel Matúš, Willem Berend Post, Victoria Elisabeth Groß, Alexander Bernd Knierim, Christina Katharina Kuhn, Franziska Fiedler, Darian Benno Tietgen, Johanna Lena Schön, Torsten Schöneberg, Simone Prömel","doi":"10.1093/g3journal/jkae206","DOIUrl":"https://doi.org/10.1093/g3journal/jkae206","url":null,"abstract":"<p><p>Adhesion G protein-coupled receptors (aGPCR) are unique molecules. They are able to transmit classical signals via G-protein activation as well as mediate functions solely through their extracellular N termini, completely independently of the seven transmembrane helices domain (7TM) and the C terminus. This dual mode of action is highly unusual for GPCRs and allows for a plethora of possible cellular consequences. However, the physiological implications and molecular details of this N terminus-mediated signaling are poorly understood. Here, we show that several distinct 7TM-independent/trans functions of the aGPCR Latrophilin homolog LAT-1 in the nematode Caenorhabditis elegans together regulate reproduction: sperm guidance, ovulation, and germ cell apoptosis. In these contexts, the receptor elicits its functions in a non-cell autonomous manner. The functions might be realized through alternative splicing of the receptor specifically generating N terminus-only variants. Thus, our findings shed light on the versatility of 7TM-independent/N terminus-only/trans functions of aGPCR and discuss possible molecular details.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Flynotyper 2.0: An updated tool for rapid quantitative assessment of Drosophila eye phenotypes.","authors":"Johnathan Ray, Deepro Banerjee, Qingyu Wang, Santhosh Girirajan","doi":"10.1093/g3journal/jkae212","DOIUrl":"10.1093/g3journal/jkae212","url":null,"abstract":"<p><p>About two-thirds of the genes in the Drosophila melanogaster genome are also involved in its eye development, making the Drosophila eye an ideal system for genetic studies. We previously developed Flynotyper, a software that uses image processing operations to identify and quantify the degree of roughness by measuring disorderliness of ommatidial arrangement in the fly eye. This software has enabled researchers to quantify morphological defects of thousands of eye images caused by genetic perturbations. Here, we present Flynotyper 2.0, a software that has an updated computer vision library, improved performance, and a streamlined pipeline for high-throughput analysis of multiple eye images. We also tested several batches of Drosophila eye images to ensure robustness and reproducibility of the updated Flynotyper 2.0 software.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142143049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jacqueline Heckenhauer, David Plotkin, Jose I Martinez, Jacob Bethin, Steffen U Pauls, Paul B Frandsen, Akito Y Kawahara
{"title":"Genomic resources of aquatic Lepidoptera, Elophila obliteralis and Hyposmocoma kahamanoa, reveal similarities with Trichoptera in amino acid composition of major silk genes.","authors":"Jacqueline Heckenhauer, David Plotkin, Jose I Martinez, Jacob Bethin, Steffen U Pauls, Paul B Frandsen, Akito Y Kawahara","doi":"10.1093/g3journal/jkae093","DOIUrl":"10.1093/g3journal/jkae093","url":null,"abstract":"<p><p>While most species of butterflies and moths (Lepidoptera) have entirely terrestrial life histories, ∼0.5% of the described species are known to have an aquatic larval stage. Larvae of aquatic Lepidoptera are similar to caddisflies (Trichoptera) in that they use silk to anchor themselves to underwater substrates or to build protective cases. However, the physical properties and genetic elements of silks in aquatic Lepidoptera remain unstudied, as most research on lepidopteran silk has focused on the commercially important silkworm, Bombyx mori. Here, we provide high-quality PacBio HiFi genome assemblies of 2 distantly-related aquatic Lepidoptera species [Elophila obliteralis (Pyraloidea: Crambidae) and Hyposmocoma kahamanoa (Gelechioidea: Cosmopterigidae)]. As a step toward understanding the evolution of underwater silk in aquatic Lepidoptera, we used the genome assemblies and compared them to published genetic data of aquatic and terrestrial Lepidoptera. Sequences of the primary silk protein, h-fibroin, in aquatic moths have conserved termini and share a basic motif structure with terrestrial Lepidoptera. However, these sequences were similar to aquatic Trichoptera in that the percentage of positively and negatively charged amino acids was much higher than in terrestrial Lepidoptera, indicating a possible adaptation of silks to aquatic environments.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gonzalo Casorzo, Luis Felipe Ferrão, Paul Adunola, Estefania Tavares Flores, Camila Azevedo, Rodrigo Amadeu, Patricio R Munoz
