Grimwood J, Grover C, Grupp K, Hu G, Lee TH, Li J, Lin L, Liu T, Marler BS, Page JT,
Roberts AW, Romanel E, Sanders WS, Szadkowski E, Tan X, Tang H, Xu C, Wang J, Wang Z,
Zhang D, Zhang L, Ashrafi H, Bedon F, Bowers JE, Brubaker CL, Chee PW, Das S, Gingle AR,
Haigler CH, Harker D, Hoffmann LV, Hovav R, Jones DC, Lemke C, Mansoor S, Rahman M,
Rainville LN, Rambani A, Reddy UK, Rong JK, Saranga Y, Scheffler BE, Scheffler JA, Stelly
DM, Triplett BA, Van Deynze A, Vaslin MF, Waghmare VN, Walford SA, Wright RJ, Zaki EA,
Zhang T, Dennis ES, Mayer KF, Peterson DG, Rokhsar DS, Wang X, Schmutz J (2012)
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
Nature 492(7429):423–427
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C (2017) Salmon provides fast and bias-aware
quantification of transcript expression. Nat Methods 14(4):417–419
Pellicer J, Fay MF, Leitch IJ (2010) The largest eukaryotic genome of them all? Bot J Linn Soc
164:10–15
Pellicer J, Hidalgo O, Dodsworth S, Leitch IJ (2018) Genome size diversity and its impact on the
evolution of land plants. Genes (Basel) 9(2):88
Perera D, Magbanua ZV, Thummasuwan S, Mukherjee D, Arick M II, Chouvarine P, Nairn CJ,
Schmutz J, Grimwood J, Dean JFD, Peterson DG (2018) Exploring the loblolly pine (Pinus
taedaL.) genome by BAC sequencing and Cot analysis. Gene. https://doi.org/10.1016/j.gene.
2018.04.024
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015) StringTie
enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol
33(3):290–295
Peterson DG (2005) Reduced representation strategies and their application to plant genomes. In:
Meksem K, Kahl G (eds) The handbook of genome mapping: genetic and physical mapping.
Wiley-VCH Verlag GmbH, KGaA, Weinheim, pp 307–335
Peterson DG (2014) Evolution of plant genome analysis. In: Paterson AH (ed) Advances in
botanical research, Genomes of herbaceous land plants, vol 69. Academic Press, Amsterdam,
pp 13–46
Peterson DG, Tomkins JP, Frisch DA, Wing RA, Paterson AH (2000) Construction of plant
bacterial artificial chromosome (BAC) libraries: an illustrated Guide. J Agric Genomics
5:1–100. http://wheat.pw.usda.gov/jag/
Philippe N, Legendre M, Doutre G, Coute Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L,
Bruley C, Garin J, Claverie JM, Abergel C (2013) Pandoraviruses: amoeba viruses with
genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science 341(6143):281–286
Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes.
Bioinformatics 21(Suppl 1):i351–i358
Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF,
Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin IT, Kuroki Y,
Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A,
Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho
SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J,
Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T,
Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL,
Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M,
Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL (2008) The Physcomitrella
genome reveals evolutionary insights into the conquest of land by plants. Science 319
(5859):64–69
Rho M, Choi JH, Kim S, Lynch M, Tang H (2007) De novo identification of LTR retrotransposons
in eukaryotic genomes. BMC Genomics 8:90
Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software
suite. Trends Genet 16(6):276–277
186
D. G. Peterson and M. Arick
Roberts AW, Romanel E, Sanders WS, Szadkowski E, Tan X, Tang H, Xu C, Wang J, Wang Z,
Zhang D, Zhang L, Ashrafi H, Bedon F, Bowers JE, Brubaker CL, Chee PW, Das S, Gingle AR,
Haigler CH, Harker D, Hoffmann LV, Hovav R, Jones DC, Lemke C, Mansoor S, Rahman M,
Rainville LN, Rambani A, Reddy UK, Rong JK, Saranga Y, Scheffler BE, Scheffler JA, Stelly
DM, Triplett BA, Van Deynze A, Vaslin MF, Waghmare VN, Walford SA, Wright RJ, Zaki EA,
Zhang T, Dennis ES, Mayer KF, Peterson DG, Rokhsar DS, Wang X, Schmutz J (2012)
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
Nature 492(7429):423–427
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C (2017) Salmon provides fast and bias-aware
quantification of transcript expression. Nat Methods 14(4):417–419
Pellicer J, Fay MF, Leitch IJ (2010) The largest eukaryotic genome of them all? Bot J Linn Soc
164:10–15
Pellicer J, Hidalgo O, Dodsworth S, Leitch IJ (2018) Genome size diversity and its impact on the
evolution of land plants. Genes (Basel) 9(2):88
Perera D, Magbanua ZV, Thummasuwan S, Mukherjee D, Arick M II, Chouvarine P, Nairn CJ,
Schmutz J, Grimwood J, Dean JFD, Peterson DG (2018) Exploring the loblolly pine (Pinus
taedaL.) genome by BAC sequencing and Cot analysis. Gene. https://doi.org/10.1016/j.gene.
2018.04.024
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015) StringTie
enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol
33(3):290–295
Peterson DG (2005) Reduced representation strategies and their application to plant genomes. In:
Meksem K, Kahl G (eds) The handbook of genome mapping: genetic and physical mapping.
Wiley-VCH Verlag GmbH, KGaA, Weinheim, pp 307–335
Peterson DG (2014) Evolution of plant genome analysis. In: Paterson AH (ed) Advances in
botanical research, Genomes of herbaceous land plants, vol 69. Academic Press, Amsterdam,
pp 13–46
Peterson DG, Tomkins JP, Frisch DA, Wing RA, Paterson AH (2000) Construction of plant
bacterial artificial chromosome (BAC) libraries: an illustrated Guide. J Agric Genomics
5:1–100. http://wheat.pw.usda.gov/jag/
Philippe N, Legendre M, Doutre G, Coute Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L,
Bruley C, Garin J, Claverie JM, Abergel C (2013) Pandoraviruses: amoeba viruses with
genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science 341(6143):281–286
Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes.
Bioinformatics 21(Suppl 1):i351–i358
Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF,
Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin IT, Kuroki Y,
Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A,
Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho
SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J,
Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T,
Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL,
Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M,
Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL (2008) The Physcomitrella
genome reveals evolutionary insights into the conquest of land by plants. Science 319
(5859):64–69
Rho M, Choi JH, Kim S, Lynch M, Tang H (2007) De novo identification of LTR retrotransposons
in eukaryotic genomes. BMC Genomics 8:90
Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software
suite. Trends Genet 16(6):276–277
186
D. G. Peterson and M. Arick