ArticlePlant biotechnology journal2022
Transposon insertions regulate genome-wide allele-specific expression and underpin flower colour variations in apple (Malus spp.).
Article in Plant biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed, 70 citations in OpenAlex.
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- 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
- A 725-bp quadruple repeat in the promoter ofHorticulture research · 2026Article
- Haplotype-resolved chromosome-level genome assemblies of nineteen apple (Malus domestica Borkh.) cultivars.Scientific data · 2026Article
- Inheritance of DNA Methylation Patterns and Its Role in Modulating Allelic Expression inPlants (Basel, Switzerland) · 2025Article
- Evolutionary dynamics of the proanthocyanidin biosynthesis gene LAR.BMC genomics · 2025Article
- Convergent domestication of bitter apples and pears by selecting mutations of MYB transcription factors to reduce proanthocyanidin levels.Molecular horticulture · 2025Article
- Transcriptome dynamics and allele-specific regulation underlie wheat heterosis at the anthesis and grain-filling stages.BMC genomics · 2025Article
- Comprehensive transposon-insertion profiling unravels the asexual breeding history of sweet orange cultivars.Plant communications · 2025Article
- The road less taken: Dihydroflavonol 4-reductase inactivation and delphinidin anthocyanin loss underpins a natural intraspecific flower colour variation.Molecular ecology · 2025Article
- Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus.Genome research · 2025Article
- Construction of the super pan-genome for the genusHorticulture research · 2025Article
- Pan-genome analysis reveals the evolution and diversity of Malus.Nature genetics · 2025Article
- Impact of Allele-Specific Expression on Ripening and Quality Characteristics of ABB Banana Fruit.International journal of molecular sciences · 2025Article
- Genome Assembly and Winged Fruit Gene Regulation of Chinese Wingnut: Insights from Genomic and Transcriptomic Analyses.Genomics, proteomics & bioinformatics · 2025Article
- Genome sequencing of 'Fuji' apple clonal varieties reveals genetic mechanism of the spur-type morphology.Nature communications · 2024Article
- Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits.Plant communications · 2024Article
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Authors and funding
24 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Allele-specific expression (ASE) can lead to phenotypic diversity and evolution. However, the mechanisms regulating ASE are not well understood, particularly in woody perennial plants. In this study, we investigated ASE genes in the apple cultivar 'Royal Gala' (RG). A high quality chromosome-level genome was assembled using a homozygous tetra-haploid RG plant, derived from anther cultures. Using RNA-sequencing (RNA-seq) data from RG flower and fruit tissues, we identified 2091 ASE genes. Compared with the haploid genome of 'Golden Delicious' (GD), a parent of RG, we distinguished the genomic sequences between the two alleles of 817 ASE genes, and further identified allele-specific presence of a transposable element (TE) in the upstream region of 354 ASE genes. These included MYB110a that encodes a transcription factor regulating anthocyanin biosynthesis. Interestingly, another ASE gene, MYB10 also showed an allele-specific TE insertion and was identified using genome data of other apple cultivars. The presence of the TE insertion in both MYB genes was positively associated with ASE and anthocyanin accumulation in apple petals through analysis of 231 apple accessions, and thus underpins apple flower colour evolution. Our study demonstrated the importance of TEs in regulating ASE on a genome-wide scale and presents a novel method for rapid identification of ASE genes and their regulatory elements in plants.
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