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The Cucumber Genome—An Update

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The Cucumber Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

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Abstract

Cucumber, Cucumis sativus L. (2n = 2x = 14), is both an economically and biologically important vegetable crop. Cucumber was the first horticultural crop with a publicly released genome. Draft genomes with varying qualities of four cucumber genotypes (‘9930’, ‘Gy14’, B10, and PI 183967) were developed using Illumina short-read sequencing or 454 technologies. In recent years, high throughput long-read sequencing and new scaffolding technologies have significantly improved assembly quality of genomes. The low cost of sequencing also allows most crops to afford a draft genome. In cucumber, using single molecule, real-time (SMRT), and Illumina sequencing and 10 × Genomics and Hi-C scaffolding methods, new versions of genome assemblies have been developed for both 9930 (v3.0) and B10 (v3.0). In this chapter, I will summarize major improvements and new insights from these new assemblies. I will also review recent progress in cucumber organelle genomes. I will discuss the cucumber genome in the context of comparative analysis with other cucurbits, cucumber genome evolution, domestication, and population genomics perspectives.

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References

  • Adams KL, Qiu YL, Stoutemyer M, Palmer JD (2002) Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc Natl Acad Sci USA 99:9905–9912

    Google Scholar 

  • Alverson AJ, Wei X, Rice DW, Stern DB, Barry K, Palmer JD (2010) Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Mol Biol Evol 27:1436–1448

    Google Scholar 

  • Alverson AJ, Rice DW, Dickinson S, Barry K, Palmer JD (2011) Origins and recombination of the bacterial-sized multi-chromosomal mitochondrial genome of cucumber. Plant Cell 23:2499–2513

    Google Scholar 

  • Arumuganathan K, Earle E (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208

    Google Scholar 

  • Bo KL, Ma Z, Chen JF, Weng Y (2015) Molecular mapping reveals structural rearrangements and quantitative trait loci underlying traits with local adaptation in semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis Qi et Yuan). Theor Appl Genet 128:25–39

    Google Scholar 

  • Burger G, Gray MW, Lang BF (2003) Mitochondrial genomes: anything goes. Trends Genet 19:709–716

    Google Scholar 

  • Castanera R, Ruggieri V, Pujol M, Garcia-Mas J, Casacuberta JM (2020) An improved melon reference genome with Single-Molecule Sequencing uncovers a recent burst of transposable elements with potential impact on genes. Front Plant Sci 10:1815

    Google Scholar 

  • Chung SM, Gordon VS, Staub JE (2007) Sequencing cucumber (Cucumis sativus L.) chloroplast genomes identifies differences between chilling-tolerant and -susceptible cucumber lines. Genome 50:215–225

    Google Scholar 

  • Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM, Hénaff E et al (2012) The genome of melon (Cucumis melo L.). Proc Natl Acad Sci USA 109:11872–11877

    Google Scholar 

  • Ghurye J, Pop M (2019) Modern technologies and algorithms for scaffolding assembled genomes. PLOS Comput Biol 15:e1006994

    Google Scholar 

  • Guo S, Zhang J, Sun H, Salse J, Lucas WJ, Zhang H, Zheng Y, Mao L et al (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45:51–58

    Google Scholar 

  • Guo SG, Zhao SJ, Sun HH, Wang X et al (2019) Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits. Nat Genet 51:1616–1623

    Google Scholar 

  • Havey MJ (1997) Predominant paternal transmission of the cucumber mitochondrial genome. J Heredity 88:232–235

    Google Scholar 

  • Havey MJ, McCreight JD, Rhodes B, Taurick G (1998) Differential transmission of the Cucumis organellar genomes. Theor Appl Genet 97:122–128

    Google Scholar 

  • Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B et al (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41:1275–1281

    Google Scholar 

  • Jain M, Olsen HE, Paten B, Akeson M (2016) The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 17:239

    Google Scholar 

  • Kim JS, Jung JD, Lee JA, Park HW, Oh KH, Jeong WJ, Choi DW, Liu JR, Cho KY (2006) Complete sequence and organization of the cucumber (Cucumis sativus L. cv. Baekmibaekdadagi) chloroplast genome. Plant Cell Rep 25:334–340

    Google Scholar 

  • Kocyan A, Zhang LB, Schaefer H, Renner SS (2007) A multi-locus phylogeny for the Cucurbitaceae and its implications for character evolution and classification. Mol Phylogen Evol 44:553–577

