Skip to main content
SpringerLink
Log in

Diospyros Lotus Genome

  • Chapter
  • First Online:
The Persimmon Genome

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

  • 180 Accesses

Abstract

Crop genomics and genetics have been radically progressed in this past decade, as a whole genome-wide sequencing era. Notwithstanding, it is still hard to exploit the genome sequence information in most of the highly polyploid crops, including hexaploid persimmon (Diospyros kaki). In this chapter, we focus on the genome sequences of a diploid persimmon, D. lotus, which is a close wild relative of D. kaki, and discuss their applications and contribution to evolutionary aspects. The whole-genome sequences of a male D. lotus were drafted recently with one of the next generation sequencing (NGS) technologies, PacBio sequencing, to be defined with 15 pseudomolecules consistent with the basic chromosome numbers of the genus Diospyros. As one of the representative characteristics in plant genomes, the Diospyros genome also underwent at least two genome-wide duplication events. One of the two, named Dd-α, is a lineage-specific duplication that occurred at approx. 60–70 million years ago. This duplication is thought to drive some lineage-specific neofunctionalization in both protein (trans-acting) and expression (cis-regulatory) functions, including an important transition into separated sexualities. Furthermore, the D. lotus genome sequences provided critical insights into sex chromosome evolution. The draft genome sequences have been already widely applied as an alternative reference of the D. kaki genome, in transcriptomic, genomic, and epigenomic analyses. Further exploration in the frontiers of various Diospyros genomes for comparative approaches would expand the possibilities of genomic analysis in persimmon, and shed light on more for the evolution of the genus Diospyros.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Akagi T, Henry IM, Tao R, Comai L (2014) A Y-chromosome–encoded small RNA acts as a sex determinant in persimmons. Science 346(6209):646–650

    Article  CAS  PubMed  Google Scholar 

  • Akagi T, Pilkington SM, Varkonyi-Gasic E, Henry IM et al (2019) Two Y-chromosome-encoded genes determine sex in kiwifruit. Nat Plants 5(8):801–809

    Article  CAS  PubMed  Google Scholar 

  • Akagi T, Shirasawa K, Nagasaki H, Hirakawa H, Tao R, Comai L, Henry IM (2020) The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants. PLoS Genet 16(2):e1008566

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Akagi T, Kajita K, Kibe T, Morimura H, Tsujimoto T, Nishiyama S, Kawai T, Tao, R (2013) Development of molecular markers associated with sexuality in Diospyros lotus L. and their Application in D. kaki Thunb J Jpn Soc Hort Sci, CH-109

    Google Scholar 

  • Akagi T, Henry IM, Ohtani H, Morimoto T, Beppu K, Kataoka I, Tao R (2018) A Y-encoded suppressor of feminization arose via lineage-specific duplication of a cytokinin response regulator in kiwifruit. Plant Cell 30(4):780–795

    Google Scholar 

  • Bachtrog D, Mank JE, Peichel CL, Kirkpatrick M, Otto SP, Ashman TL, Hahn MW, Kitano J, Mayrose I, Ming R, Perrin N, Ross L, Vamosi, Tree of Sex Consortium (2014) Sex determination: why so many ways of doing it?. PLoS Biol 12(7):e1001899

    Google Scholar 

  • Badenes M, Garcés A, Romero C, Romero M, Clavé J, Rovira M, Llácer G (2003) Genetic diversity of introduced and local Spanish persimmon cultivars revealed by RAPD markers. Genet Resour Crop Evol 50(6):579–585

    Article  CAS  Google Scholar 

  • Bergero R, Forrest A, Kamau E, Charlesworth D (2007) Evolutionary strata on the X chromosomes of the dioecious plant Silene latifolia: evidence from new sex-linked genes. Genetics 175(4):1945–1954

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blackburn KB (1923) Sex chromosomes in plants. Nature 112(2819):687–688

    Article  Google Scholar 

  • Charlesworth B, Charlesworth D (1978a) A model for the evolution of dioecy and gynodioecy. Am Nat 112(988):975–997

