ArticleThe plant genome2021
An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids.
Article in The plant genome, 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.
- Pan-NLRome ofFrontiers in plant science · 2026Article
- Spinach (Foods (Basel, Switzerland) · 2025Article
- QTL mapping and candidate gene identification of the full flowering date trait in olive trees (Olea Europaea L.).BMC plant biology · 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
- 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
- Cross-species analysis of abiotic stress in hydroponic leafy crops reveals conserved regulatory networks and key divergences.Frontiers in plant science · 2025Article
- 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
- Systematic Analysis of theInternational journal of molecular sciences · 2024Article
- A chromosome-level genome assembly provides insights into the local adaptation of Tamarix austromongolica in the Yellow River Basin, China.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Evolutionary assembly of the plant terrestrialization toolkit from protein domains.Proceedings. Biological sciences · 2024Article
- Spinach genomes reveal migration history and candidate genes for important crop traits.NAR genomics and bioinformatics · 2024Article
- Article
- Chromosome-level genome assembly of a xerophytic plant, Haloxylon ammodendron.DNA research : an international journal for rapid publication of reports on genes and genomes · 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
- An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids.The plant genome · 2021Article
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15 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Spinach (Spinacia oleracea L.) is a member of the Caryophyllales family, a basal eudicot asterid that consists of sugar beet (Beta vulgaris L. subsp. vulgaris), quinoa (Chenopodium quinoa Willd.), and amaranth (Amaranthus hypochondriacus L.). With the introduction of baby leaf types, spinach has become a staple food in many homes. Production issues focus on yield, nitrogen-use efficiency and resistance to downy mildew (Peronospora effusa). Although genomes are available for the above species, a chromosome-level assembly exists only for quinoa, allowing for proper annotation and structural analyses to enhance crop improvement. We independently assembled and annotated genomes of the cultivar Viroflay using short-read strategy (Illumina) and long-read strategies (Pacific Biosciences) to develop a chromosome-level, genetically anchored assembly for spinach. Scaffold N50 for the Illumina assembly was 389 kb, whereas that for Pacific BioSciences was 4.43 Mb, representing 911 Mb (93% of the genome) in 221 scaffolds, 80% of which are anchored and oriented on a sequence-based genetic map, also described within this work. The two assemblies were 99.5% collinear. Independent annotation of the two assemblies with the same comprehensive transcriptome dataset show that the quality of the assembly directly affects the annotation with significantly more genes predicted (26,862 vs. 34,877) in the long-read assembly. Analysis of resistance genes confirms a bias in resistant gene motifs more typical of monocots. Evolutionary analysis indicates that Spinacia is a paleohexaploid with a whole-genome triplication followed by extensive gene rearrangements identified in this work. Diversity analysis of 75 lines indicate that variation in genes is ample for hypothesis-driven, genomic-assisted breeding enabled by this work.
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