1,721,047 research outputs found
Minimizing detection bias of somatic mutations in a highly heterozygous oak genome
Full text linkSomatic mutations are particularly relevant for long-lived organisms. Sources of somatic mutations include imperfect DNA repair, replication errors, and exogenous damage such as ultraviolet radiation. A previous study estimated a surprisingly low number of somatic mutations in a 234-year-old individual of the pedunculate oak (Quercus robur), known as the Napoleon Oak. It has been suggested that the true number of somatic mutations was underestimated due to gaps in the reference genome and too conservative filtering of potential mutations. We therefore generated new high-fidelity long-read data for the Napoleon Oak (n = 12) to produce both a pseudo-haploid genome assembly and a partially phased diploid assembly. The high heterozygosity allowed for complete reconstruction of phased and gapless centromeres for 22 of the 24 chromosomes. On the other hand, the high heterozygosity posed challenges for short-read alignments. Use of only the pseudo-haploid assembly as a reference led to potential misalignments, while use of only the diploid assembly reduced variant detection sensitivity. Since most somatic mutations are layer-specific, the fraction of reads covering a specific somatic mutation is expected to be relatively low, even where all cells in a single layer contain a specific mutation. To address this challenge, we employed a read assignment strategy, selecting the appropriate reference sequence (pseudo-haploid or diploid) based on alignment score and mapping quality. Ultimately, we identified 198 high-confidence somatic mutations, compared with 17 somatic mutations identified before with the same set of short reads. Our approach thus increased the total estimated annual mutation rate by a factor of 5.
© The Author(s) 2025. Published by Oxford University Press on behalf of The Genetics Society of America
Reducing sampling bias in molecular studies of grapevine fruit ripening: transcriptomic assessment of the density sorting method
No full textThe interplay between environmental and genetic factors conditions the fruit ripening program in plants. Transcriptome analysis of grapevine fruits can help understanding these interactions to consciously cope with conditions leading to detrimental effects for viticultural purposes. However, considering the grapevine characteristic ripening asynchrony, which can be intensified by contrasting conditions, accurate grape sampling may be essential for molecular comparisons. In this study, berry density sorting according to floatability in NaCl solutions was transcriptomically assessed as a grape ripening staging strategy. The transcriptome was compared between three density classes collected near commercial maturity using grapevine whole-genome NimbleGen microarrays. Expression profiles clearly related with ripening progression were detected in a density series simultaneously collected from a vineyard of Albariño. By contrast, considerable differences were detected when the same density series was sampled on two different dates from the same vineyard of Tempranillo. Functional analysis indicated that environmental differences between both sampling moments determined most of these expression differences. Ripening degree-dependent responses to the environment were also detected. Finally, the effect of the sorting procedures on the grape transcriptome showed negligible when it was directly tested. Altogether, these findings evidence the convenience of homogenizing the developmental stage and the sampling time conditions for transcriptome comparisons. Berry density sorting proved useful to this end, although this method could be limited when berry sugar concentration increases through dehydration.This work was carried out in the context of the CENIT-DEMETER Project, funded by the Spanish Centre for Technological and Industrial Development (CDTI) from the Spanish Ministry of Science and Innovation (MICINN). The authors express their gratitude to all entities participating in the CENIT-DEMETER Consortium, and especially to Bodegas Miguel Torres S. A., Bodegas Martín Códax, Bodegas Roda, and Bodegas Matarromera S. L. for their support and for providing the plants and the growing conditions. Collaboration between authors’ research groups was established in the context of COST (European Cooperation in Science and Technology) Action FA1106 “QualityFruit”.Peer Reviewe
Deciphering the origin of improved agronomic traits in grape and pistachio from genome assemblies and Iso-Seq analysis
No full textTrabajo presentado en el PacBio Discoveries Roadshow, celebrado en Barcelona (España), el 16 de mayo de 202
Deciphering the origin of improved agronomic traits in grape and pistachio from genome assemblies and Iso-Seq analysis
No full textTrabajo presentado en el PacBio Day Tübingen, celebrado en Bonn (Alemania), el 21 de septiembre de 202
Identificación del origen de variantes clonales de Tempranillo y Garnacha empleando ensamblajes de genomas varietales
No full textTrabajo presentado en las XV Jornadas del Instituto de Ciencias de la Vid y del Vino, celebradas en Logroño (España), el 15 de diciembre de 202
Genome assemblies and long-read sequencing to search for functional variation in grapevine
No full textTrabajo presentado en GRAPEDIA Annual Meeting, celebrado en Valencia (España), del 11 al 13 de septiembre de 2023Domesticated grapevines exhibit a high level of genome diversity
among cultivars. In addition, grapevine cultivars are usually highly
heterozygous, with great diversity between the two haploid
complements comprising their diploid genome. Therefore, to increase
the possibilities of capturing the genome variants responsible for phenotype variation in traits of agronomic interest, we have developed
