Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data

  • Dan BolserEmail author
  • Daniel M. Staines
  • Emily Pritchard
  • Paul Kersey
Part of the Methods in Molecular Biology book series (MIMB, volume 1374)


Ensembl Plants ( is an integrative resource presenting genome-scale information for a growing number of sequenced plant species (currently 33). Data provided includes genome sequence, gene models, functional annotation, and polymorphic loci. Various additional information are provided for variation data, including population structure, individual genotypes, linkage, and phenotype data. In each release, comparative analyses are performed on whole genome and protein sequences, and genome alignments and gene trees are made available that show the implied evolutionary history of each gene family. Access to the data is provided through a genome browser incorporating many specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These access routes are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests, and pollinators.

Ensembl Plants is updated 4–5 times a year and is developed in collaboration with our international partners in the Gramene ( and transPLANT projects (

Key words

Databases Genomebrowser Genomics Transcriptomics Functional genomics Comparative genomics Geneticvariation Phenotype Crops Cereals 



“The transPLANT project is funded by the European Commission within its 7th Framework Programme, under the thematic area “Infrastructures”, contract number 283496”.


  1. 1.
    Ribaut JM, Hoisington D (1998) Marker-assisted selection: new tools and strategies. Trends Plant Sci 3(6):236–239CrossRefGoogle Scholar
  2. 2.
    Goddard ME, Hayes BJ (2007) Genomic selection. J Anim Breed Genet 124(6):323–330CrossRefPubMedGoogle Scholar
  3. 3.
    Rafalski JA (2010) Association genetics in crop improvement. Curr Opin Plant Biol 13(2):174–180CrossRefPubMedGoogle Scholar
  4. 4.
    Kleinhofs A, Behki R (1977) Prospects for plant genome modification by nonconventional methods. Annu Rev Genet 11(1):79–101CrossRefPubMedGoogle Scholar
  5. 5.
    Hartung F, Schiemann J (2014) Precise plant breeding using new genome editing techniques: opportunities, safety and regulation in the EU. Plant J 78(5):742–752CrossRefPubMedGoogle Scholar
  6. 6.
  7. 7.
  8. 8.
    Kersey PJ, Allen JE, Christensen M et al (2014) Ensembl genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res 42(D1):D546–D552PubMedCentralCrossRefPubMedGoogle Scholar
  9. 9.
    Monaco MK, Stein J, Naithani S et al (2014) Gramene 2013: comparative plant genomics resources. Nucleic Acids Res 42(D1):D1193–D1199PubMedCentralCrossRefPubMedGoogle Scholar
  10. 10.
    Kasprzyk A (2011) BioMart: driving a paradigm change in biological data management. Database 2011:bar049PubMedCentralCrossRefPubMedGoogle Scholar
  11. 11.
    Jones P, Binns D, Chang H-Y et al (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30(9):1236–1240PubMedCentralCrossRefPubMedGoogle Scholar
  12. 12.
    McLaren W, Pritchard B, Rios D et al (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP effect predictor. Bioinformatics 26(16):2069–2070PubMedCentralCrossRefPubMedGoogle Scholar
  13. 13.
    Harris RS (2007) Improved pairwise alignment of genomic DNA. ProQuest, Ann Arbor, p 84Google Scholar
  14. 14.
    Schwartz S, James Kent W, Smit A et al (2003) Human–mouse alignments with BLASTZ. Genome Res 13(1):103–107PubMedCentralCrossRefPubMedGoogle Scholar
  15. 15.
    Kent WJ (2002) BLAT—the BLAST-like alignment tool. Genome Res 12(4):656–664PubMedCentralCrossRefPubMedGoogle Scholar
  16. 16.
    Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D (2003) Evolution’s cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci 100(20):11484–11489PubMedCentralCrossRefPubMedGoogle Scholar
  17. 17.
    Vilella AJ, Severin J, Ureta-Vidal A et al (2009) EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 19(2):327–335PubMedCentralCrossRefPubMedGoogle Scholar
  18. 18.
    Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25(1):25–29PubMedCentralCrossRefPubMedGoogle Scholar
  19. 19.
    Cooper L, Ramona L, Walls JE et al (2013) The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol 54(2):e1PubMedCentralCrossRefPubMedGoogle Scholar
  20. 20.
    Burge S, Kelly E, Lonsdale D et al (2012) Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database 2012:bar068PubMedCentralPubMedGoogle Scholar
  21. 21.
    Eilbeck K, Lewis SE, Mungall CJ et al (2005) The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol 6(5):R44PubMedCentralCrossRefPubMedGoogle Scholar
  22. 22.
    Chamala S, Chanderbali AS, Der JP et al (2013) Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science 342(6165):1516–1517CrossRefPubMedGoogle Scholar
  23. 23.
    Hu TT, Pattyn P, Bakker EG et al (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet 43(5):476–481PubMedCentralCrossRefPubMedGoogle Scholar
  24. 24.
    Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408(6814):796CrossRefGoogle Scholar
  25. 25.
    D’Hont A, Denoeud F, Aury JM et al (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410):213–217CrossRefPubMedGoogle Scholar
  26. 26.
    International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491(7426):711–716Google Scholar
  27. 27.
    International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463(7282):763–768CrossRefGoogle Scholar
  28. 28.
    Brassica rapa Genome Sequencing Project Consortium (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43(10):1035–1039CrossRefGoogle Scholar
  29. 29.
    Merchant SS, Prochnik SE, Vallon O et al (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318(5848):245–250PubMedCentralCrossRefPubMedGoogle Scholar
  30. 30.
    Matsuzaki M, Misumi O, Shin-I T et al (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428(6983):653–657CrossRefPubMedGoogle Scholar
  31. 31.
    Consortium for Grapevine Genome Characterization, (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463–467CrossRefGoogle Scholar
  32. 32.
    Schnable PS, Ware D, Fulton RS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956):1112–1115CrossRefPubMedGoogle Scholar
  33. 33.
    Young ND, Debellé F, Oldroyd GE et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480(7378):520–524PubMedCentralPubMedGoogle Scholar
  34. 34.
    Bennetzen JL, Schmutz J, Wang H et al (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30(6):555–561CrossRefPubMedGoogle Scholar
  35. 35.
    Rensing SA, Lang D, Zimmer AD et al (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319(5859):64–69CrossRefPubMedGoogle Scholar
  36. 36.
    Tuskan GA, Difazio S, Jansson S et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793):1596–1604CrossRefPubMedGoogle Scholar
  37. 37.
    Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475(7355):189–195CrossRefGoogle Scholar
  38. 38.
    International Peach Genome Initiative (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45(5):487–494Google Scholar
  39. 39.
    Chen J, Huang Q, Gao D et al (2013) Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat Commun 4:1595PubMedCentralCrossRefPubMedGoogle Scholar
  40. 40.
  41. 41.
    Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296(5565):79–92CrossRefPubMedGoogle Scholar
  42. 42.
    International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436(7052):793–800CrossRefGoogle Scholar
  43. 43.
    Banks JA, Nishiyama T, Hasebe M et al (2011) The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332(6032):960–963PubMedCentralCrossRefPubMedGoogle Scholar
  44. 44.
    Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229):551–556CrossRefPubMedGoogle Scholar
  45. 45.
    Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463(7278):178–183CrossRefPubMedGoogle Scholar
  46. 46.
    Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485(7400):635–641CrossRefGoogle Scholar
  47. 47.
    Jia J, Zhao S, Kong X et al (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496(7443):91–95CrossRefPubMedGoogle Scholar
  48. 48.
  49. 49.
    Ling HQ, Zhao S, Liu D et al (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496(7443):87–90CrossRefPubMedGoogle Scholar
  50. 50.
    Clark RM, Schweikert G, Toomajian C et al (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317(5836):338–342CrossRefPubMedGoogle Scholar
  51. 51.
    Atwell S, Huang YS, Vilhjálmsson BJ et al (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465(7298):627–631PubMedCentralCrossRefPubMedGoogle Scholar
  52. 52.
    Fox SE, Preece J, Kimbrel JA et al (2013) Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae). Appl Plant Sci 1(3)Google Scholar
  53. 53.
    Yu J, Wang J, Lin W et al (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3(2), e38PubMedCentralCrossRefPubMedGoogle Scholar
  54. 54.
    Zhao K, Wright M, Kimball J et al (2010) Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One 5(5):e10780PubMedCentralCrossRefPubMedGoogle Scholar
  55. 55.
    McNally KL, Childs KL, Bohnert R et al (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci 106(30):12273–12278PubMedCentralCrossRefPubMedGoogle Scholar
  56. 56.
    Morris GP, Ramu P, Deshpande SP et al (2013) Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci 110(2):453–458PubMedCentralCrossRefPubMedGoogle Scholar
  57. 57.
    Myles S, Chia J-M, Hurwitz B et al (2010) Rapid genomic characterization of the genus vitis. PLoS One 5(1), e8219PubMedCentralCrossRefPubMedGoogle Scholar
  58. 58.
    Chia JM, Song C, Bradbury PJ et al (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 44(7):803–807CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Dan Bolser
    • 1
    Email author
  • Daniel M. Staines
    • 1
  • Emily Pritchard
    • 1
  • Paul Kersey
    • 1
  1. 1.European Molecular Biology LaboratoryEuropean Bioinformatics InstituteHinxton, CambridgeUK

Personalised recommendations