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variant detection and genome assembly improvement. PLoS One 9(11):e112963
Wan T, Liu ZM, Li LF, Leitch AR, Leitch IJ, Lohaus R, Liu ZJ, Xin HP, Gong YB, Liu Y, Wang
WC, Chen LY, Yang Y, Kelly LJ, Yang J, Huang JL, Li Z, Liu P, Zhang L, Liu HM, Wang H,
Deng SH, Liu M, Li J, Ma L, Liu Y, Lei Y, Xu W, Wu LQ, Liu F, Ma Q, Yu XR, Jiang Z, Zhang
GQ, Li SH, Li RQ, Zhang SZ, Wang QF, Van de Peer Y, Zhang JB, Wang XM (2018) A
genome for gnetophytes and early evolution of seed plants. Nat Plants 4(2):82–89
Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S,
Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B,
Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C,
Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F,
190
D. G. Peterson and M. Arick
Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo MC, Thudi M, Gowda CL, Singh
NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel J, Bansal KC, Xu X, Edwards D,
Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J, Cook DR (2013) Draft
genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat
Biotechnol 31(3):240–246
Varshney RK, Shi C, Thudi M, Mariac C, Wallace J, Qi P, Zhang H, Zhao Y, Wang X, Rathore A,
Srivastava RK, Chitikineni A, Fan G, Bajaj P, Punnuri S, Gupta SK, Wang H, Jiang Y,
Couderc M, Katta M, Paudel DR, Mungra KD, Chen W, Harris-Shultz KR, Garg V, Desai N,
Doddamani D, Kane NA, Conner JA, Ghatak A, Chaturvedi P, Subramaniam S, Yadav OP,
Berthouly-Salazar C, Hamidou F, Wang J, Liang X, Clotault J, Upadhyaya HD, Cubry P,
Rhone B, Gueye MC, Sunkar R, Dupuy C, Sparvoli F, Cheng S, Mahala RS, Singh B, Yadav
RS, Lyons E, Datta SK, Hash CT, Devos KM, Buckler E, Bennetzen JL, Paterson AH,
Ozias-Akins P, Grando S, Wang J, Mohapatra T, Weckwerth W, Reif JC, Liu X,
Vigouroux Y, Xu X (2017) Pearl millet genome sequence provides a resource to improve
agronomic traits in arid environments. Nat Biotechnol 35(10):969–976
Vaser R, Sovic I, Nagarajan N, Sikic M (2017) Fast and accurate de novo genome assembly from
long uncorrected reads. Genome Res 27(5):737–746
Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar
SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G,
Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G,
Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E,
Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J,
Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D,
Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A,
Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P,
Lespinasse Y, Allan AC, Bus V, Chagne D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA,
Proost S, Rouze P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner
RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R (2010) The
genome of the domesticated apple (Malus x domestica Borkh.) Nat Genet 42(10):833–839
Vlasova A, Capella-Gutierrez S, Rendon-Anaya M, Hernandez-Onate M, Minoche AE, Erb I,
Camara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ Jr,
Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gomez-Garrido J, Aguilar-Moron MA,
Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vazquez MP, Delgado-Salinas A,
Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, Garcia JL, Alioto T, Sanchez F,
Himmelbauer H, Santalla M, Notredame C, Gabaldon T, Herrera-Estrella A, Guigo R (2016)
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene
duplications in establishing tissue and temporal specialization of genes. Genome Biol 17:32
Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, Schatz MC (2017)
GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33
(14):2202–2204
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q,
Wortman J, Young SK, Earl AM (2014) Pilon: an integrated tool for comprehensive microbial
variant detection and genome assembly improvement. PLoS One 9(11):e112963
Wan T, Liu ZM, Li LF, Leitch AR, Leitch IJ, Lohaus R, Liu ZJ, Xin HP, Gong YB, Liu Y, Wang
WC, Chen LY, Yang Y, Kelly LJ, Yang J, Huang JL, Li Z, Liu P, Zhang L, Liu HM, Wang H,
Deng SH, Liu M, Li J, Ma L, Liu Y, Lei Y, Xu W, Wu LQ, Liu F, Ma Q, Yu XR, Jiang Z, Zhang
GQ, Li SH, Li RQ, Zhang SZ, Wang QF, Van de Peer Y, Zhang JB, Wang XM (2018) A
genome for gnetophytes and early evolution of seed plants. Nat Plants 4(2):82–89
Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S,
Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B,
Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C,
Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F,
190
D. G. Peterson and M. Arick