dc.contributor.author | Castanera, Raúl | |
dc.contributor.author | de Tomás, Carlos | |
dc.contributor.author | Ruggieri, Valentino | |
dc.contributor.author | Vicient, Carlos | |
dc.contributor.author | Eduardo, Iban | |
dc.contributor.author | Aranzana, Maria Jose | |
dc.contributor.author | Arús, Pere | |
dc.contributor.author | Casacuberta, Josep M. | |
dc.contributor.other | Producció Vegetal | ca |
dc.date.accessioned | 2024-06-26T08:36:09Z | |
dc.date.available | 2024-06-26T08:36:09Z | |
dc.date.issued | 2024-04-09 | |
dc.identifier.citation | Castanera, Raúl, Carlos de Tomás, Valentino Ruggieri, Carlos Vicient, Iban Eduardo, Maria José Aranzana, Pere Arús, and Josep M Casacuberta. 2024. “A Phased Genome of the Highly Heterozygous ‘Texas’ Almond Uncovers Patterns of Allele-Specific Expression Linked to Heterozygous Structural Variants.” Horticulture Research 11 (6). https://doi.org/10.1093/hr/uhae106. | ca |
dc.identifier.issn | 2052-7276 | ca |
dc.identifier.uri | http://hdl.handle.net/20.500.12327/3055 | |
dc.description.abstract | The vast majority of traditional almond varieties are self-incompatible, and the level of variability of the species is very high, resulting in a high-heterozygosity genome. Therefore, information on the different haplotypes is particularly relevant to understand the genetic basis of trait variability in this species. However, although reference genomes for several almond varieties exist, none of them is phased and has genome information at the haplotype level. Here, we present a phased assembly of genome of the almond cv. Texas. This new assembly has 13% more assembled sequence than the previous version of the Texas genome and has an increased contiguity, in particular in repetitive regions such as the centromeres. Our analysis shows that the ‘Texas’ genome has a high degree of heterozygosity, both at SNPs, short indels, and structural variants level. Many of the SVs are the result of heterozygous transposable element insertions, and in many cases, they also contain genic sequences. In addition to the direct consequences of this genic variability on the presence/absence of genes, our results show that variants located close to genes are often associated with allele-specific gene expression, which highlights the importance of heterozygous SVs in almond. | ca |
dc.description.sponsorship | This work was supported by the Spanish Ministerio de Ciencia e Innovación PID2019-106374RB-I00 and PID2022-143167NB-I00 grants to J.C. and IJC2020-045949-I fellowship to R.C., and RTI2018-100795-B-I00 and PID2021-128885OB-I00 both funded by MCIN/AEI/10.13039/501100011033 and by ‘ERDF A way of making Europe’ to M.J.A. We also acknowledge the support from the CERCA Programme (‘Generalitat de Catalunya’) and the ‘Severo Ochoa Programme for Centres of Excellence in R&D’ 2016–2019 (SEV-2015-0533) and 2020–2023 (CEX2019-000902-S). | ca |
dc.format.extent | 11 | ca |
dc.language.iso | eng | ca |
dc.publisher | Oxford University Press | ca |
dc.relation.ispartof | Horticulture Research | ca |
dc.rights | Attribution 4.0 International | ca |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | * |
dc.title | A phased genome of the highly heterozygous ‘Texas’ almond uncovers patterns of allele-specific expression linked to heterozygous structural variants | ca |
dc.type | info:eu-repo/semantics/article | ca |
dc.description.version | info:eu-repo/semantics/publishedVersion | ca |
dc.rights.accessLevel | info:eu-repo/semantics/openAccess | |
dc.embargo.terms | cap | ca |
dc.relation.projectID | MICIU/Programa Estatal de generación del conocimiento y fortalecimiento científico y tecnológico del sistema I+D+I y Programa Estatal de I+D+I orientada a los retos de la sociedad/PID2019-106374RB-I00/ES/TRANSPOSONES, UNA FUENTE IMPORTANTE DE VARIABILIDAD GENETICA EN PLANTAS CULTIVADAS/ | ca |
dc.relation.projectID | MICINN/Programa Estatal para impulsar la investigación científico-técnica y su transferencia/ PID2022-143167NB-I00/ES/Los Transposones, un motor de la evolución de los genomas de plantas/ | ca |
dc.relation.projectID | MICINN/Programa Estatal de promoción del talento y su empleabilidad en I+D+I/IJC2020-045949-I/ES/ / | ca |
dc.relation.projectID | MICIU/Programa Estatal de I+D+I orientada a los retos de la sociedad/RTI2018-100795-B-I00/ES/HERRAMIENTAS MOLECULARES PARA LA MEJORA GENETICA DE CARACTERES DE CALIDAD EN MELOCOTONERO Y OTROS PRUNUS/ | ca |
dc.relation.projectID | MICINN/Programa Estatal para impulsar la investigación científico-técnica y su transferencia/PID2021-128885OB-I00/ES/ / | ca |
dc.relation.projectID | MINECO/Programa Estatal de fomento de la investigación científica y técnica de excelencia/SEV-2015-0533/ES/ / | ca |
dc.relation.projectID | MICIU/Programa Estatal de generación del conocimiento y fortalecimiento científico y tecnológico del sistema I+D+I/CEX2019-000902-S/ES/ / | ca |
dc.relation.projectID | FEDER/ / /EU/ / | ca |
dc.subject.udc | 633 | ca |
dc.identifier.doi | https://doi.org/10.1093/hr/uhae106 | ca |
dc.contributor.group | Genòmica i Biotecnologia | ca |