cultivar-specific and diploid genome assemblies for relevant grapevine
cultivars. To overcome the highly repetitive and heterozygous nature of
grapevine genomes, we either combined noisy PacBio and Nanopore
long reads with trio binning of haplotypes or used accurate HiFi PacBio
long reads. The obtained genome assemblies, combined in specific
cases with long read-based gene annotations and methylation analysis,
were useful for detecting genome and epigenome variations associated
with intra-cultivar variants displaying diversity in fruit colour or
decreased bunch compactness
Estudio del origen genético de la variedad de vid Garnacha Blanca, de su diversidad fenotípica y de los efectos moleculares asociados a la variación en el color de la uva
No full textBecause of their high heterocygosity, grapevine cultivars are reproduced by vegetative multiplication in order to keep their varietal characteristic traits. In this way, somatic variation is the main source of genetic divsersity to improve traditional varieties either by clonal selection, or for the generation of new derivative varieties, like berry color variants. Garnacha Blanca (GB) is a white-berried variety derived from Garnacha Tinta (GT). Both varieties display fruit set problems that can limit production. In order to understand potential in GB for clonal selection improvement regarding production and bunch compactness, we studied the variation of related traits at plant, bunch and berry level, in several accessions during two years. We also analyzed the genetic and molecular origin of color loss variation and its relation with production and bunch compactness by SNP genotyping of chromosome 2 and next- generation sequencing strategies. In addition, we used white variants of Garnacha and Tempranillo to assess for direct and indirect consequences of the absence of anthocyanins in berry composition using metabolomic and transcriptomic analyses. Results showed us that the main variable determining variation in production and bunch compactness is fruitset rate and it has strong environmental dependece. Traits related with berry size are less relevant in determining production and bunch compactness. Regarding the genetic origin of GB, the SNP genotyping chip for chromosome 2, allowed us to detect loss of heterozigosity around the region of the berry color locus that regulates anthocyanin biosynthesis in the berry. Sequencing and comparison of GT and GB genomes confirmed that the loss of heterocigosity was caused by deletions of the functional copies of VviMYBA1 and VviMYBA2 genes. Segregation and gamete viability analyses showed that these deletions have no negative effects neither in gamete transmission nor in gamete viability, and consequently do not affect production and bunch compactness in GB. Finally, metabolome and transcriptome comparisons between berry color somatic variants unveiled the regulatory role of VviMYBA1 and VviMYBA2 genes in phenylpropanoid biosynthesis pathway and in triggering protection againts pathogens and abiotic stress in the berry skin during berry ripening. In addition, white grapes accumulated higher levels of alternative photoprotective molecules (carotenoids, phenilpropanoids and terpenoids) correlating with the transcriptional activation of light responses in white berries. These responses associate with important changes in the berry composition and may contribute to floral, white fruit and herbaceous aromatic character, typical of white wines. Altogether, the results contribute to a deeper understanding of somatic variation mechanisms and its phenotypic effects in terms of production and quality in grapes. This knowledge could help to optimize clonal selection programs and increase their efficiency.Estudio del origen genético de la variedad de vid Garnacha Blanca, de su diversidad fenotípica y de los efectos moleculares asociados a la variación en el color de la uva
La vid cultivada se propaga mediante reproducción vegetativa ya que, dada su alta heterocigosidad, es el único modo de mantener las características varietales. En relación con esto, la variación somática es la principal fuente de diversidad genética para la mejora de las variedades tradicionales de vid mediante selección clonal y para la obtención de nuevas variedades derivadas como es el caso de las variantes de color de la uva. Garnacha Blanca (GB) es una variedad de uva blanca derivada de Garnacha Tinta (GT), ambas caracterizadas por problemas en el cuajado de frutos que limitan su producción. Con el objetivo de estudiar el potencial de la variación intravarietal recolectada en GB para la mejora mediante selección clonal de su producción y compacidad de racimo, se estudió el comportamiento de distintas accesiones a lo largo de dos años para variables relacionadas a nivel de planta, racimo y baya. También se analizó, mediante estrategias de genotipado de SNP y de secuenciación masiva, el origen genético y molecular de la pérdida de color de la uva y su posible relación con la producción y la compacidad. Además, la disponibilidad de variantes blancas tanto en Garnacha como en Tempranillo se utilizó para estudiar en detalle los efectos directos e indirectos que la pérdida de antocianinas determina en la composición de la baya, tanto a nivel metabolómico como de expresión génica. Los resultados ponen de manifiesto que la tasa de cuajado es la variable más determinante de la variación para la compacidad y la producción en GB y que tiene además una gran dependencia ambiental. Otras variables relacionadas con el tamaño de los frutos tienen sin embargo un menor impacto en la producción y en la compacidad de los racimos. En lo relativo al origen genético de GB, el desarrollo de un chip