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A-, B-, and Z-DNA. Science 216(4545):475–485
DiFazio SP, Slavov GT, Joshi CP (2011) Populus: a premier pioneer system for plant genomics. In:
Joshi CP, Di Fazio SP, Kole C (eds) Genetics, genomics and breeding of poplar. CRC Press,
Boca Raton, pp 1–28
Dodsworth S, Chase MW, Leitch AR (2016) Is post-polyploidization diploidization the key to the
evolutionary success of angiosperms? Bot J Linn Soc 180(1):1–5
Dohm JC, Minoche AE, Holtgrawe D, Capella-Gutierrez S, Zakrzewski F, Tafer H, Rupp O,
Sorensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF,
Schmidt T, Gabaldon T, Lehrach H, Weisshaar B, Himmelbauer H (2014) The genome of the
recently domesticated crop plant sugar beet (Beta vulgaris). Nature 505(7484):546–549
Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P,
Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, Staker B, Pant KP, Baccash J,
Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R,
Curson B, Ebert JC, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V,
Koenig M, Kong C, Landers T, Le C, Liu J, McBride CE, Morenzoni M, Morey RE, Mutch K,
Perazich H, Perry K, Peters BA, Peterson J, Pethiyagoda CL, Pothuraju K, Richter C,
Rosenbaum AM, Roy S, Shafto J, Sharanhovich U, Shannon KW, Sheppy CG, Sun M,
Thakuria JV, Tran A, Vu D, Zaranek AW, Wu X, Drmanac S, Oliphant AR, Banyai WC,
Martin B, Ballinger DG, Church GM, Reid CA (2010) Human genome sequencing using
unchained base reads on self-assembling DNA nanoarrays. Science 327(5961):78–81
Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I,
Lander ES, Aiden AP, Aiden EL (2017) De novo assembly of the Aedes aegypti genome using
Hi-C yields chromosome-length scaffolds. Science 356(6333):92–95
Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space
complexity. BMC Bioinformatics 5:113
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B,
Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A,
Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G,
Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma C, Marks P, Maxham M, Murphy D,
Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K,
Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J,
Turner S (2009) Real-time DNA sequencing from single polymerase molecules. Science
323(5910):133–138
El Baidouri M, Panaud O (2013) Comparative genomic paleontology across plant kingdom reveals
the dynamics of TE-driven genome evolution. Genome Biol Evol 5(5):954–965
Fan C, Walling JG, Zhang J, Hirsch CD, Jiang J, Wing RA (2011) Conservation and purifying
selection of transcribed genes located in a rice centromere. Plant Cell 23(8):2821–2830
Farjon A (2008) A natural history of conifers. Timber Press, Portland
Farjon A (2010) The economic importance of conifers. In: A handbook of the world’s conifers. Brill
Academic Publishers, Leiden, pp 25–28
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR (2015)
HMMER web server: 2015 update. Nucleic Acids Res 43(W1):W30–W38
French-Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine
genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449
(7161):463–467
Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson
JR, Schloss JA, Schwartz DC, Vezenov DV (2009) The challenges of sequencing by synthesis.
Nat Biotechnol 27(11):1013–1023
Garsmeur O, Schnable JC, Almeida A, Jourda C, D’Hont A, Freeling M (2014) Two evolutionarily
distinct classes of paleopolyploidy. Mol Biol Evol 31(2):448–454
Sequencing Plant Genomes
179
unveils many unique features. Proc Natl Acad Sci U S A 103(31):11647–11652
Dickerson RE, Drew HR, Conner BN, Wing RM, Fratini AV, Kopka ML (1982) The anatomy of
A-, B-, and Z-DNA. Science 216(4545):475–485
DiFazio SP, Slavov GT, Joshi CP (2011) Populus: a premier pioneer system for plant genomics. In:
Joshi CP, Di Fazio SP, Kole C (eds) Genetics, genomics and breeding of poplar. CRC Press,
Boca Raton, pp 1–28
Dodsworth S, Chase MW, Leitch AR (2016) Is post-polyploidization diploidization the key to the
evolutionary success of angiosperms? Bot J Linn Soc 180(1):1–5
Dohm JC, Minoche AE, Holtgrawe D, Capella-Gutierrez S, Zakrzewski F, Tafer H, Rupp O,
Sorensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF,
Schmidt T, Gabaldon T, Lehrach H, Weisshaar B, Himmelbauer H (2014) The genome of the
recently domesticated crop plant sugar beet (Beta vulgaris). Nature 505(7484):546–549
Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P,
Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, Staker B, Pant KP, Baccash J,
Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R,
Curson B, Ebert JC, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V,
Koenig M, Kong C, Landers T, Le C, Liu J, McBride CE, Morenzoni M, Morey RE, Mutch K,
Perazich H, Perry K, Peters BA, Peterson J, Pethiyagoda CL, Pothuraju K, Richter C,
Rosenbaum AM, Roy S, Shafto J, Sharanhovich U, Shannon KW, Sheppy CG, Sun M,
Thakuria JV, Tran A, Vu D, Zaranek AW, Wu X, Drmanac S, Oliphant AR, Banyai WC,
Martin B, Ballinger DG, Church GM, Reid CA (2010) Human genome sequencing using
unchained base reads on self-assembling DNA nanoarrays. Science 327(5961):78–81
Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I,
Lander ES, Aiden AP, Aiden EL (2017) De novo assembly of the Aedes aegypti genome using
Hi-C yields chromosome-length scaffolds. Science 356(6333):92–95
Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space
complexity. BMC Bioinformatics 5:113
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B,
Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A,
Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G,
Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma C, Marks P, Maxham M, Murphy D,
Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K,
Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J,
Turner S (2009) Real-time DNA sequencing from single polymerase molecules. Science
323(5910):133–138
El Baidouri M, Panaud O (2013) Comparative genomic paleontology across plant kingdom reveals
the dynamics of TE-driven genome evolution. Genome Biol Evol 5(5):954–965
Fan C, Walling JG, Zhang J, Hirsch CD, Jiang J, Wing RA (2011) Conservation and purifying
selection of transcribed genes located in a rice centromere. Plant Cell 23(8):2821–2830
Farjon A (2008) A natural history of conifers. Timber Press, Portland
Farjon A (2010) The economic importance of conifers. In: A handbook of the world’s conifers. Brill
Academic Publishers, Leiden, pp 25–28
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR (2015)
HMMER web server: 2015 update. Nucleic Acids Res 43(W1):W30–W38
French-Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine
genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449
(7161):463–467
Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson
JR, Schloss JA, Schwartz DC, Vezenov DV (2009) The challenges of sequencing by synthesis.
Nat Biotechnol 27(11):1013–1023
Garsmeur O, Schnable JC, Almeida A, Jourda C, D’Hont A, Freeling M (2014) Two evolutionarily
distinct classes of paleopolyploidy. Mol Biol Evol 31(2):448–454
Sequencing Plant Genomes
179