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Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, Baldwin A, Bates K, Bhattacharyya
S, Bower L, Browne P, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Hoad G,
Kanz C, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, Lorenc D, McWilliam H, Mukherjee
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analysis and sequence assembly. Nat Biotechnol 30(8):771–776
182
D. G. Peterson and M. Arick
system. Nat Methods 5. https://doi.org/10.1038/nmeth.f.1212
Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS,
Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR,
Springer NM, Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe
RK, Hastie A, Rank DR, Ware D (2017) Improved maize reference genome with singlemolecule technologies. Nature 546(7659):524–527
Kagale S, Koh C, Nixon J, Bollina V, Clarke WE, Tuteja R, Spillane C, Robinson SJ, Links MG,
Clarke C, Higgins EE, Huebert T, Sharpe AG, Parkin IA (2014) The emerging biofuel crop
Camelina sativa retains a highly undifferentiated hexaploid genome structure. Nat Commun 5:3706
Kang YJ, Kim SK, Kim MY, Lestari P, Kim KH, Ha BK, Jun TH, Hwang WJ, Lee T, Lee J, Shim S,
Yoon MY, Jang YE, Han KS, Taeprayoon P, Yoon N, Somta P, Tanya P, Kim KS, Gwag JG,
Moon JK, Lee YH, Park BS, Bombarely A, Doyle JJ, Jackson SA, Schafleitner R, Srinives P,
Varshney RK, Lee SH (2014) Genome sequence of mungbean and insights into evolution within
Vigna species. Nat Commun 5:5443
Karger BL, Guttman A (2009) DNA sequencing by capillary electrophoresis. Electrophoresis
30(Suppl 1):S196–S202
Katayama T (1995) Cytogenetical studies on the genus Oryza. XIV. Intergeneric hybridizations
between tetraploid Oryza species and diploid Leersia species. Jpn J Genet 70:47–55
Keeling PJ (2010) The endosymbiotic origin, diversification and fate of plastids. Philos Trans R Soc
Lond Ser B Biol Sci 365(1541):729–748
Kelly LJ, Renny-Byfield S, Pellicer J, Macas J, Novak P, Neumann P, Lysak MA, Day PD,
Berger M, Fay MF, Nichols RA, Leitch AR, Leitch IJ (2015) Analysis of the giant genomes
of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions
in genome size. New Phytol 208(2):596–607
Kent WJ (2002) BLAT – the BLAST-like alignment tool. Genome Res 12(4):656–664
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory
requirements. Nat Methods 12(4):357–360
Kircher M, Sawyer S, Meyer M (2012) Double indexing overcomes inaccuracies in multiplex
sequencing on the Illumina platform. Nucleic Acids Res 40(1):e3
Knuth DE (1984) Literate programming. Comput J 27(2):97–111
Kolesnikov AA, Gerasimov ES (2012) Diversity of mitochondrial genome organization.
Biochemistry (Mosc) 77(13):1424–1435
Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R,
Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV,
Vasudevan S, Wolf YI, Yin JJ, Natale DA (2004) A comprehensive evolutionary classification
of proteins encoded in complete eukaryotic genomes. Genome Biol 5(2):R7
Koornneef M, Meinke D (2010) The development of Arabidopsis as a model plant. Plant J
61(6):909–921
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM (2017) Canu: scalable and
accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res
27(5):722–736
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009)
Circos: an information aesthetic for comparative genomics. Genome Res 19(9):1639–1645
Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, Baldwin A, Bates K, Bhattacharyya
S, Bower L, Browne P, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Hoad G,
Kanz C, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, Lorenc D, McWilliam H, Mukherjee
G, Nardone F, Pastor MP, Plaister S, Sobhany S, Stoehr P, Vaughan R, Wu D, Zhu W, Apweiler
R (2007) EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res 35(Database issue):
D16–D20
Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, Deshpande P, Cao H, Nagarajan N,
Xiao M, Kwok PY (2012) Genome mapping on nanochannel arrays for structural variation
analysis and sequence assembly. Nat Biotechnol 30(8):771–776
182
D. G. Peterson and M. Arick