Abstract
Spinach (Spinacia olracea L.) is a dioecious leafy vegetable with a highly repetitive genome of around 990 Mb, which is challenging for de-novo genome assembly. In our study, a segregating F1 (double pseudo-testcross) population from ‘Viroflay’ × ‘Cornell-NO. 9′ was used for genetic mapping by resequencing genotyping. In the paternal ‘Cornell-NO. 9′ map, 212,414 SNPs were mapped, and the total linkage distance was 476.83 cM; the maternal ‘Viroflay’ map included 29,282 SNPs with 401.28 cM total genetic distance. Both paternal and maternal maps have the expected number of six linkage groups (LGs). A non-recombining region with 5678 SNPs (39 bin markers) co-segregates with sex type which located at 45.2 cM of LG1 in the ‘Cornell-NO. 9′ map while indicates the sex determination region (SDR). Integration of two maps into a consensus map guided us to anchor additional 1242 contigs to six pseudomolecules from the published reference genome, which improved additional 233 Mb (23.4%) assembly based on spinach estimated genome size. Particularly, the X counterpart of SDR in our assembly is estimated around 18.4 Mb which locates at the largest chromosome, as consensus with sex-biased FISH signals from previous cytogenetics studies. The region is featured by reduced gene density, higher percentage of repetitive sequences, and no recombination. Our linkage maps provide the resource for improving spinach genome de-novo assembly and identification of sex-determining genes in spinach.
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Data availability statements
The genomic sequences of spinach reference genome and gene annotation can be downloaded in the SpinachBase (https://www.spinachbase.org/). The improved genome assembly has been deposit in NCBI submission portal (ID: SUB7892681).
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Acknowledgements
This work was supported by the National Science Foundation (NSF) Plant Genome Research Program Award BI-1546890, Natural Science Foundation of Fujian Province, China 2018J01606, and startup fund from Fujian Agriculture and Forestry University. We appreciate the suggestions from Dr. Jun Wu and Wei Wei for projects and manuscript.
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RM conceived the spinach sex chromosomes project, and LY constructed the spinach population, extracted the DNA, conducted the data analysis, and wrote the manuscript. XM and BD prepared the sequencing libraries. JY and XM proofread the manuscript. RM revised the manuscript.
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Supplementary file1Supplementary S1 Summary of re-sequencing data. The numbers of clean reads, average depth, GC content, Q20, and Q30 information were summarized (XLSX 10 kb)
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Supplementary file2Supplementary S2 Segregation patterns of F1 plants. Types of segregation patterns of F1 plants were summarized (XLSX 10 kb)
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Supplementary file3Supplementary S3 Selected SNPs for ‘Viroflay’ map construction. The file includes all selected SNP with ‘nnxnp’ genotype code from transformed variant calling files (VCFs) (TXT 6969 kb)
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Supplementary file4Supplementary S4 Selected SNPs for ‘Cornell-NO. 9’ map construction. The file includes all selected loci with ‘lmxll’ genotype code from transformed variant calling files (VCFs) (TXT 44937 kb)
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Supplementary file5Supplementary S5 Linkage map of ‘Viroflay’ × ‘Cornell-NO. 9’. The table includes genotypes for each F1 individual across all bins from ‘Virofaly’ map and ‘Cornell-NO. 9’ map. The first column represents the genetic distance, second column represents name for each bin, third column represents genomic size for each bin and the fourth column represent numbers of SNPs within each bin (XLSX 1009 kb)
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Supplementary file6Supplementary S6 AGP table of map-based spinach genome assembly. The table includes corresponded genomic region coordinates between map-based genome assembly and published reference genome (XLSX 2330 kb)
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Supplementary file7Supplementary S7 Genotype for SNPs identified from sex-linked region derived from ‘Cornell-NO. 9’ map. The worksheet includes genotypes identified from sex-linked region based on coordinates from each contig or scaffold (XLSX 1624 kb)
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Supplementary file8Supplementary S8 Statistics of segregation distorted bins from two maps. The Chi-square test value, ratio between numbers of homozygous and heterozygous genotypes for 80 individuals were summarized (XLSX 135 kb)
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Supplementary file9Supplementary S9 Summary of sex-linked genomic regions. The corresponded genomic region between map-based assembly and published reference genome was summarized, includes numbers of genes, numbers of SNPs, SNP coverage (XLSX 12 kb)
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Supplementary file10Supplementary S10 Summary of sex-linked uni-genes from previous studies. Uni-genes identified from previous studies were summarized based on coordinate from corresponded genomic position and occurrence in X counterpart of SDR defined from map-based genome assembly (XLSX 16 kb)
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Yu, L., Ma, X., Deng, B. et al. Construction of high-density genetic maps defined sex determination region of the Y chromosome in spinach. Mol Genet Genomics 296, 41–53 (2021). https://doi.org/10.1007/s00438-020-01723-4
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DOI: https://doi.org/10.1007/s00438-020-01723-4