Sequencing and Assembly of the Pineapple Genome

  • Jishan Lin
  • Ray MingEmail author
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 22)


Pineapple (Ananas comosus L.) is an important tropical fruit crop, not only because of its economic value but also due to its CAM photosynthesis that exhibits the highest water-use efficiency comparing to plants with C3 and C4 photosynthesis. The genome of pineapple variety F153 was sequenced using a combination of DNA sequencing technologies, including Illumina, Moleculo, 454, and PacBio single-molecule long reads. Pooled bacterial artificial chromosome (BAC) sequences were used to assist the genome assembly, and the final assembly reached 382 Mb, 72.6% of the estimated 526 Mb. An ultrahigh-density genetic map with 25 linkage groups was used to correct chimeric scaffolds and anchored 564 scaffolds, covering 316 Mb, or 82.7%, of the assembled genome. The pineapple genome was annotated by MAKER and 27,024 genes, and 10,151 alternative splicing events were identified. Transposable elements (TEs) accounted for 44% of the assembly. The 27.4% unassembled sequences are all highly repetitive centromere, telomere, and rDNA clusters (2.4%) and TEs (25%), indicating that TEs accounted for 69% of the pineapple genome. LTR retrotransposons were the most abundant of TEs, representing 33% of the assembly. Intragenomic syntenic analysis of pineapple genome traced karyotype evolution from seven monocot ancestral chromosomes to current 25 chromosomes, and two ancient whole-genome duplication (WGD) events (σ and τ) in pineapple genome were detected, but not the more recent ρ WGD. Candidate genes involved in the carbon fixation module of CAM were identified in the pineapple genome, and nine genes were found to have a diurnal expression pattern in the green leaf tissue. CAM-related genes were enriched with circadian clock cis-regulatory elements. The pineapple genome will accelerate the progress relevant to fundamental biology and/or pineapple production, including drought tolerance.


Ananas comosus Cis-element Genome sequencing Karyotype Whole-genome duplication 



We thank Duane Bartholomew for providing the historic information of Smooth Cayenne clone Champaka F153.


  1. Borland AM, Hartwell J, Weston DJ, Schlauch KA, Tschaplinski TJ, Tuskan GA, Yang X, Cushman JC (2014) Engineering crassulacean acid metabolism to improve water-use efficiency. Trends Plant Sci 19:327–338CrossRefGoogle Scholar
  2. Brewbaker JL, Gorrez DD (1967) Genetics of self-incompatibility in the monocot genera, Ananas (pineapple) and Gasteria. Am J Bot 54(5):611–616CrossRefGoogle Scholar
  3. Butcher D, Gouda E (2014) Most Ananas are cultivars. Newsletter Pineapple Working Group Int Soc Hortic Sci 21:9–11Google Scholar
  4. Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Yandell M et al (2008) MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res 18(1):188–196CrossRefGoogle Scholar
  5. Carlier JD, Nancheva D, Leitao JM, Coppens D’Eeckenbrugge G (2006) Genetic mapping of DNA markers in pineapple. Acta Hortic 702(702):79–86CrossRefGoogle Scholar
  6. Carlier JD, Reis A, Duval MF, Coppens dG, Leitao JM (2004) Genetic maps of rapd, aflp and issr markers in Ananas bracteatus and A. comosus using the pseudo-testcross strategy. Plant Breed 123(2):186–192CrossRefGoogle Scholar
  7. Carlier JD, Sousa NH, Santo TE, D’Eeckenbrugge GC, Leitão JM (2012) A genetic map of pineapple (Ananas comosus (L.) Merr.) including scar, caps, ssr and est-ssr markers. Mol Breeding 29(1):245–260CrossRefGoogle Scholar
  8. Givnish TJ, Barfuss MH, Van Ee B, Riina R, Schulte K, Horres R, Gonsiska PA, Jabaily RS, Crayn DM, Smith JA, Winter K, Brown GK, Evans TM, Holst BK, Luther H, Till W, Zizka G, Berry PE, Sytsma KJ (2014) Adaptive radiation, correlated and contingent evolution, and net species diversification in Bromeliaceae. Mol Phylogenet Evol 71(2):55–78CrossRefGoogle Scholar
  9. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644CrossRefGoogle Scholar
  10. Luo R (2012) Soapdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1(1):1–6CrossRefGoogle Scholar
  11. Magallón S, Gómez-Acevedo S, Sánchez-Reyes LL, Hernández-Hernández T (2015) A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. New Phytol 207(2):437CrossRefGoogle Scholar
  12. Michael TP, Mockler TC, Breton G, Mcentee C, Byer A, Trout JD et al (2008) Network discovery pipeline elucidates conserved time-of-day–specific cis-regulatory modules. PLoS Genet 4(2):e14CrossRefGoogle Scholar
  13. Ming R, Vanburen R, Wai CM, Tang H, Schatz MC, Bowers JE et al (2015) The pineapple genome and the evolution of cam photosynthesis. Nat Genet 47(12):1435–1442CrossRefGoogle Scholar
  14. Morrison SE (1963) Journals and other documents of the life and voyages of Christopher Columbus. Heritage Press, New YorkGoogle Scholar
  15. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ et al (2000) A whole-genome assembly of Drosophila. Science 287(5461):2196–2204CrossRefGoogle Scholar
  16. Newcomb RD, Crowhurst RN, Gleave AP, Rikkerink EHA, Allan AC, Beuning LL et al (2006) Analyses of expressed sequence tags from apple. Plant Physiol 141(1):147–166CrossRefGoogle Scholar
  17. Osmond CB (2003) Crassulacean acid metabolism: a curiosity in context. Annu Rev Plant Biol 29(1):379–414CrossRefGoogle Scholar
  18. Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A 101(26):9903CrossRefGoogle Scholar
  19. Schmid KJ, Sorensen TR, Stracke R, Torjek O, Altmann T, Mitchellolds T et al (2003) Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res 13(6A):1250–1257CrossRefGoogle Scholar
  20. Sousa ND, Carlier J, Santo T, Leitão J (2013) An integrated genetic map of pineapple (Ananas comosus, (L.) Merr.). Sci Hortic-Amsterdam 157(3):113–118CrossRefGoogle Scholar
  21. Tang H, Soltis DE (2010) Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci U S A 107(1):472–477CrossRefGoogle Scholar
  22. Wang W, Haberer G, Gundlach H, Glässer C, Nussbaumer T, Luo MC et al (2014) The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat Commun 5:3311CrossRefGoogle Scholar
  23. Woodhouse MR, Tang H, Freeling M (2011) Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids. Plant Cell 23(12):4241–4253CrossRefGoogle Scholar
  24. Yang X, Cushman JC, Borland AM, Edwards EJ, Wullschleger SD, Tuskan GA et al (2015) A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world. New Phytol 207(3):491–504CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
  2. 2.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA

Personalised recommendations