{"title":"Understanding the genetic basis of blueberry postharvest traits to define better breeding strategies.","authors":"Gonzalo Casorzo, Luis Felipe Ferrão, Paul Adunola, Estefania Tavares Flores, Camila Azevedo, Rodrigo Amadeu, Patricio R Munoz","doi":"10.1093/g3journal/jkae163","DOIUrl":"10.1093/g3journal/jkae163","url":null,"abstract":"<p><p>Blueberry (Vaccinium spp.) is among the most-consumed soft fruit and has been recognized as an important source of health-promoting compounds. Highly perishable and susceptible to rapid spoilage due to fruit softening and decay during postharvest storage, modern breeding programs are looking to maximize the quality and extend the market life of fresh blueberries. However, it is uncertain how genetically controlled postharvest quality traits are in blueberries. This study aimed to investigate the prediction ability and the genetic basis of the main fruit quality traits affected during blueberry postharvest to create breeding strategies for developing cultivars with an extended shelf life. To achieve this goal, we carried out target genotyping in a breeding population of 588 individuals and evaluated several fruit quality traits after 1 day, 1 week, 3 weeks, and 7 weeks of postharvest storage at 1°C. Using longitudinal genome-based methods, we estimated genetic parameters and predicted unobserved phenotypes. Our results showed large diversity, moderate heritability, and consistent predictive accuracies along the postharvest storage for most of the traits. Regarding the fruit quality, firmness showed the largest variation during postharvest storage, with a surprising number of genotypes maintaining or increasing their firmness, even after 7 weeks of cold storage. Our results suggest that we can effectively improve the blueberry postharvest quality through breeding and use genomic prediction to maximize the genetic gains in the long term. We also emphasize the potential of using longitudinal genomic prediction models to predict the fruit quality at extended postharvest periods by integrating known phenotypic data from harvest.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373639/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Eng-Ti Leslie Low, Kuang-Lim Chan, Noorhariza Mohd Zaki, Elizaveta Taranenko, Jared M Ordway, Corey Wischmeyer, Jaap Buntjer, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Jayanthi Nagappan, Rozana Rosli, Eugeniya Bondar, Nadzirah Amiruddin, Norashikin Sarpan, Ngoot-Chin Ting, Pek-Lan Chan, Meilina Ong-Abdullah, Marhalil Marjuni, Suzana Mustaffa, Norziha Abdullah, Norazah Azizi, Blaire Bacher, Nathan Lakey, Tatiana V Tatarinova, Mohamad Arif Abd Manaf, Ravigadevi Sambanthamurti, Rajinder Singh
{"title":"Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae.","authors":"Eng-Ti Leslie Low, Kuang-Lim Chan, Noorhariza Mohd Zaki, Elizaveta Taranenko, Jared M Ordway, Corey Wischmeyer, Jaap Buntjer, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Jayanthi Nagappan, Rozana Rosli, Eugeniya Bondar, Nadzirah Amiruddin, Norashikin Sarpan, Ngoot-Chin Ting, Pek-Lan Chan, Meilina Ong-Abdullah, Marhalil Marjuni, Suzana Mustaffa, Norziha Abdullah, Norazah Azizi, Blaire Bacher, Nathan Lakey, Tatiana V Tatarinova, Mohamad Arif Abd Manaf, Ravigadevi Sambanthamurti, Rajinder Singh","doi":"10.1093/g3journal/jkae135","DOIUrl":"10.1093/g3journal/jkae135","url":null,"abstract":"<p><p>Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141450237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Krista G Freeman, Michael J Lauer, Danny Jiang, Jennifer Roscher, Sterling Sandler, Nicholas Mercado, Robert Fryberger, Julia Kovalski, Abigail R Lutz, Lee E Hughes, Andrew P VanDemark, Graham F Hatfull