    Article  Google Scholar 

  • Charlesworth D, Charlesworth B (1978b) Population genetics of partial male-sterility and the evolution of monoecy and dioecy. Heredity 41(2):137–153

    Article  Google Scholar 

  • Collard BC, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 363(1491):557–572

    Article  CAS  PubMed  Google Scholar 

  • Cornille A, Gladieux P, Smulders MJ, Roldan-Ruiz I, Laurens F, Le Cam B, Nersesyan A, Clavel J, Olonova M, Feugey L, Gabrielyan I, Zhang XG, Tenalillon M, Giraud T (2012) New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genet 8(5):e1002703

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dong Y, Ye X, Xiong A, Zhu N, Jiang L, Qu S (2021) The regulatory role of gibberellin related genes DKGA2ox1 and MIR171f_3 in persimmon dwarfism. Plant Sci 310:110958

    Article  CAS  PubMed  Google Scholar 

  • Flagel LE, Wendel JF (2009) Gene duplication and evolutionary novelty in plants. New Phytol 183(3):557–564

    Article  PubMed  Google Scholar 

  • González-Grandío E, Pajoro A, Franco-Zorrilla JM, Tarancón C, Immink RG, Cubas P (2017) Abscisic acid signaling is controlled by a BRANCHED1/HD-ZIP I cascade in Arabidopsis axillary buds. Proc Natl Acad Sci USA 114(2):E245–E254

    Article  PubMed  CAS  Google Scholar 

  • Harkess A, Zhou J, Xu C, Bowers JE et al (2017) The asparagus genome sheds light on the origin and evolution of a young Y chromosome. Nat Commun 8(1):1–10

    Article  CAS  Google Scholar 

  • Huang S, Ding J, Deng D, Tang W et al (2013) Draft genome of the kiwifruit Actinidia chinensis. Nat Commun 4(1):1–9

    Article  Google Scholar 

  • Iorizzo M, Ellison S, Senalik D, Zeng P et al (2016) A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nature Genet 48(6):657–666

    Article  CAS  PubMed  Google Scholar 

  • Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Cassagrande A, Wincker P (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463–467

    Article  CAS  PubMed  Google Scholar 

  • Kanzaki S, Yonemori K, Sugiura A, Sato A, Yamada M (2001) Identification of molecular markers linked to the trait of natural astringency loss of Japanese persimmon (Diospyros kaki) fruit. J Am Soc Hortic Sci 126(1):51–55

    Article  CAS  Google Scholar 

  • Kanzaki S, Akagi T, Masuko T, Kimura M, Yamada M, Sato A, Mitani N, Ustunomiya N, Yonemori K (2010) SCAR markers for practical application of marker-assisted selection in persimmon (Diospyros kaki Thunb.) breeding. J Jpn Soc Hort Sci 79(2):150–155

    Google Scholar 

  • Kihara H, Ono T (1923) Cytological studies on rumex L. II on the relation of chromosome number and sexes in rumex acetosa L. Bot Mag Tokyo 37:147–149

    Article  Google Scholar 

  • Komatsuda T, Pourkheirandish M, He C, Azhaguvel P et al (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci USA 104(4):1424–1429

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin Z, Hong Y, Yin M, Li C, Zhang K, Grierson D (2008) A tomato HD-Zip homeobox protein, LeHB-1, plays an important role in floral organogenesis and ripening. Plant J 55(2):301–310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luo ZR, Yonemori K, Sugiura A (1995) Evaluation of RAPD analysis for cultivar identification of persimmons. J Jpn Soc Hort Sci 64(3):535–541

    Article  CAS  Google Scholar 

  • Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290(5494):1151–1155

    Article  CAS  PubMed  Google Scholar 

  • Maeda H, Akagi T, Onoue N, Kono A, Tao R (2019) Evolution of lineage-specific gene netorks underlying the considerable fruit shape diversity in persimmon. Plant Cell Physiol 60(11):2464–2477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Masuda K, Akagi T, Esumi T, Tao R (2020a) Epigenetic flexibility underlies somaclonal sex conversions in hexaploid persimmon. Plant Cell Physiol 61(2):393–402

