ArticleGenome biology2022
The spinach YY genome reveals sex chromosome evolution, domestication, and introgression history of the species.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 47 citations in OpenAlex.
- Gibberellic acid modulates drought stress signaling, antioxidant defense, and ionic homeostasis in spinach.Plant signaling & behavior · 2026Article
- Haplotype-resolved genome assembly of femaleHorticulture research · 2026Article
- Transposons drove the evolution of a male sex-determining gene from a female gene with deep introgression across cichlids.Science advances · 2026Article
- Genome-wide association and genomic prediction of anthracnose (Colletotrichum dematium) resistance in spinach.The plant genome · 2026Article
- Pan-NLRome ofFrontiers in plant science · 2026Article
- A haplotype-resolved genome assembly of seed hemp (Horticulture research · 2026Article
- Spinach (Foods (Basel, Switzerland) · 2025Article
- Genetic Mapping and Transcriptomic Analysis of Sepal-Derived Seed Shape in Spinach.International journal of molecular sciences · 2025Article
- Analyses of contiguous reference genomes of Amaranthus tuberculatus highlight the landscape of the sex-associated region and PEBP gene family diversity.BMC genomics · 2025Article
- Gibberellin Disrupts Hormonal Homeostasis and Anther Integrity to Trigger Sex Reversal in Spinach.International journal of molecular sciences · 2025Article
- A complete telomere-to-telomere assembly of the Spinacia oleracea genome reveals Y chromosome evolution and centromere landscape.Plant communications · 2025Article
- Spatiotemporal Transcriptomic Atlas Reveals the Regulatory Mechanisms Underlying Early Inflorescence Development and Sex Differentiation in Spinach.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Integration of crop modeling and sensing into molecular breeding for nutritional quality and stress tolerance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Identification of a candidate sex determination region and sex-specific molecular markers based on whole-genome re‑sequencing in the sea star Asterias amurensis.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- ZW sex chromosome structure in Amborella trichopoda.Nature plants · 2024Article
- Evolution of Sex-linked Genes and the Role of Pericentromeric Regions in Sex Chromosomes: Insights from Diploid Willows.Molecular biology and evolution · 2024Article
- Pan-genome analysis of 13 Spinacia accessions reveals structural variations associated with sex chromosome evolution and domestication traits in spinach.Plant biotechnology journal · 2024Article
- Transcriptome-guided selection of stable reference genes for expression analysis in spinach.Scientific reports · 2024Article
- Spinach genomes reveal migration history and candidate genes for important crop traits.NAR genomics and bioinformatics · 2024Article
- Gene Regulatory Network Controlling Flower Development in Spinach (International journal of molecular sciences · 2024Article
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Authors and funding
18 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSpinach (Spinacia oleracea L.) is a dioecious species with an XY sex chromosome system, but its Y chromosome has not been fully characterized. Our knowledge about the history of its domestication and improvement remains limited.
resultsA high-quality YY genome of spinach is assembled into 952 Mb in six pseudo-chromosomes. By a combination of genetic mapping, Genome-Wide Association Studies, and genomic analysis, we characterize a 17.42-Mb sex determination region (SDR) on chromosome 1. The sex chromosomes of spinach evolved when an insertion containing sex determination genes occurred, followed by a large genomic inversion about 1.98 Mya. A subsequent burst of SDR-specific repeats (0.1-0.15 Mya) explains the large size of this SDR. We identify a Y-specific gene, NRT1/PTR 6.4 which resides in this insertion, as a strong candidate for the sex determination or differentiation factor. Resequencing of 112 spinach genomes reveals a severe domestication bottleneck approximately 10.87 Kya, which dates the domestication of spinach 7000 years earlier than the archeological record. We demonstrate that a strong selection signal associated with internode elongation and leaf area expansion is associated with domestication of edibility traits in spinach. We find that several strong genomic introgressions from the wild species Spinacia turkestanica and Spinacia tetrandra harbor desirable alleles of genes related to downy mildew resistance, frost resistance, leaf morphology, and flowering-time shift, which likely contribute to spinach improvement.
conclusionsAnalysis of the YY genome uncovers evolutionary forces shaping nascent sex chromosome evolution in spinach. Our findings provide novel insights about the domestication and improvement of spinach.
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