{"title":"Characterization of mycobacteriophage Adephagia cytotoxic proteins.","authors":"Krista G Freeman, Michael J Lauer, Danny Jiang, Jennifer Roscher, Sterling Sandler, Nicholas Mercado, Robert Fryberger, Julia Kovalski, Abigail R Lutz, Lee E Hughes, Andrew P VanDemark, Graham F Hatfull","doi":"10.1093/g3journal/jkae166","DOIUrl":"10.1093/g3journal/jkae166","url":null,"abstract":"<p><p>Mycobacterium phage Adephagia is a cluster K phage that infects Mycobacterium smegmatis and some strains of Mycobacterium pathogens. Adephagia has a siphoviral virion morphology and is temperate. Its genome is 59,646 bp long and codes for one tRNA gene and 94 predicted protein-coding genes; most genes not associated with virion structure and assembly are functionally ill-defined. Here, we determined the Adephagia gene expression patterns in lytic and lysogenic growth and used structural predictions to assign additional gene functions. We characterized 66 nonstructural genes for their toxic phenotypes when expressed in M. smegmatis, and we show that 25 of these (38%) are either toxic or strongly inhibit growth, resulting in either reduced viability or small colony sizes. Some of these genes are predicted to be involved in DNA metabolism or regulation, but others are of unknown function. We also characterize the HicAB-like toxin-antitoxin (TA) system encoded by Adephagia (gp91 and gp90, respectively) and show that the gp90 antitoxin is lysogenically expressed, abrogates gp91 toxicity, and is required for normal lytic and lysogenic growth.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141731061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Selection with two alleles of X-linkage and its application to the fitness component analysis of OdsH in Drosophila.","authors":"Sha Sun, Chau-Ti Ting, Chung-I Wu","doi":"10.1093/g3journal/jkae157","DOIUrl":"10.1093/g3journal/jkae157","url":null,"abstract":"<p><p>In organisms with the XY sex-determination system, there is an imbalance in the inheritance and transmission of the X chromosome between males and females. Unlike an autosomal allele, an X-linked recessive allele in a female will have phenotypic effects on its male counterpart. Thus, genes located on the X chromosome are of particular interest to researchers in molecular evolution and genetics. Here we present a model for selection with two alleles of X-linkage to understand fitness components associated with genes on the X chromosome. We apply this model to the fitness analysis of an X-linked gene, OdsH (16D), in the fruit fly Drosophila melanogaster. The function of OdsH is involved in sperm production and the gene is rapidly evolving under positive selection. Using site-directed gene targeting, we generated functional and defective OdsH variants tagged with the eye-color marker gene white. We compare the allele frequency changes of the two OdsH variants, each directly competing against a wild-type OdsH allele in concurrent but separate experimental populations. After 20 generations, the two genetically modified OdsH variants displayed a 40% difference in allele frequencies, with the functional OdsH variant demonstrating an advantage over the defective variant. Using maximum likelihood estimation, we determined the fitness components associated with the OdsH alleles in males and females. Our analysis revealed functional aspects of the fitness determinants associated with OdsH, and that sex-specific fertility and viability consequences both contribute to selection on an X-linked gene.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141603505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sixin Liu, Kyle E Martin, Warren M Snelling, Roseanna Long, Timothy D Leeds, Roger L Vallejo, Gregory D Wiens, Yniv Palti
{"title":"Accurate genotype imputation from low-coverage whole-genome sequencing data of rainbow trout.","authors":"Sixin Liu, Kyle E Martin, Warren M Snelling, Roseanna Long, Timothy D Leeds, Roger L Vallejo, Gregory D Wiens, Yniv Palti","doi":"10.1093/g3journal/jkae168","DOIUrl":"10.1093/g3journal/jkae168","url":null,"abstract":"<p><p>With the rapid and significant cost reduction of next-generation sequencing, low-coverage whole-genome sequencing (lcWGS), followed by genotype imputation, is becoming a cost-effective alternative to single-nucleotide polymorphism (SNP)-array genotyping. The objectives of this study were 2-fold: (1) construct a haplotype reference panel for genotype imputation from lcWGS data in rainbow trout (Oncorhynchus mykiss); and (2) evaluate the