    Article  CAS  PubMed  Google Scholar 

  • Masuda K, Fujita N, Yang HW, Ushijima K, Kubo Y, Tao R, Akagi T (2020b) Molecular mechanism underlying derepressed male production in hexaploid persimmon. Front Plant Sci 11:567249

    Article  PubMed  PubMed Central  Google Scholar 

  • Masuda K, Yamamoto E, Shirasawa K, Onoue N, Kono A, Ushijima K, Kubo Y, Tao R, Henry IM, Akagi T (2020c) Genome-wide study on the polysomic genetic factors conferring plasticity of flower sexuality in hexaploid persimmon. DNA Res 27(3):dsaa012

    Google Scholar 

  • Ming R, Bendahmane A, Renner SS (2011) Sex chromosomes in land plants. Annu Rev Plant Biol 62:485–514

    Article  CAS  PubMed  Google Scholar 

  • Müller NA, Kersten B, Leite Montalvão AP, Mähler N, Bernhardsson C, Bräutigam K, Lorenzo ZC, Hoenicka H, Kumar V, Mader M, Pakull B, Robinson KM, Sabatti M, Vettori C, Ingvarsson PK, Cronk Q, Street NR, Fladung M (2020) A single gene underlies the dynamic evolution of poplar sex determination. Nature Plants 6(6):630–637

    Google Scholar 

  • Nishiyama S, Onoue N, Kono A, Sato A, Yonemori K, Tao R (2018) Characterization of a gene regulatory network underlying astringency loss in persimmon fruit. Planta 247(3):733–743

    Article  CAS  PubMed  Google Scholar 

  • Numaguchi K, Akagi T, Kitamura Y, Ishikawa R, Ishii T (2020) Interspecific introgression and natural selection in the evolution of Japanese apricot (Prunus mume). Plant J 104(6):1551–1567

    Article  CAS  PubMed  Google Scholar 

  • Parfitt DE, Yonemori K, Honsho C, Nozaka M, Kanzaki S, Sato A, Yamada M (2015) Relationships among Asian persimmon cultivars, astringent and non-astringent types. Tree Genet Genomes 11(2):24

    Article  Google Scholar 

  • Renner SS, Müller NA (2021) Plant sex chromosomes defy evolutionary models of expanding recombination suppression and genetic degeneration. Nat Plants 7(4):392–402

    Article  PubMed  Google Scholar 

  • Reyes-Chin-Wo S, Wang Z, Yang X, Kozik A et al (2017) Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat Commun 8(1):1–11

    Article  CAS  Google Scholar 

  • Ribaut JM, Hoisington D (1998) Marker-assisted selection: new tools and strategies. Trends Plant Sci 3(6):236–239

    Article  Google Scholar 

  • Roulin A, Auer PL, Libault M, Schlueter J, Farmer A, May G, Stacey G, Doerge RW, Jackson SA (2013) The fate of duplicated genes in a polyploid plant genome. Plant J 73(1):143–153

    Article  CAS  PubMed  Google Scholar 

  • Sakuma S, Pourkheirandish M, Hensel G, Kumlehn J, Stein N, Tagiri A, Yamaji N, Ma JF, Sassa H, Koda T, Komatsuda T (2013) Divergence of expression pattern contributed to neofunctionalization of duplicated HD-Z ip I transcription factor in barley. New Phytol 197(3):939–948

    Google Scholar 

  • Shi T, Huang H, Barker MS (2010) Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales. Ann Bot 106(3):497–504

    Article  PubMed  PubMed Central  Google Scholar 

  • Shulaev V, Sargent DJ, Crowhurst RN et al (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43(2):109–116

    Article  CAS  PubMed  Google Scholar 

  • Suo Y, Sun P, Cheng H, Han W, Diao S, Li H, Mai Y, Zhao X, Fu J (2020) A high-quality chromosomal genome assembly of Diospyros oleifera Cheng. GigaScience 9(1):giz164

