Abstract
Gramene is an integrated informatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for economically important and research model crops, including wheat, potato, tomato, banana, grape, poplar, and Chlamydomonas. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) view a phylogenetic tree for a family of transcription factors, (2) explore genetic variation in the orthologues of a gene with a known trait association, and (3) upload, visualize, and privately share end user data into a new genome browser track.
Moreover, this is the first publication describing Gramene’s new web interface—intended to provide a simplified portal to the most complete and up-to-date set of plant genome and pathway annotations.
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References
Jia J, Zhao S, Kong X et al (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496(7443):91–95
Amborella Genome Project (2013) The Amborella genome and the evolution of flowering plants. Science 342(6165):1241089
Chamala S, Chanderbali AS, Der JP et al (2013) Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science 342(6165):1516–1517
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):476–481
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408(6814):796–815
The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463(7282):763–768
Wang X, Wang H, Wang J et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43(10):1035–1039
Merchant SS, Prochnik SE, Vallon O et al (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318(5848):245–250
Matsuzaki M, Misumi O, Shin IT et al (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428(6983):653–657
Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463(7278):178–183
International Barley Genome Sequencing Consortium, Mayer KF, Waugh R et al (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491(7426):711–716
Young ND, Debelle F, Oldroyd GE et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480(7378):520–524
D’Hont A, Denoeud F, Aury JM et al (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410):213–217
Chen J, Huang Q, Gao D et al (2013) Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat Commun 4:1595
Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296(5565):79–92
Zhao W, Wang J, He X et al (2004) BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res 32(Database issue):D377–D382
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436(7052):793–800
Kawahara Y, de la Bastide M, Hamilton JP et al (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) 6(1):4
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):64–69
Tuskan GA, Difazio S, Jansson S et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793):1596–1604
The International Peach Genome Initiative, Verde I, Abbott AG et al (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45(5):487–494
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):960–963
Bennetzen JL, Schmutz J, Wang H et al (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30(6):555–561
Zhang G, Liu X, Quan Z et al (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol 30(6):549–554
Tomato Genome C (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485(7400):635–641
Potato Genome Sequencing Consortium, Xu X, Pan S et al (2011) Genome sequence and analysis of the tuber crop potato. Nature 475(7355):189–195
Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229):551–556
Brenchley R, Spannagl M, Pfeifer M et al (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491(7426):705–710
Ling HQ, Zhao S, Liu D et al (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496(7443):87–90
Jaillon O, Aury JM, Noel B et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463–467
Myles S, Chia JM, Hurwitz B et al (2010) Rapid genomic characterization of the genus vitis. PLoS One 5(1), e8219
Atwell S, Huang YS, Vilhjalmsson BJ et al (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465(7298):627–631
Fox SE, Preece J, Kimbrel JA et al (2013) Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae). Appl Plant Sci 1(3):1200011
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 U S A 106(30):12273–12278
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), e10780
Yu J, Wang J, Lin W et al (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3(2), e38
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 U S A 110(2):453–458
Zheng LY, Guo XS, He B et al (2011) Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol 12(11):R114
Gore MA, Chia JM, Elshire RJ et al (2009) A first-generation haplotype map of maize. Science 326(5956):1115–1117
Chia JM, Song C, Bradbury PJ et al (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 44(7):803–807
Flicek P, Amode MR, Barrell D et al (2014) Ensembl 2014. Nucleic Acids Res 42(Database issue):D749–D755
Kersey PJ, Allen JE, Christensen M et al (2014) Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res 42(Database issue):D546–D552
Ware D (2007) Gramene. Methods Mol Biol 406:315–329
Dharmawardhana P, Ren L, Amarasinghe V et al (2013) A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. Rice (N Y) 6(1):15
Monaco MK, Sen TZ, Dharmawardhana PD et al (2013) Maize metabolic network construction and transcriptome analysis. Plant Genome 6(1):1–12
Youens-Clark K, Buckler E, Casstevens T et al (2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res 39(Database issue):D1085–D1094
Karp PD, Paley SM, Krummenacker M et al (2010) Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform 11(1):40–79
Caspi R, Altman T, Billington R et al (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 42(Database issue):D459–D471
Mueller LA, Zhang P, Rhee SY (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol 132(2):453–460
Urbanczyk-Wochniak E, Sumner LW (2007) MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics 23(11):1418–1423
Zhang P, Dreher K, Karthikeyan A et al (2010) Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiol 153(4):1479–1491
Bombarely A, Menda N, Tecle IY et al (2011) The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res 39(Database issue):D1149–D1155
Croft D, O’Kelly G, Wu G et al (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39(Database issue):D691–D697
Spooner W, Youens-Clark K, Staines D et al (2012) GrameneMart: the BioMart data portal for the Gramene project. Database (Oxford) 2012:bar056
Monaco MK, Stein J, Naithani S et al (2014) Gramene 2013: comparative plant genomics resources. Nucleic Acids Res 42(Database issue):D1193–D1199
Doebley J, Stec A, Hubbard L (1997) The evolution of apical dominance in maize. Nature 386(6624):485–488
Harjes CE, Rocheford TR, Bai L et al (2008) Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science 319(5861):330–333
Regulski M, Lu Z, Kendall J et al (2013) The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Res 23(10):1651–1662
Acknowledgements
The authors would like to thank all members of the Gramene Project, especially Bo Wang for going through the exercises and providing feedback for clarity in the protocols and Peter van Buren for system technolology support. We are also grateful to Gramene’s users for valuable suggestions, and our collaborators for sharing genomic-scale data sets that make Gramene an outstanding community resource. The Genomes and Pathways modules in Gramene would not have been possible without the synergistic collaborations with the Ensembl Genomes project at the EMBL-European Bioinformatics Institute, and the Reactome project at the Ontario Institute for Cancer Research, respectively.
Gramene is supported by an NSF grant (IOS-1127112).
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Tello-Ruiz, M.K., Stein, J., Wei, S., Youens-Clark, K., Jaiswal, P., Ware, D. (2016). Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 1374. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3167-5_7
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DOI: https://doi.org/10.1007/978-1-4939-3167-5_7
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3166-8
Online ISBN: 978-1-4939-3167-5
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