Smith LM, Sanders JZ, Kaiser RJ, Hughes P, Dodd C, Connell CR, Heiner C, Kent SBH, Hood LE
(1986) Fluorescence detection in automated DNA sequence analysis. Nature 321:674
Smith SA, Beaulieu JM, Donoghue MJ (2009) Mega-phylogeny approach for comparative biology:
an alternative to supertree and supermatrix approaches. BMC Evol Biol 9:37
Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006) Automatic annotation of eukaryotic genes,
pseudogenes and promoters. Genome Biol 7(Suppl 1):S10.11–S10.12
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG,
Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P,
Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E (2002) The Bioperl toolkit: perl
modules for the life sciences. Genome Res 12(10):1611–1618
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with
thousands of taxa and mixed models. Bioinformatics 22(21):2688–2690
Stanke M, Steinkamp R, Waack S, Morgenstern B (2004) AUGUSTUS: a web server for gene
finding in eukaryotes. Nucleic Acids Res 32(Web Server issue):W309–W312
Supek F, Bosnjak M, Skunca N, Smuc T (2011) REVIGO summarizes and visualizes long lists of
gene ontology terms. PLoS One 6(7):e21800
Swift H (1950) The constancy of desoxyribose nucleic acid in plant nuclei. Proc Natl Acad Sci
U S A 36(11):643–654
Thrash A, Arick M 2nd, Peterson DG (2018) Quack: a quality assurance tool for high throughput
sequence data. Anal Biochem 548:38–43
Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy
fruit evolution. Nature 485(7400):635–641
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL,
Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments
with TopHat and Cufflinks. Nat Protoc 7(3):562–578
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S,
Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D,
Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen
GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J,
Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S,
Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L,
Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, IslamFaridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J,
Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple
JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C,
Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J,
Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B,
Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K,
Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (2006)
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313
(5793):1596–1604
van den Berg BH, Konieczka JH, McCarthy FM, Burgess SC (2009) ArrayIDer: automated
structural re-annotation pipeline for DNA microarrays. BMC Bioinformatics 10:30
van Regenmortel MH, Mahy BW (2004) Emerging issues in virus taxonomy. Emerg Infect Dis
10(1):8–13
Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MT, Azam S,
Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV, Wu W,
Upadhyaya HD, Yang SP, Shah T, Saxena KB, Michael T, McCombie WR, Yang B,
Zhang G, Yang H, Wang J, Spillane C, Cook DR, May GD, Xu X, Jackson SA (2011) Draft
genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor
farmers. Nat Biotechnol 30(1):83–89
Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD,
Tar'an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM,
Sequencing Plant Genomes
189
(1986) Fluorescence detection in automated DNA sequence analysis. Nature 321:674
Smith SA, Beaulieu JM, Donoghue MJ (2009) Mega-phylogeny approach for comparative biology:
an alternative to supertree and supermatrix approaches. BMC Evol Biol 9:37
Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006) Automatic annotation of eukaryotic genes,
pseudogenes and promoters. Genome Biol 7(Suppl 1):S10.11–S10.12
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG,
Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P,
Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E (2002) The Bioperl toolkit: perl
modules for the life sciences. Genome Res 12(10):1611–1618
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with
thousands of taxa and mixed models. Bioinformatics 22(21):2688–2690
Stanke M, Steinkamp R, Waack S, Morgenstern B (2004) AUGUSTUS: a web server for gene
finding in eukaryotes. Nucleic Acids Res 32(Web Server issue):W309–W312
Supek F, Bosnjak M, Skunca N, Smuc T (2011) REVIGO summarizes and visualizes long lists of
gene ontology terms. PLoS One 6(7):e21800
Swift H (1950) The constancy of desoxyribose nucleic acid in plant nuclei. Proc Natl Acad Sci
U S A 36(11):643–654
Thrash A, Arick M 2nd, Peterson DG (2018) Quack: a quality assurance tool for high throughput
sequence data. Anal Biochem 548:38–43
Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy
fruit evolution. Nature 485(7400):635–641
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL,
Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments
with TopHat and Cufflinks. Nat Protoc 7(3):562–578
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S,
Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D,
Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen
GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J,
Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S,
Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L,
Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, IslamFaridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J,
Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple
JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C,
Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J,
Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B,
Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K,
Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (2006)
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313
(5793):1596–1604
van den Berg BH, Konieczka JH, McCarthy FM, Burgess SC (2009) ArrayIDer: automated
structural re-annotation pipeline for DNA microarrays. BMC Bioinformatics 10:30
van Regenmortel MH, Mahy BW (2004) Emerging issues in virus taxonomy. Emerg Infect Dis
10(1):8–13
Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MT, Azam S,
Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV, Wu W,
Upadhyaya HD, Yang SP, Shah T, Saxena KB, Michael T, McCombie WR, Yang B,
Zhang G, Yang H, Wang J, Spillane C, Cook DR, May GD, Xu X, Jackson SA (2011) Draft
genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor
farmers. Nat Biotechnol 30(1):83–89
Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD,
Tar'an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM,
Sequencing Plant Genomes
189