    Google Scholar 

  • Tamura M, Tao R, Yonemori K, Utsunomiya N, Sugiura A (1998) Ploidy level and genome size of several Diospyros species. J Jpn Soc Hort Sci 67(3):306–312

    Article  CAS  Google Scholar 

  • Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485(7400):635

    Article  CAS  Google Scholar 

  • Unver T, Wu Z, Sterck L, Turktas M et al (2017) Genome of wild olive and the evolution of oil biosynthesis. Proc Natl Acad Sci USA 114(44):E9413–E9422

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van de Peer Y, Mizrachi E, Marchal K (2017) The evolutionary significance of polyploidy. Nat Rev Genet 18(7):411–424

    Google Scholar 

  • Vanneste K, Baele G, Maere S, Van de Peer Y (2014) Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. Genome Res 24(8):1334–1347

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Varkonyi-Gasic E, Wang T, Voogd C, Jeon S, Drummond RS, Gleave AP, Allan AC (2019) Mutagenesis of kiwifruit CENTRORADIALIS-like genes transforms a climbing woody perennial with long juvenility and axillary flowering into a compact plant with rapid terminal flowering. Plant Biotechnol J 17(5):869–880

    Article  CAS  PubMed  Google Scholar 

  • Varkonyi‐Gasic E, Wang T, Cooney J, Jeon S, Voogd C, Douglas MJ, Pilkington SM, Akagi T, Allan AC (2021) Shy Girl, a kiwifruit suppressor of feminization, restricts gynoecium development via regulation of cytokinin metabolism and signalling. New Phytol 230(4):1461–1475

    Google Scholar 

  • Wang Y, Chen F, Ma Y, Zhang T, Sun P, Lan M, Li F, Fang W (2021) An ancient whole-genome duplication event and its contribution to flavor compounds in the tea plant (Camellia sinensis). Hortic Res 8(1):1–12

    Article  CAS  Google Scholar 

  • Whipple CJ, Kebrom TH, Weber AL, Yang F, Hall D, Meeley R, Schmidt R, Doebley J, Brutnell TP, Jackson DP (2011) grassy tillers1 promotes apical dominance in maize and responds to shade signals in the grasses. Proc Natl Acad Sci USA 108(33):E506–E512

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Winge O (1923) On sex chromosomes, sex determination and preponderance of female in some dioecious plants. Comp Rend Trav Lab Carlsberg 15(5):1–25

    Google Scholar 

  • Wu S, Lau KH, Cao Q et al (2018) Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nat Commun 9(1):1–12

    Article  CAS  Google Scholar 

  • Yonemori K, Honsho C, Kanzaki S, Ino H, Ikegami A, Kitajima A, Sugiura A, Parfitt DE (2008) Sequence analyses of the ITS regions and the mat K gene for determining phylogenetic relationships of Diospyros kaki (persimmon) with other wild Diospyros (Ebenaceae) species. Tree Genet Genomes 4(2):149–158

    Article  Google Scholar 

  • Zhu QG, Xu Y, Yang Y, Guan CF, Zhang QY, Huang JW, Grierson D, Chen KS, Gong BC, Yin XR (2019) The persimmon (Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolution. Hortic Res 6(1):1–15

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank Dr. Deborah Charlesworth for the extensive discussions on the interpretation of D. lotus genome evolution, especially on the parts involving sex determination, and the many thoughtful pieces of advice provided through this work.

Author information

Authors and Affiliations

  1. Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan

    Takashi Akagi

  2. Japan Science and Technology Agency (JST), PRESTO, Kawaguchi-shi, Saitama, 332-0012, Japan

    Takashi Akagi

Authors
  1. Takashi Akagi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Takashi Akagi .

Editor information

Editors and Affiliations

  1. Graduate School of Agriculture, Kyoto University, Kyoto, Japan

    Ryutaro Tao

  2. Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China

    Zhengrong Luo

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Akagi, T. (2022). Diospyros Lotus Genome. In: Tao, R., Luo, Z. (eds) The Persimmon Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-031-05584-3_5

Download citation

Publish with us

Policies and ethics

Search

Navigation