ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2021
A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Genome-wide association and genomic prediction of anthracnose (Colletotrichum dematium) resistance in spinach.The plant genome · 2026Article
- Genome-wide association study and genomic prediction of fruit weight in spinach.Scientific reports · 2026Article
- Genome-wide association study and genomic prediction of bolting trait in spinach (Frontiers in plant science · 2026Article
- Article
- Pan-NLRome ofFrontiers in plant science · 2026Article
- Transcriptome-Based miR156-Mediated Expression Dynamics of SPL Transcription Factors During Vegetative to Reproductive Transition in Spinach.Plants (Basel, Switzerland) · 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
- Pan-genome analysis of 13 Spinacia accessions reveals structural variations associated with sex chromosome evolution and domestication traits in spinach.Plant biotechnology journal · 2024Article
- Dual transcriptional characterization of spinach and Peronospora effusa during resistant and susceptible race-cultivar interactions.BMC genomics · 2024Article
- Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum).DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Spinach genomes reveal migration history and candidate genes for important crop traits.NAR genomics and bioinformatics · 2024Article
- Improvement of crop production in controlled environment agriculture through breeding.Frontiers in plant science · 2024Review
- Article
- Chromosome-scale genome assembly of Glycyrrhiza uralensis revealed metabolic gene cluster centred specialized metabolites biosynthesis.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Identification of Sex Differentiation-Related microRNAs in Spinach Female and Male Flower.International journal of molecular sciences · 2022Article
- Quantitative Trait Locus Mapping and Identification of Candidate Genes Controlling Bolting in Spinach (Frontiers in plant science · 2022Article
- Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasm.Horticulture research · 2022Article
- Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits.Nature communications · 2021Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Spinach (Spinacia oleracea) is grown as a nutritious leafy vegetable worldwide. To accelerate spinach breeding efficiency, a high-quality reference genome sequence with great completeness and continuity is needed as a basic infrastructure. Here, we used long-read and linked-read technologies to construct a de novo spinach genome assembly, designated SOL_r1.1, which was comprised of 287 scaffolds (total size: 935.7 Mb; N50 = 11.3 Mb) with a low proportion of undetermined nucleotides (Ns = 0.34%) and with high gene completeness (BUSCO complete 96.9%). A genome-wide survey of resistance gene analogues identified 695 genes encoding nucleotide-binding site domains, receptor-like protein kinases, receptor-like proteins and transmembrane-coiled coil domains. Based on a high-density double-digest restriction-site associated DNA sequencing-based linkage map, the genome assembly was anchored to six pseudomolecules representing ∼73.5% of the whole genome assembly. In addition, we used SOL_r1.1 to identify quantitative trait loci for bolting timing and fruit/seed shape, which harbour biologically plausible candidate genes, such as homologues of the FLOWERING LOCUS T and EPIDERMAL PATTERNING FACTOR-LIKE genes. The new genome assembly, SOL_r1.1, will serve as a useful resource for identifying loci associated with important agronomic traits and for developing molecular markers for spinach breeding/selection programs.
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Registered trials
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