    Google Scholar 

  • Lee S-C, Lee HO, Hj J, Kim I, Lee W-K, Yang T-J, Song K (2017) The complete chloroplast genome sequence with a novel 24-bp deletion of a Korean solid green-type cucumber variety (Cucumis sativus var. sativus). J Mitochondrial DNA Part B 2:755–756

    Google Scholar 

  • Levene MJ, Korlach J, Turner SW et al (2003) Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299:682–686

    Google Scholar 

  • Li Z, Zhang Z, Yan P, Huang S, Fei Z, Lin K (2011) RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics 12:540

    Google Scholar 

  • Li DW, Cuevas H, Yang LM, Li YH, Garcia-Mas J, Zalapa J, Staub JE, Luan FS, Reddy U, He XM, Gong ZH, Weng Y (2011b) Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping. BMC Genomics 2011, 12:396

    Google Scholar 

  • Li Q, Li H, Huang W, Xu Y, Zhou Q, Wang S, Ruan J, Huang S, Zhang Z (2019) A chromosome-scale genome assembly of cucumber (Cucumis sativus L.). GigaScience 8:giz072

    Google Scholar 

  • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293

    Google Scholar 

  • Lim H, Gounaris I, Hardison RC, Boyer CD (1990) Restriction site and genetic map of Cucurbita pepo chloroplast DNA. Curr Genet 18:273–275

    Google Scholar 

  • Lv J, Qi JJ, Shi QX, Shen D, Zhang SP, Shao GJ, Li H, Sun ZY, Weng Y, Shang Y et al. (2012) Genetic diversity and population structure of cucumber (Cucumis sativus L.). PLoS ONE 7:e46919

    Google Scholar 

  • McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, et al. (2014) Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS ONE 9(9): e106689

    Google Scholar 

  • Osipowski P, Pawełkowicz M, Wojcieszek M et al (2020) A high-quality cucumber genome assembly enhances computational comparative genomics. Mol Genet Genomics 295:177–193

    Google Scholar 

  • Palmer J (1982) Physical and gene mapping of chloroplast DNA from Atriplex triangularis and Cucumis sativus. Nucleic Acids Res 10:1593–1605

    Google Scholar 

  • Pan YP, Wang YH, McGregor C, Liu S, Luan FS, Gao ML, Weng Y (2020) Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective. Theor Appl Genet 133:1–21

    Google Scholar 

  • Paris HS, Daunay MC, Janick J (2012) Occidental diffusion of cucumber (Cucumis sativus) 500–1300 CE, two routes to Europe. Ann Bot 109:117–126

    Google Scholar 

  • Perl-Treves R, Galun E (1985) The Cucumis plastome: physical map, intrageneric variation, and phylogenetic relationships. Theor Appl Genet 71:417–429

    Google Scholar 

  • Plader W, YukawaY SM, Malepszy S (2007) The complete structure of the cucumber (Cucumis sativus L.) chloroplast genome: its composition and comparative analysis. Cell Mol Biol Lett 12:584–594

    Google Scholar 

  • Putnam NH, O’Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R et al (2016) Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res 26:342–350

    Google Scholar 

  • Qi JJ, Liu X, Shen D, Miao H, Xie BY, Li XX, Zeng P, Wang SH, Shang Y, Gu XF et al (2013) A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet 45:1510–1515

    Google Scholar 

  • Ruggieri V, Alexiou KG, Morata J, Argyris J, Pujol M, Yano R et al. (2018) An improved assembly and annotation of the melon (Cucumis melo L.) reference genome. Sci Rep 8: 8088

    Google Scholar 

  • Schaefer H, Heibl C, Renner SS (2009) Gourds afloat: a dated phylogeny reveals an Asian origin of the gourd family (Cucurbitaceae) and numerous oversea dispersal events. Proc Royal Soc B 276:843–851

    Google Scholar 

  • Sebastian P, Schaefer H, Telford IR, Renner SS (2010) Phylogenetic relationships among domesticated and wild species of Cucumis (Cucurbitaceae): The sister species of melon is from Australia. Proc Natl Acad Sci USA 107:14269–14273

    Google Scholar 

  • Shen J, Kere MG, Chen JF (2013) Mitochondrial genome is paternally inherited in Cucumis allotetraploid (C. × hytivus) derived by interspecific hybridization. Sci Hortic 155:39–42

    Google Scholar 

  • Shen J, Shou WS, Zhang J, Yuan G, Zhao Y, Chen J, Harvey MJ (2019) Rare maternal and biparental transmission of the cucumber mitochondrial DNA reveals sorting of polymorphisms among progenies. Theor Appl Genet 132:1223–1233