concordance between imputed genotypes and SNP-array genotypes in 2 breeding populations. Medium-coverage (12×) whole-genome sequences were obtained from a total of 410 fish representing 5 breeding populations with various spawning dates. The short-read sequences were mapped to the rainbow trout reference genome, and genetic variants were identified using GATK. After data filtering, 20,434,612 biallelic SNPs were retained. The reference panel was phased with SHAPEIT5 and was used as a reference to impute genotypes from lcWGS data employing GLIMPSE2. A total of 90 fish from the Troutlodge November breeding population were sequenced with an average coverage of 1.3×, and these fish were also genotyped with the Axiom 57K rainbow trout SNP array. The concordance between array-based genotypes and imputed genotypes was 99.1%. After downsampling the coverage to 0.5×, 0.2×, and 0.1×, the concordance between array-based genotypes and imputed genotypes was 98.7, 97.8, and 96.7%, respectively. In the USDA odd-year breeding population, the concordance between array-based genotypes and imputed genotypes was 97.8% for 109 fish downsampled to 0.5× coverage. Therefore, the reference haplotype panel reported in this study can be used to accurately impute genotypes from lcWGS data in rainbow trout breeding populations.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Maria Fernanda Guizar Amador, Kathy Darragh, Jasen W Liu, Cheryl Dean, Diego Bogarín, Oscar A Pérez-Escobar, Zuleika Serracín, Franco Pupulin, Santiago R Ramírez
{"title":"The Gongora gibba genome assembly provides new insights into the evolution of floral scent in male euglossine bee-pollinated orchids.","authors":"Maria Fernanda Guizar Amador, Kathy Darragh, Jasen W Liu, Cheryl Dean, Diego Bogarín, Oscar A Pérez-Escobar, Zuleika Serracín, Franco Pupulin, Santiago R Ramírez","doi":"10.1093/g3journal/jkae211","DOIUrl":"https://doi.org/10.1093/g3journal/jkae211","url":null,"abstract":"<p><p>Orchidaceae is one of the most prominent flowering plant families, with many species exhibiting highly specialized reproductive and ecological adaptations. An estimated 10% of orchid species in the American tropics are pollinated by scent-collecting male euglossine bees; however, to date, there are no published genomes of species within this pollination syndrome. Here we present the first draft genome of an epiphytic orchid from the genus Gongora, a representative of the male euglossine bee-pollinated subtribe Stanhopeinae. The 1.83 Gb de novo genome with a scaffold N50 of 1.7Mb was assembled using short- and long-read sequencing and chromosome capture (Hi-C) information. Over 17,000 genes were annotated, and 82.95% of the genome was identified as repetitive content. Furthermore, we identified and manually annotated 26 terpene synthase (TPS) genes linked to floral scent biosynthesis and performed a phylogenetic analysis with other published orchid TPS genes. The Gongora gibba genome assembly will serve as the foundation for future research to understand the genetic basis of floral scent biosynthesis and diversification in orchids. Las orquídeas (Orchidaceae) son una de las familias de plantas con mayor riqueza de especies y exhiben adaptaciones reproductivas altamente especializadas. Se estima que el 10% de las especies de orquídeas en los trópicos americanos son polinizadas por abejas euglosinas; sin embargo, hasta la fecha no existen genomas publicados de especies con este síndrome de polinización. Aquí presentamos el primer genoma de una orquídea epífita del género Gongora, un representante de la subtribu Stanhopeinae, que es polinizada exclusivamente por abejas euglosinas macho. El genoma de 1,83 Gb se ensambló de novo utilizando secuenciación e información de captura de cromosomas (Hi-C), logrando un N50 de 1,7 Mb. Se anotaron más de 17.000 genes y se identificó que el 82,95% del genoma presenta elementos repetitivos. Además, identificamos y anotamos manualmente 26 genes de la familia de genes terpeno sintasa (TPS) y realizamos un análisis filogenético con otros genes TPS de orquídeas publicados. El ensamblaje del genoma de Gongora gibba servirá como base para futuras investigaciones para comprender la base genética de la biosíntesis y la diversificación de los aromas florales en las orquídeas.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}