Current Status of Octoploid Strawberry (Fragaria × ananassa) Genome Study

  • Sachiko N. IsobeEmail author
  • Kenta Shirasawa
  • Soichiro Nagano
  • Hideki Hirakawa
Part of the Compendium of Plant Genomes book series (CPG)


The complex structure of the polyploid genome has inhibited advances in genomics and genetic analysis in polyploid species. Octoploid strawberry (Fragaria × ananassa) is allopolyploidy species (2n = 8x  = 56) with an estimated genome size of 1C = 708–720 Mb. The recent study reported by Tennessen et al. (2014) suggested that the genome of F. × ananassa consisted of each one pair of F. vesca-like and Fragaria iinumae-like genomes and two other pairs of subgenomes. Therefore, while the genome sequences of F. vesca have played an important role, the whole genome sequences of F. × ananassa are also essential for a more detailed and thorough understanding in studies about F. × ananassa. The construction of high-quality subgenome-specific reference sequences in F. × ananassa has been a long-dreamt goal, due to its potential for analyzing the expression of previously unexplored genes, such as in the evolution in Fragaria species, and for accelerating molecular breeding. In this chapter, we review the recent results of large-scale genome and transcriptome analyses related to genome sequence dissection in F. × ananassa.


  1. Aguiar D, Istrail S (2013) Haplotype assembly in polyploid genomes and identical by descent shared tracts. Bioinformatics 29(13):352–360CrossRefGoogle Scholar
  2. Akiyama Y, Yamamoto Y, Ohmido N et al (2001) Estimation of the nuclear DNA content of strawberries (Fragaria spp.) compared with Arabidopsis thaliana by using dual system flow cytometry. Cytologia 66:431–436CrossRefGoogle Scholar
  3. Amil-Ruiz F, Garrido-Gala J, Blanco-Portales R et al (2013) Kevin M. Folta, Juan Muñoz-Blanco, José L. Caballero Identification and validation of reference genes for transcript normalization in strawberry (Fragaria × ananassa) defense responses. PLoS ONE 8(8):e70603CrossRefPubMedPubMedCentralGoogle Scholar
  4. Bassil NV, Davis TM, Zhang H et al (2015) Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa. BMC Genom 16:155CrossRefGoogle Scholar
  5. Bertioli DJ, Cannon SB, Froenicke L et al (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 48:438–446CrossRefPubMedGoogle Scholar
  6. Bringhurst RS (1990) Cytogenetics and evolution in american Fragaria. Hort Sci 106:679–683Google Scholar
  7. Chalhoub B, Denoeud F, Wincker P et al (2014) Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345(6199):950–953CrossRefPubMedPubMedCentralGoogle Scholar
  8. Chambers AH, Pillet J, Plotto A et al (2014) Identification of a strawberry flavor gene candidate using an integrated genetic-genomic-analytical chemistry approach. BMC Genom 15:217CrossRefGoogle Scholar
  9. Chen J, Mao L, Lu W et al (2016) Transcriptome profiling of postharvest strawberry fruit in response to exogenous auxin and abscisic acid. Planta 243(1):183–197CrossRefPubMedGoogle Scholar
  10. Darwish O, Shahan R, Liu Z et al (2015) Re-annotation of the woodland strawberry (Fragaria vesca) genome. BMC Genom 16:29CrossRefGoogle Scholar
  11. Davik J, Sargent DJ, Brurberg MB (2015) A ddRAD based linkage map of the cultivated strawberry, Fragaria xananassa. PLoS One 10(9):e0137746CrossRefPubMedPubMedCentralGoogle Scholar
  12. Davis TM, Denoyes-Rothan B, Lerceteau-Köhler E (2007) Strawberry. In: Kole C (ed) Genome mapping and molecular breeding inplants, vol 4. Fruit and Nuts. Springer, Berlin, pp 189–205Google Scholar
  13. D’Hont A, Denoeud F, Aury JM et al (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488:213–217CrossRefPubMedGoogle Scholar
  14. Federova NJ (1946) Crossability and phylogenetic relations in the main European species of Fragaria. Compte-rendu de l’académie des Sciences de l’URSS 52:545–547Google Scholar
  15. Glover NM, Redestig H, Dessimoz C (2016) Homoeologs: what are they and how do we infer them? Trends Plant Sci 21(7):609–621CrossRefPubMedPubMedCentralGoogle Scholar
  16. Govindarajulu R, Parks M, Tennessen JA et al (2015) Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species. Am J Bot. Scholar
  17. Han J, Li A, Liu H et al (2014) Computational identification of microRNAs in the strawberry (Fragaria x ananassa) genome sequence and validation of their precise sequences by miR-RACE. Gene 536(1):151–162CrossRefPubMedGoogle Scholar
  18. Hirakawa H, Shirasawa K, Isobe SN et al (2014) Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. DNA Res 21(2):169–181CrossRefPubMedGoogle Scholar
  19. Honjo M, Kataoka S, Yui S et al (2009) Maternal lineages of the cultivated strawberry, Fragaria × ananassa, revealed by chloroplast DNA variation. HortScience 44(6):1562–1565Google Scholar
