Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize
genome: complexity, diversity, and dynamics. Science 326(5956):1112–1115
Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S,
Bode E, Bode HB, Bolten CJ, Choudhuri JV, Doss S, Elnakady YA, Frank B, Gaigalat L,
Goesmann A, Groeger C, Gross F, Jelsbak L, Jelsbak L, Kalinowski J, Kegler C, Knauber T,
Konietzny S, Kopp M, Krause L, Krug D, Linke B, Mahmud T, Martinez-Arias R, McHardy
AC, Merai M, Meyer F, Mormann S, Munoz-Dorado J, Perez J, Pradella S, Rachid S,
Raddatz G, Rosenau F, Ruckert C, Sasse F, Scharfe M, Schuster SC, Suen G, Treuner-Lange A,
Velicer GJ, Vorholter FJ, Weissman KJ, Welch RD, Wenzel SC, Whitworth DE, Wilhelm S,
Wittmann C, Blocker H, Puhler A, Muller R (2007) Complete genome sequence of the
myxobacterium Sorangium cellulosum. Nat Biotechnol 25(11):1281–1289
Schubert I, Vu GT (2016) Genome stability and evolution: attempting a holistic view. Trends Plant
Sci 21(9):749–757
Shahinnia F, Druka A, Franckowiak J, Morgante M, Waugh R, Stein N (2012) High resolution
mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H. Theor
Appl Genet 124(2):373–384
Shapiro B, Hofreiter M (2014) A paleogenomic perspective on evolution and gene function: new
insights from ancient DNA. Science 343(6169):1236573
Shearer LA, Anderson LK, de Jong H, Smit S, Goicoechea JL, Roe BA, Hua A, Giovannoni JJ,
Stack SM (2014) Fluorescence in situ hybridization and optical mapping to correct scaffold
arrangement in the tomato genome. G3 (Bethesda) 4(8):1395–1405
Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH
(2017) DNA sequencing at 40: past, present and future. Nature 550:345–353
Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P,
Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP,
Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP,
Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, Liu B,
Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H,
Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm
LJ, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W,
Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P,
Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R,
Borodovsky M, Veilleux RE, Folta KM (2011) The genome of woodland strawberry (Fragaria
vesca). Nat Genet 43(2):109–116
Shuter BJ, Thomas JE, Taylor WD, Zimmerman AM (1983) Phenotypic correlates of genomic
DNA content in unicellular eukaryotes and other cells. Am Nat 122(1):26–44
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing
genome assembly and annotation completeness with single-copy orthologs. Bioinformatics
31(19):3210–3212
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I (2009) ABySS: a parallel
assembler for short read sequence data. Genome Res 19(6):1117–1123
Singh R, Ong-Abdullah M, Low ET, Manaf MA, Rosli R, Nookiah R, Ooi LC, Ooi SE, Chan KL,
Halim MA, Azizi N, Nagappan J, Bacher B, Lakey N, Smith SW, He D, Hogan M, Budiman
MA, Lee EK, DeSalle R, Kudrna D, Goicoechea JL, Wing RA, Wilson RK, Fulton RS, Ordway
JM, Martienssen RA, Sambanthamurthi R (2013) Oil palm genome sequence reveals divergence
of interfertile species in old and new worlds. Nature 500(7462):335–339
Slater GS, Birney E (2005) Automated generation of heuristics for biological sequence comparison.
BMC Bioinformatics 6:31
Smit AFA, Hubley R, Green P (2013) RepeatMasker open-4.0. 2013–2015. http://www.
repeatmasker.org. Accessed 18 Feb 2018
Smith DR, Lee RW (2014) A plastid without a genome: evidence from the nonphotosynthetic green
algal genus Polytomella. Plant Physiol 164(4):1812–1819
188
D. G. Peterson and M. Arick
genome: complexity, diversity, and dynamics. Science 326(5956):1112–1115
Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S,
Bode E, Bode HB, Bolten CJ, Choudhuri JV, Doss S, Elnakady YA, Frank B, Gaigalat L,
Goesmann A, Groeger C, Gross F, Jelsbak L, Jelsbak L, Kalinowski J, Kegler C, Knauber T,
Konietzny S, Kopp M, Krause L, Krug D, Linke B, Mahmud T, Martinez-Arias R, McHardy
AC, Merai M, Meyer F, Mormann S, Munoz-Dorado J, Perez J, Pradella S, Rachid S,
Raddatz G, Rosenau F, Ruckert C, Sasse F, Scharfe M, Schuster SC, Suen G, Treuner-Lange A,
Velicer GJ, Vorholter FJ, Weissman KJ, Welch RD, Wenzel SC, Whitworth DE, Wilhelm S,
Wittmann C, Blocker H, Puhler A, Muller R (2007) Complete genome sequence of the
myxobacterium Sorangium cellulosum. Nat Biotechnol 25(11):1281–1289
Schubert I, Vu GT (2016) Genome stability and evolution: attempting a holistic view. Trends Plant
Sci 21(9):749–757
Shahinnia F, Druka A, Franckowiak J, Morgante M, Waugh R, Stein N (2012) High resolution
mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H. Theor
Appl Genet 124(2):373–384
Shapiro B, Hofreiter M (2014) A paleogenomic perspective on evolution and gene function: new
insights from ancient DNA. Science 343(6169):1236573
Shearer LA, Anderson LK, de Jong H, Smit S, Goicoechea JL, Roe BA, Hua A, Giovannoni JJ,
Stack SM (2014) Fluorescence in situ hybridization and optical mapping to correct scaffold
arrangement in the tomato genome. G3 (Bethesda) 4(8):1395–1405
Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH
(2017) DNA sequencing at 40: past, present and future. Nature 550:345–353
Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P,
Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP,
Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP,
Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, Liu B,
Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H,
Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm
LJ, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W,
Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P,
Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R,
Borodovsky M, Veilleux RE, Folta KM (2011) The genome of woodland strawberry (Fragaria
vesca). Nat Genet 43(2):109–116
Shuter BJ, Thomas JE, Taylor WD, Zimmerman AM (1983) Phenotypic correlates of genomic
DNA content in unicellular eukaryotes and other cells. Am Nat 122(1):26–44
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing
genome assembly and annotation completeness with single-copy orthologs. Bioinformatics
31(19):3210–3212
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I (2009) ABySS: a parallel
assembler for short read sequence data. Genome Res 19(6):1117–1123
Singh R, Ong-Abdullah M, Low ET, Manaf MA, Rosli R, Nookiah R, Ooi LC, Ooi SE, Chan KL,
Halim MA, Azizi N, Nagappan J, Bacher B, Lakey N, Smith SW, He D, Hogan M, Budiman
MA, Lee EK, DeSalle R, Kudrna D, Goicoechea JL, Wing RA, Wilson RK, Fulton RS, Ordway
JM, Martienssen RA, Sambanthamurthi R (2013) Oil palm genome sequence reveals divergence
of interfertile species in old and new worlds. Nature 500(7462):335–339
Slater GS, Birney E (2005) Automated generation of heuristics for biological sequence comparison.
BMC Bioinformatics 6:31
Smit AFA, Hubley R, Green P (2013) RepeatMasker open-4.0. 2013–2015. http://www.
repeatmasker.org. Accessed 18 Feb 2018
Smith DR, Lee RW (2014) A plastid without a genome: evidence from the nonphotosynthetic green
algal genus Polytomella. Plant Physiol 164(4):1812–1819
188
D. G. Peterson and M. Arick