ArticleHorticulture research2023
A chromosome-level phased genome enabling allele-level studies in sweet orange: a case study on citrus Huanglongbing tolerance.
Article in Horticulture research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 38 citations in OpenAlex.
- Highly heterozygous Citrus changshan-huyou Y. B. Chang originated from ancient hybridization between mandarin and pummelo and displayed distinct tissue-specific allelic imbalance.The plant genome · 2026Article
- A Super-Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution.Plant biotechnology journal · 2026Article
- Haplotype-resolved genome of Citrus × sinensis 'Pera IAC', the most widely cultivated sweet orange in Brazil.Scientific data · 2026Article
- High-quality genome assembly of Aglaia odorata reveals evolution, terpenes diversity and abundance in Meliaceae.Molecular horticulture · 2026Article
- AlleleMiner: a long-read pipeline for gene-wise de novo allele phasing and variant detection in diploid citrus cultivars.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- The genome of a low-seeded mandarin, Premier, displays major structural changes due to gamma irradiation.The plant genome · 2026Article
- Genotyping-by-Sequencing Reveals Marker-Based Genome Stability in Tetraploid Clementines for Triploid Breeding.Plants (Basel, Switzerland) · 2026Article
- Genetic mapping reveals QTLs associated with HLB response determined byFrontiers in plant science · 2026Article
- Pollen performance under controlled temperatures and chromosome stability of diploid and tetraploid citrus.BMC plant biology · 2025Article
- Diploid assembly of the Mexican lime genome.G3 (Bethesda, Md.) · 2025Article
- A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus.BMC genomics · 2025Article
- Substantial enhancement ofHorticulture research · 2025Article
- Comprehensive transposon-insertion profiling unravels the asexual breeding history of sweet orange cultivars.Plant communications · 2025Article
- Exploring the Genetic Networks of HLB Tolerance in Citrus: Insights Across Species and Tissues.Plants (Basel, Switzerland) · 2025Article
- Citrus genomes: past, present and future.Horticulture research · 2025Article
- Construction of a comprehensive library of repeated sequences for the annotation of Citrus genomes.BMC genomic data · 2025Article
- Distinctive acidity in citrus fruit is linked to loss of proanthocyanidin biosynthesis.iScience · 2024Article
- Chromosome-level genome assembly and annotation of Flueggea virosa (Phyllanthaceae).Scientific data · 2024Article
- Chromosome-Scale, De Novo, Phased Genome Assemblies of Three Australian Limes:Plants (Basel, Switzerland) · 2024Article
- A high-quality chromosome-scale genome assembly of blood orange, an important pigmented sweet orange variety.Scientific data · 2024Article
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sweet orange originated from the introgressive hybridizations of pummelo and mandarin resulting in a highly heterozygous genome. How alleles from the two species cooperate in shaping sweet orange phenotypes under distinct circumstances is unknown. Here, we assembled a chromosome-level phased diploid Valencia sweet orange (DVS) genome with over 99.999% base accuracy and 99.2% gene annotation BUSCO completeness. DVS enables allele-level studies for sweet orange and other hybrids between pummelo and mandarin. We first configured an allele-aware transcriptomic profiling pipeline and applied it to 740 sweet orange transcriptomes. On average, 32.5% of genes have a significantly biased allelic expression in the transcriptomes. Different cultivars, transgenic lineages, tissues, development stages, and disease status all impacted allelic expressions and resulted in diversified allelic expression patterns in sweet orange, but particularly citrus Huanglongbing (HLB) shifted the allelic expression of hundreds of genes in leaves and calyx abscission zones. In addition, we detected allelic structural mutations in an HLB-tolerant mutant (T19) and a more sensitive mutant (T78) through long-read sequencing. The irradiation-induced structural mutations mostly involved double-strand breaks, while most spontaneous structural mutations were transposon insertions. In the mutants, most genes with significant allelic expression ratio alterations (≥1.5-fold) were directly affected by those structural mutations. In T19, alleles located at a translocated segment terminal were upregulated, including
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.