  20. Isobe SN, Hirakawa H, Sato S et al (2013) Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability. DNA Res 20(1):79–92CrossRefPubMedGoogle Scholar
  21. Kunihisa M (2011) Studies using DNA markers in F. × ananassa: genetic analysis, genome structure, and cultivar identification. J Jpn Soc Hort Sci 80:231–243CrossRefGoogle Scholar
  22. Li F, Fan G, Lu C et al (2015) Genome sequence of cultivated upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol 33:524–530CrossRefPubMedGoogle Scholar
  23. Ling HQ, Zhao S, Liu D et al (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496:87–90CrossRefPubMedGoogle Scholar
  24. Ma Y, Sun H, Zhao G et al (2008) Isolation and characterization of genomic retrotransposon sequences from octoploid strawberry (Fragaria × ananassa Duch.). Plant Cell Rep 27:499CrossRefPubMedGoogle Scholar
  25. Ma Y, He P, Sun H et al (2010) Isolation and characterization of transcriptionally active Ty1-copia retrotransposons in Fragaria × ananassa. Agric sci China 9(3):337–345CrossRefGoogle Scholar
  26. Mahoney LL, Quimby ML, Shields ME, Davis TM (2010) Mitochondrial DNA transmission, ancestry, and sequencing in Fragaria. Acta Hort 859:301–308CrossRefGoogle Scholar
  27. Michael TP, VanBuren R (2015) Progress, challenges and the future of crop genomes. Curr Opin Plant Biol 24:71–81CrossRefPubMedGoogle Scholar
  28. Monden Y, Fujii N, Yamaguchi K et al (2014) Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site. Genome 57(5):245–252CrossRefPubMedGoogle Scholar
  29. Njuguna W, Liston A, Cronn R et al (2013) Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing. Mol Phylogenet Evol 66(1):17–29CrossRefPubMedGoogle Scholar
  30. Pillet J, Yu HW, Chambers AH et al (2015) Identification of candidate flavonoid pathway genes using transcriptome correlation network analysis in ripe strawberry (Fragaria × ananassa) fruits. J Exp Bot 66(15):4455–4467CrossRefPubMedPubMedCentralGoogle Scholar
  31. Sánchez-Sevilla JF, Cruz-Rus E, Valpuesta V et al (2014) Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses. BMC Genom 15:218CrossRefGoogle Scholar
  32. Sánchez-Sevilla JF, Horvath A, Botella MA et al (2015) Diversity arrays technology (DArT) marker platforms for diversity analysis and linkage mapping in a complex crop, the octoploid cultivated strawberry (Fragaria × ananassa). PLoS ONE 10(12):e0144960CrossRefPubMedPubMedCentralGoogle Scholar
  33. Sargent DJ, Yang Y, Šurbanovski N (2016) HaploSNP affinities and linkage map positions illuminate subgenome composition in the octoploid, cultivated strawberry (Fragaria × ananassa). Plant Sci 242:140–150CrossRefPubMedGoogle Scholar
  34. Senanayake YDA, Bringhurst RS (1967) Origin of Fragaria polyploids. I. Cytological analysis. Am J Bot 54:221–228CrossRefGoogle Scholar
  35. Shirasawa K, Nagano S, Hirakawa H et al (2017) De novo whole genome assembly in allo-octoploid strawberry. In: Abstracts of international plant & animal genome XXV. San Diego, 14–18 Jan 2017Google Scholar
  36. Shulaev V, Sargent DJ, Crowhurst RN et al (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43:109–116CrossRefPubMedGoogle Scholar
  37. Song L, Shankar DS, Florea L (2016) Rascaf: improving genome assembly with RNA sequencing data. Plant Genome. Scholar
  38. Tennessen JA, Govindarajulu R, Ashman TL, Liston A (2014) Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps. Genome Biol Evol 6(12):3295–3313CrossRefPubMedPubMedCentralGoogle Scholar
  39. Tewhey R, Bansal V, Torkamani A (2011) The importance of phase information for human genomics. Nat Rev Genet 12:215–223CrossRefPubMedPubMedCentralGoogle Scholar
  40. The International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345(6194):1251788CrossRefGoogle Scholar
  41. Wang K, Wang Z, Li F et al (2012) The draft genome of a diploid cotton Gossypium raimondii. Nat Genet 44:1098–1103CrossRefPubMedPubMedCentralGoogle Scholar
  42. Wang T, Liu L, Ning C (2016) Alterations of DNA methylation and gene expression during hybridization and polyploidization in Fragaria spp. Sci Hortic 201:218–224CrossRefGoogle Scholar
  43. Xu X, Yin L, Ying Q et al (2013) High-throughput sequencing and degradome analysis identify miRNAs and their targets involved in fruit senescence of Fragaria ananassa. PLoS ONE 8(8):e70959CrossRefPubMedPubMedCentralGoogle Scholar
  44. Yanagi T, Noguchi Y (2016) Strawberry (Plants in the genus Fragaria) In: Mason AS (ed) Polyploidy and hybridization for crop improvement. CRC press, FL, US, pp 115–151Google Scholar
  45. Yang J, Liu D, Wang X et al (2016) The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nat Genet 48:1225–1232CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Sachiko N. Isobe
    • 1
    Email author
  • Kenta Shirasawa
    • 1
  • Soichiro Nagano
    • 1
  • Hideki Hirakawa
    • 1
  1. 1.Kazusa DNA Research InstituteKisarazuJapan

Personalised recommendations