Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M,
Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O,
Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE,
McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar
DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thummler F, Tillich M, Villarreal Aguilar
JC, Widiez T, Wong GK, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX,
Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F,
Salse J, Schmutz J, Rensing SA (2018) The Physcomitrella patens chromosome-scale assembly
reveals moss genome structure and evolution. Plant J 93(3):515–533
Langmead B (2010) Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics
32:11.17.11–11.17.14
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods
9(4):357–359
Leggett RM, Clavijo BJ, Clissold L, Clark MD, Caccamo M (2014) NextClip: an analysis and read
preparation tool for Nextera Long Mate Pair libraries. Bioinformatics 30(4):566–568
Leitch AR, Leitch IJ (2008) Genomic plasticity and the diversity of polyploid plants. Science 320
(5875):481–483
Lesk AM (2012) Introduction to genomics, 2nd edn. Oxford University Press, New York
Li H (2016) Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
Bioinformatics 32(14):2103–2110
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform.
Bioinformatics 25(14):1754–1760
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000
Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and
SAMtools. Bioinformatics 25(16):2078–2079
Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, Ma Z, Shang H, Ma X, Wu J, Liang X, Huang G,
Percy RG, Liu K, Yang W, Chen W, Du X, Shi C, Yuan Y, Ye W, Liu X, Zhang X, Liu W,
Wei H, Wei S, Huang G, Zhang X, Zhu S, Zhang H, Sun F, Wang X, Liang J, Wang J, He Q,
Huang L, Wang J, Cui J, Song G, Wang K, Xu X, Yu JZ, Zhu Y, Yu S (2015a) Genome
sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into
genome evolution. Nat Biotechnol 33(5):524–530
Li Z, Baniaga AE, Sessa EB, Scascitelli M, Graham SW, Rieseberg LH, Barker MS (2015b) Early
genome duplications in conifers and other seed plants. Sci Adv 1(10):e1501084
Liu C, Weigel D (2015) Chromatin in 3D: progress and prospects for plants. Genome Biol 16:170
Liu MJ, Zhao J, Cai QL, Liu GC, Wang JR, Zhao ZH, Liu P, Dai L, Yan G, Wang WJ, Li XS,
Chen Y, Sun YD, Liu ZG, Lin MJ, Xiao J, Chen YY, Li XF, Wu B, Ma Y, Jian JB, Yang W,
Yuan Z, Sun XC, Wei YL, Yu LL, Zhang C, Liao SG, He RJ, Guang XM, Wang Z, Zhang YY,
Luo LH (2014) The complex jujube genome provides insights into fruit tree biology. Nat
Commun 5:5315
Love RR, Weisenfeld NI, Jaffe DB, Besansky NJ, Neafsey DE (2016) Evaluation of DISCOVAR
de novo using a mosquito sample for cost-effective short-read genome assembly. BMC Genomics 17:187
Lowry DB, Purmal CT, Juenger TE (2013) A population genetic transect of Panicum hallii
(Poaceae). Am J Bot 100(3):592–601
Manda P, Freeman MG, Bridges SM, Jankun-Kelly TJ, Nanduri B, McCarthy FM, Burgess SC
(2010) GOModeler – a tool for hypothesis-testing of functional genomics datasets. BMC
Bioinformatics 11(Suppl 6):S29
Mankertz P (2008) Molecular biology of porcine circoviruses. In: Animal viruses: molecular
biology. Academic Press, Caister, pp 355–374
Marcais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A (2018) MUMmer4: a fast
and versatile genome alignment system. PLoS Comput Biol 14(1):e1005944
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS,
Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S,
Sequencing Plant Genomes
183
Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O,
Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE,
McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar
DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thummler F, Tillich M, Villarreal Aguilar
JC, Widiez T, Wong GK, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX,
Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F,
Salse J, Schmutz J, Rensing SA (2018) The Physcomitrella patens chromosome-scale assembly
reveals moss genome structure and evolution. Plant J 93(3):515–533
Langmead B (2010) Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics
32:11.17.11–11.17.14
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods
9(4):357–359
Leggett RM, Clavijo BJ, Clissold L, Clark MD, Caccamo M (2014) NextClip: an analysis and read
preparation tool for Nextera Long Mate Pair libraries. Bioinformatics 30(4):566–568
Leitch AR, Leitch IJ (2008) Genomic plasticity and the diversity of polyploid plants. Science 320
(5875):481–483
Lesk AM (2012) Introduction to genomics, 2nd edn. Oxford University Press, New York
Li H (2016) Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
Bioinformatics 32(14):2103–2110
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform.
Bioinformatics 25(14):1754–1760
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000
Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and
SAMtools. Bioinformatics 25(16):2078–2079
Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, Ma Z, Shang H, Ma X, Wu J, Liang X, Huang G,
Percy RG, Liu K, Yang W, Chen W, Du X, Shi C, Yuan Y, Ye W, Liu X, Zhang X, Liu W,
Wei H, Wei S, Huang G, Zhang X, Zhu S, Zhang H, Sun F, Wang X, Liang J, Wang J, He Q,
Huang L, Wang J, Cui J, Song G, Wang K, Xu X, Yu JZ, Zhu Y, Yu S (2015a) Genome
sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into
genome evolution. Nat Biotechnol 33(5):524–530
Li Z, Baniaga AE, Sessa EB, Scascitelli M, Graham SW, Rieseberg LH, Barker MS (2015b) Early
genome duplications in conifers and other seed plants. Sci Adv 1(10):e1501084
Liu C, Weigel D (2015) Chromatin in 3D: progress and prospects for plants. Genome Biol 16:170
Liu MJ, Zhao J, Cai QL, Liu GC, Wang JR, Zhao ZH, Liu P, Dai L, Yan G, Wang WJ, Li XS,
Chen Y, Sun YD, Liu ZG, Lin MJ, Xiao J, Chen YY, Li XF, Wu B, Ma Y, Jian JB, Yang W,
Yuan Z, Sun XC, Wei YL, Yu LL, Zhang C, Liao SG, He RJ, Guang XM, Wang Z, Zhang YY,
Luo LH (2014) The complex jujube genome provides insights into fruit tree biology. Nat
Commun 5:5315
Love RR, Weisenfeld NI, Jaffe DB, Besansky NJ, Neafsey DE (2016) Evaluation of DISCOVAR
de novo using a mosquito sample for cost-effective short-read genome assembly. BMC Genomics 17:187
Lowry DB, Purmal CT, Juenger TE (2013) A population genetic transect of Panicum hallii
(Poaceae). Am J Bot 100(3):592–601
Manda P, Freeman MG, Bridges SM, Jankun-Kelly TJ, Nanduri B, McCarthy FM, Burgess SC
(2010) GOModeler – a tool for hypothesis-testing of functional genomics datasets. BMC
Bioinformatics 11(Suppl 6):S29
Mankertz P (2008) Molecular biology of porcine circoviruses. In: Animal viruses: molecular
biology. Academic Press, Caister, pp 355–374
Marcais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A (2018) MUMmer4: a fast
and versatile genome alignment system. PLoS Comput Biol 14(1):e1005944
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS,
Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S,
Sequencing Plant Genomes
183