ArticleHorticulture research2024
A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous structural variants.
Article in Horticulture research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026Review
- Comparative transcriptomics among peach, almond and their interspecific F1 hybrid reveal key common and species-specific regulatory pathways involved in fruit development.BMC plant biology · 2026Article
- Improved genome assembly of double haploid Prunus persica siblings 'Lovell 2D' and 'Lovell 5D' and the peach NLRome.Scientific reports · 2026Article
- The Combination of Start-Codon-Targeted (SCoT) andInternational journal of molecular sciences · 2025Article
- Tandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes.Mobile DNA · 2025Article
- Mapping the genomic landscape ofHorticulture research · 2025Article
- Exploring additive and non-additive genetic models to decipher the genetic regulation of almond tolerance toFrontiers in plant science · 2025Article
- Article
- QTL mapping of almond kernel quality traits in the FFrontiers in plant science · 2024Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
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