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Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L,
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Hernandez A, Lambert GM, Inan G, Galbraith DW, Bressan RA, Yun DJ, Zhu JK, Cheeseman
JM, Bohnert HJ (2010) Genome structures and halophyte-specific gene expression of the
extremophile Thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella
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Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV (2007) The tiny eukaryote
Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl
Acad Sci U S A 104(18):7705–7710
Pandey V, Nutter RC, Prediger E (2008) Applied biosystems SOLiD™ system: ligation-based
sequencing. In: Janitz M (ed) Next generation genome sequencing: towards personalized
medicine. Wiley-VCH, Weinheim, pp 29–41
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):9903–9908
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G,
Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti
AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M,
Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC,
Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R,
Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS
(2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457
(7229):551–556
Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC,
Shu S, Udall J, Yoo MJ, Byers R, Chen W, Doron-Faigenboim A, Duke MV, Gong L,
Sequencing Plant Genomes
185
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Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M,
Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ,
Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C,
Yandell M, Davis JM, Smith KE, Dean JFD, Lorenz WW, Whetten RW, Sederoff R,
Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, deJong PJ, Yorke JA, Salzberg
SL, Langley CH (2014) Decoding the massive genome of loblolly pine using haploid DNA and
novel assembly strategies. Genome Biol 15(3):R59
Ng MP, Vergara IA, Frech C, Chen Q, Zeng X, Pei J, Chen N (2009) OrthoClusterDB: an online
platform for synteny blocks. BMC Bioinformatics 10:192
Nickerson DA, Tobe VO, Taylor SL (1997) PolyPhred: automating the detection and genotyping of
single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res
25(14):2745–2751
Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N,
Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L,
Holmberg K, Hallman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Kaller M,
Luthman J, Lysholm F, Niittyla T, Olson A, Rilakovic N, Ritland C, Rossello JA, Sena J,
Svensson T, Talavera-Lopez C, Theissen G, Tuominen H, Vanneste K, Wu ZQ, Zhang B,
Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia GR, Hvidsten TR, de Jong P,
MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, Van de Peer Y, Andersson B,
Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S (2013) The Norway spruce genome
sequence and conifer genome evolution. Nature 497(7451):579–584
Ocana K, de Oliveira D (2015) Parallel computing in genomic research: advances and applications.
Adv Appl Bioinforma Chem 8:23–35
Oh DH, Dassanayake M, Haas JS, Kropornika A, Wright C, d’Urzo MP, Hong H, Ali S,
Hernandez A, Lambert GM, Inan G, Galbraith DW, Bressan RA, Yun DJ, Zhu JK, Cheeseman
JM, Bohnert HJ (2010) Genome structures and halophyte-specific gene expression of the
extremophile Thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella
halophila) and Arabidopsis. Plant Physiol 154(3):1040–1052
Palenik B, Grimwood J, Aerts A, Rouze P, Salamov A, Putnam N, Dupont C, Jorgensen R,
Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C,
Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C,
Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C,
Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV (2007) The tiny eukaryote
Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl
Acad Sci U S A 104(18):7705–7710
Pandey V, Nutter RC, Prediger E (2008) Applied biosystems SOLiD™ system: ligation-based
sequencing. In: Janitz M (ed) Next generation genome sequencing: towards personalized
medicine. Wiley-VCH, Weinheim, pp 29–41
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):9903–9908
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G,
Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti
AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M,
Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC,
Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R,
Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS
(2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457
(7229):551–556
Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC,
Shu S, Udall J, Yoo MJ, Byers R, Chen W, Doron-Faigenboim A, Duke MV, Gong L,
Sequencing Plant Genomes
185