BUSCADOR RECOLECTA

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., 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)., info:eu-repo/semantics/publishedVersion

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., 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)., With funding from the Spanish goverment throught the "Severo Ochoa Centre of Excellence" accreditation (SEV-2015-0533 and CEX2019-000902-S)., Peer reviewed

Peer reviewed