Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N,
Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR,
Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna
Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G,
Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ,
Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks
FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ (2008) Accurate whole human genome
sequencing using reversible terminator chemistry. Nature 456(7218):53–59
Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Cannon EK, Liu X, Gao D,
Clevenger J, Dash S, Ren L, Moretzsohn MC, Shirasawa K, Huang W, Vidigal B,
Abernathy B, Chu Y, Niederhuth CE, Umale P, Araujo AC, Kozik A, Kim KD, Burow MD,
Varshney RK, Wang X, Zhang X, Barkley N, Guimaraes PM, Isobe S, Guo B, Liao B, Stalker
HT, Schmitz RJ, Scheffler BE, Leal-Bertioli SC, Xun X, Jackson SA, Michelmore R,
Ozias-Akins P (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the
diploid ancestors of cultivated peanut. Nat Genet 48(4):438–446
Bio-IT World Staff (2013) Six years after acquisition, Roche quietly shutters 454. Bio-IT World.
http://www.bio-itworld.com/2013/10/16/six-years-after-acquisition-roche-quietly-shutters-454.
html
Birol I, Raymond A, Jackman SD, Pleasance S, Coope R, Taylor GA, Yuen MM, Keeling CI,
Brand D, Vandervalk BP, Kirk H, Pandoh P, Moore RA, Zhao Y, Mungall AJ, Jaquish B,
Yanchuk A, Ritland C, Boyle B, Bousquet J, Ritland K, Mackay J, Bohlmann J, Jones SJ (2013)
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun
sequencing data. Bioinformatics 29(12):1492–1497
Blanc-Mathieu R, Verhelst B, Derelle E, Rombauts S, Bouget FY, Carre I, Chateau A,
Eyre-Walker A, Grimsley N, Moreau H, Piegu B, Rivals E, Schackwitz W, Van de Peer Y,
Piganeau G (2014) An improved genome of the model marine alga Ostreococcus tauri unfolds
by assessing Illumina de novo assemblies. BMC Genomics 15:1103
Boivin A, Vendrely R, Vendrely C (1948) L’acide désoxyribonuclèique du noyau cellulaire
dépositaire des caractères héréditaires; arguments d'ordre analytique. C R Acad Sci
226:1061–1063
Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S,
Sorensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R,
Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jimenez-Gomez JM,
Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham
RC, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JK, Zamir D,
Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR (2014a) The genome of the stresstolerant wild tomato species Solanum pennellii. Nat Genet 46(9):1034–1038
Bolger AM, Lohse M, Usadel B (2014b) Trimmomatic: a flexible trimmer for Illumina sequence
data. Bioinformatics 30(15):2114–2120
Bridges SM, Magee GB, Wang N, Williams WP, Burgess SC, Nanduri B (2007) ProtQuant: a tool
for the label-free quantification of MudPIT proteomics data. BMC Bioinformatics 8(Suppl 7):
S24
Buermans HP, den Dunnen JT (2014) Next generation sequencing technology: advances and
applications. Biochim Biophys Acta 1842(10):1932–1941
Butler JM (2015) The future of forensic DNA analysis. Philos Trans R Soc Lond Ser B Biol Sci 370
(1674):20140252
Buza TJ, McCarthy FM, Wang N, Bridges SM, Burgess SC (2008) Gene Ontology annotation
quality analysis in model eukaryotes. Nucleic Acids Res 36(2):e12
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009)
BLAST+: architecture and applications. BMC Bioinformatics 10:421
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sanchez Alvarado A, Yandell M
(2008) MAKER: an easy-to-use annotation pipeline designed for emerging model organism
genomes. Genome Res 18(1):188–196
Sequencing Plant Genomes
177
Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR,
Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna
Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G,
Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ,
Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks
FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ (2008) Accurate whole human genome
sequencing using reversible terminator chemistry. Nature 456(7218):53–59
Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Cannon EK, Liu X, Gao D,
Clevenger J, Dash S, Ren L, Moretzsohn MC, Shirasawa K, Huang W, Vidigal B,
Abernathy B, Chu Y, Niederhuth CE, Umale P, Araujo AC, Kozik A, Kim KD, Burow MD,
Varshney RK, Wang X, Zhang X, Barkley N, Guimaraes PM, Isobe S, Guo B, Liao B, Stalker
HT, Schmitz RJ, Scheffler BE, Leal-Bertioli SC, Xun X, Jackson SA, Michelmore R,
Ozias-Akins P (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the
diploid ancestors of cultivated peanut. Nat Genet 48(4):438–446
Bio-IT World Staff (2013) Six years after acquisition, Roche quietly shutters 454. Bio-IT World.
http://www.bio-itworld.com/2013/10/16/six-years-after-acquisition-roche-quietly-shutters-454.
html
Birol I, Raymond A, Jackman SD, Pleasance S, Coope R, Taylor GA, Yuen MM, Keeling CI,
Brand D, Vandervalk BP, Kirk H, Pandoh P, Moore RA, Zhao Y, Mungall AJ, Jaquish B,
Yanchuk A, Ritland C, Boyle B, Bousquet J, Ritland K, Mackay J, Bohlmann J, Jones SJ (2013)
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun
sequencing data. Bioinformatics 29(12):1492–1497
Blanc-Mathieu R, Verhelst B, Derelle E, Rombauts S, Bouget FY, Carre I, Chateau A,
Eyre-Walker A, Grimsley N, Moreau H, Piegu B, Rivals E, Schackwitz W, Van de Peer Y,
Piganeau G (2014) An improved genome of the model marine alga Ostreococcus tauri unfolds
by assessing Illumina de novo assemblies. BMC Genomics 15:1103
Boivin A, Vendrely R, Vendrely C (1948) L’acide désoxyribonuclèique du noyau cellulaire
dépositaire des caractères héréditaires; arguments d'ordre analytique. C R Acad Sci
226:1061–1063
Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S,
Sorensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R,
Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jimenez-Gomez JM,
Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham
RC, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JK, Zamir D,
Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR (2014a) The genome of the stresstolerant wild tomato species Solanum pennellii. Nat Genet 46(9):1034–1038
Bolger AM, Lohse M, Usadel B (2014b) Trimmomatic: a flexible trimmer for Illumina sequence
data. Bioinformatics 30(15):2114–2120
Bridges SM, Magee GB, Wang N, Williams WP, Burgess SC, Nanduri B (2007) ProtQuant: a tool
for the label-free quantification of MudPIT proteomics data. BMC Bioinformatics 8(Suppl 7):
S24
Buermans HP, den Dunnen JT (2014) Next generation sequencing technology: advances and
applications. Biochim Biophys Acta 1842(10):1932–1941
Butler JM (2015) The future of forensic DNA analysis. Philos Trans R Soc Lond Ser B Biol Sci 370
(1674):20140252
Buza TJ, McCarthy FM, Wang N, Bridges SM, Burgess SC (2008) Gene Ontology annotation
quality analysis in model eukaryotes. Nucleic Acids Res 36(2):e12
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009)
BLAST+: architecture and applications. BMC Bioinformatics 10:421
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sanchez Alvarado A, Yandell M
(2008) MAKER: an easy-to-use annotation pipeline designed for emerging model organism
genomes. Genome Res 18(1):188–196
Sequencing Plant Genomes
177