de genotipado de SNP para el cromosoma 2 ha permitido detectar regiones de pérdida de heterocigosidad alrededor de la posición en la que se encuentra el locus que regula la síntesis de antocianinas en el fruto. La secuenciación y comparación de genomas de GT y GB confirmaron que dicha pérdida de heterocigosidad se da como resultado de deleciones que incluyen la copia funcional de los genes VviMYBA1 y VviMYBA2. Los resultados indican que la presencia de deleciones en hemicigosis no afecta a la transmisión de las regiones mutadas ni reduce la viabilidad de los gametos y por lo tanto no tiene consecuencias a nivel de producción ni de compacidad en GB. Finalmente, la comparación de metaboloma y transcriptoma entre variantes somáticas de color tanto en Garnacha como en Tempranillo identificó el papel regulador de los genes VviMYBA1 y VviMYBA2 en la ruta de síntesis de fenilpropanoides y en rutas de respuesta de defensa y protección frente a condiciones de estrés en el hollejo durante la maduración de la baya. Además, en ausencia de antocianos, las uvas blancas acumularon mayores niveles de moléculas fotoprotectoras y antioxidantes alternativas (carotenoides, fenilpropanoides y terpenoides), lo que correlaciona con un aumento de respuestas trasncriptómicas a la luz en las bayas blancas. Estas respuestas se asocian con cambios importantes en la composición de las bayas que pueden contribuir al carácter aromático floral, de fruta blanca y herbáceo que caracteriza a los vinos blancos. En conjunto, los resultados contribuyen a un conocimiento más profundo de la variación somática y de sus efectos fenotípicos en lo relativo a la producción del cultivo de la vid y su calidad. Este conocimiento puede servir para optimizar el diseño de los programas de selección clonal y mejorar su eficacia
Sequencing methods and bioinformatics to make sense of genome variation
No full textSeminario de 3 horas impartido en el Master Bioinformatics and Computational Biology students, en la Universidad de Lisboa (Portugal), el 3 de noviembre de 202
Fast biofoundries: coping with the challenges of biomanufacturing
No full textBiofoundries are highly automated facilities that enable the rapid and efficient design, build, test, and learn cycle of biomanufacturing and engineering biology, which is applicable to both research and industrial production. However, developing a biofoundry platform can be expensive and time consuming. A biofoundry should grow organically, starting from a basic platform but with a vision for automation, equipment interoperability, and efficiency. By thinking about strategies early in the process through process planning, simulation, and optimization, bottlenecks can be identified and resolved. Here, we provide a survey of technological solutions in biofoundries and their advantages and limitations. We explore possible pathways towards the creation of a functional, early-phase biofoundry, and strategies towards long-term sustainability.The authors thank Dr Rosalind Le Feuvre, Manchester SYNBIOCHEM Centre, for providing insightful discussions. J.T.-L. was supported by the Next Generation EU (NGEU) fund through the Spanish Recovery, Transformation and Resilience Plan via a Margarita Salas personal grant from the Spanish Ministry of Universities (UNI/551/2021). I.O.-M. was supported by CSIC intramural project PIE 20211CT006. A.G.-M. was supported by the grants BioSinT-CM (Y2020/TCS-6555) and CONTEXT (Atracción de Talento Program; 2019-T1/BIO-14053) Projects of the Comunidad de Madrid, MULTI-SYSBIO (PID2020-117205GA-I00), and the Severo Ochoa Program for Centres of Excellence in R&D (SEV-2016-0672) (2017–2021) from Ministe. P.C. was supported by MCIN/AEI/10.13039/501100011033 BIODYNAMICS grant number PID2020-117271RB-C21, and Universitat Politécnica de València Talento Programme.Peer reviewe
Comparative analysis of grapevine whole-genome gene predictions, functional annotation, categorization and integration of the predicted gene sequences
Full text linkAbstract Background The first draft assembly and gene prediction of the grapevine genome (8X base coverage) was made available to the scientific community in 2007, and functional annotation was developed on this gene prediction. Since then additional Sanger sequences were added to the 8X sequences pool and a new version of the genomic sequence with superior base coverage (12X) was produced. Results In order to more efficiently annotate the function of the genes predicted in the new assembly, it is important to build on as much of the previous work as possible, by transferring 8X annotation of the genome to the 12X version. The 8X and 12X assemblies and gene predictions of the grapevine genome were compared to answer the question, “Can we uniquely map 8X predicted genes to 12X predicted genes?” The results show that while the assemblies and gene structure predictions are too different to make a complete mapping between them, most genes (18,725) showed a one-to-one relationship between 8X predicted genes and the last version of 12X predicted genes. In addition, reshuffled genomic sequence structures appeared. These highlight regions of the genome where the gene predictions need to be taken with caution. Based on the new grapevine gene functional annotation and in-depth functional categorization, twenty eight new molecular networks have been created for VitisNet while the existing networks were updated. Conclusions The outcomes of this study provide a functional annotation of the 12X genes, an update of VitisNet, the system of the grapevine molecular networks, and a new functional categorization of genes. Data are available at the VitisNet website (http://www.sdstate.edu/ps/research/vitis/pathways.cfm).</p
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