    Google Scholar 

  • Simão PA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212

    Google Scholar 

  • Sloan DB, Alverson AJ, Storchova H, Palmer JD, Taylor DR (2010) Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia. BMC Evol Biol 10:274

    Google Scholar 

  • Wang X, Bao K, Reddy UK, Bai Y, Hammer SA, Jiao C, Wehner TC, Ramirez Madera A, Weng Y, Grumet R, Fei ZJ (2018) The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies and core collection development. Hort Res 5: 64

    Google Scholar 

  • Wang YH, Bo KL, Gu XF, Pan JS, Li YH, Chen JF, Wen CL, Ren ZH, Ren HZ, Chen XH, Grumet G, Weng Y (2019) Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature. Hort Res 7:3

    Google Scholar 

  • Wang Y, Jiang B, Dymerski R, Xu XW, Weng Y (2021) Quantitative trait loci for horticulturally important traits defining the Sikkim cucumber. Cucumis sativus var. sikkimensis. Theor Appl Genet 134:229–247

    Google Scholar 

  • Ward B, Anderson R, Bendich A (1981) The mitochondrial genome is large and variable in a family of plants (Cucurbitaceae). Cell 25:793–803

    Google Scholar 

  • Weng Y, Sun ZY (2011) Chapter 1 Major Cucurbit Crops. In: Genetics, Genomics and Breeding in Crop Plants. Cucurbits. Wang YH, Behera T (eds). Science Publishers Inc. Enfield NH. CRC Press, Boca Raton FL, pp 1–16

    Google Scholar 

  • Weng Y (2016) Chapter 9. The cucumber genome. In (R. Grumet et al. eds.), Genetics and Genomics of Cucurbitaceae, Plant Genetics and Genomics: Crops and Models. https://doi.org/10.1007/7397_2016_6. Springer International Publishing AG 2016. pp 183–198

  • Weng Y (2021) Cucumis sativus: Chromosome Evolution, Domestication, and Genetic Diversity: Implications for Cucumber Breeding. Plant Breed Rev 49:77–111

    Google Scholar 

  • Wóycicki R, Witkowicz J, Gawroński P, Dąbrowska J, Lomsadze A, Pawełkowicz M, et al. (2011) The genome sequence of the North European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PLoS One 2011, 6:e22728

    Google Scholar 

  • Wu S, Shamimuzzaman M, Sun H, Salse J, Sui X, Wilder A, Wu Z, Levi A, Xu Y, Ling KS, Fei Z (2017) The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a papaya ring-spot virus resistance locus. Plant J 92:963–975

    Google Scholar 

  • Yang LM, Koo DH, Li YH, Zhang XJ, Luan FS, Havey MJ, Jiang JM, Weng Y (2012) Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly. Plant J 71:895–906

    Google Scholar 

  • Yang LM, Koo D-H, Li DW, Zhang T, Jiang JM, Luan FS et al (2014) Next-generation sequencing, FISH mapping, and synteny-based modeling reveal mechanisms of dysploid chromosome reduction in Cucumis. Plant J 77:16–30

    Google Scholar 

  • Yang JH, Deng GC, Lian JM, Garraway J, Niu YC, Hu ZY, Yu JQ, Zhang MF (2020) The chromosome-scale genome of melon dissects genetic architecture of important agronomic traits. Science 23:1010422

    Google Scholar 

  • Yano R, Ariizumi T, Nonaka S et al (2020) Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression. Commun Biol 3:432

    Google Scholar 

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Authors and Affiliations

  1. Horticulture Department, USDA-ARS Vegetable Crops Research Unit, University of Wisconsin, Madison, WI, USA

    Yiqun Weng

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  1. Yiqun Weng
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Correspondence to Yiqun Weng .

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Editors and Affiliations

  1. Indian Institute of Vegetable Research, Indian Council of Agricultural Research, Varanasi, Uttar Pradesh, India

    Sudhakar Pandey

  2. USDA-ARS, Horticulture Department, University of Wisconsin, Madison, WI, USA

    Yiqun Weng

  3. Indian Institute of Vegetable Research, Indian Council of Agricultural Research, Varanasi, Uttar Pradesh, India

    Tusar Kanti Behera

  4. The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China

    Kailiang Bo

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Weng, Y. (2022). The Cucumber Genome—An Update. In: Pandey, S., Weng, Y., Behera, T.K., Bo, K. (eds) The Cucumber Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-88647-9_3

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