[1] | Jiao WB, Schneeberger K . The impact of third generation genomic technologies on plant genome assembly. Curr Opin Plant Biol, 2017,36:64-70. | [2] | Tang C, Yang M, Fang Y, Luo Y, Gao S, Xiao X, An Z, Zhou B, Zhang B, Tan X, Yeang HY, Qin Y, Yang J, Lin Q, Mei H, Montoro P, Long X, Qi J, Hua Y, He Z, Sun M, Li W, Zeng X, Cheng H, Liu Y, Yang J, Tian W, Zhuang N, Zeng R, Li D, He P, Li Z, Zou Z, Li S, Li C, Wang J, Wei D, Lai CQ, Luo W, Yu J, Hu S, Huang H . The rubber tree genome reveals new insights into rubber production and species adaptation. Nat Plants, 2016,2(6):16073. | [3] | Nowoshilow S, Schloissnig S, Fei JF, Dahl A, Pang AWC, Pippel M, Winkler S, Hastie AR, Young G, Roscito JG, Falcon F, Knapp D, Powell S, Cruz A, Cao H, Habermann B, Hiller M, Tanaka EM, Myers EW . The axolotl genome and the evolution of key tissue formation regulators. Nature, 2018,554(7690):50-55. | [4] | Wei C, Yang H, Wang S, Zhao J, Liu C, Gao L, Xia E, Lu Y, Tai Y, She G, Sun J, Cao H, Tong W, Gao Q, Li Y, Deng W, Jiang X, Wang W, Chen Q, Zhang S, Li H, Wu J, Wang P, Li P, Shi C, Zheng F, Jian J, Huang B, Shan D, Shi M, Fang C, Yue Y, Li F, Li D, Wei S, Han B, Jiang C, Yin Y, Xia T, Zhang Z, Bennetzen JL, Zhao S, Wan X . Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality. Proc Natl Acad Sci USA, 2018,115(18):E4151-E4158. | [5] | Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T . Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res, 2014,24(8):1384-1395. | [6] | 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 . Genome sequence of cultivated upland cotton ( Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol, 2015,33(5):524-530. | [7] | Sun F, Fan G, Hu Q, Zhou Y, Guan M, Tong C, Li J, Du D, Qi C, Jiang L, Liu W, Huang S, Chen W, Yu J, Mei D, Meng J, Zeng P, Shi J, Liu K, Wang X, Wang X, Long Y, Liang X, Hu Z, Huang G, Dong C, Zhang H, Li J, Zhang Y, Li L, Shi C, Wang J, Lee SM, Guan C, Xu X, Liu S, Liu X, Chalhoub B, Hua W, Wang H . The high-quality genome of Brassica napus cultivar ‘ZS11’ reveals the introgression history in semi-winter morphotype. Plant J, 2017,92(3):452-468. | [8] | Chen YC, Liu T, Yu CH, Chiang TY, Hwang CC . Effects of GC bias in next-generation-sequencing data on de novo genome assembly. PLoS One, 2013,8(4):e62856. | [9] | Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ . Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods, 2009,6(4):291-295. | [10] | Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Chan CX, Marriage TN, Bhattacharya D, Klein AS, Badis Y, Brodie J, Cao Y, Collen J, Dittami SM, Gachon CMM, Green BR, Karpowicz SJ, Kim JW, Kudahl UJ, Lin S, Michel G, Mittag M, Olson B, Pangilinan JL, Peng Y, Qiu H, Shu S, Singer JT, Smith AG, Sprecher BN, Wagner V, Wang W, Wang ZY, Yan J, Yarish C, Zauner- Riek S, Zhuang Y, Zou Y, Lindquist EA, Grimwood J, Barry KW, Rokhsar DS, Schmutz J, Stiller JW, Grossman AR, Prochnik SE . Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis( Bangiophyceae, Rhodophyta). Proc Natl Acad Sci USA, 2017,114(31):E6361-E6370. | [11] | Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, Maroon H, Thomas F, Aboobaker AA, Blaxter M . No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. Proc Natl Acad Sci USA, 2016,113(18):5053-5058. | [12] | Boothby TC, Tenlen JR, Smith FW, Wang JR, Patanella KA, Nishimura EO, Tintori SC, Li Q, Jones CD, Yandell M, Messina DN, Glasscock J, Goldstein B . Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc Natl Acad Sci USA, 2015,112(52):15976-15981. | [13] | Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL, SanMiguel P, Lakey N, Bedell J, Yuan Y, Budiman MA, Resnick A, Van Aken S, Utterback T, Riedmuller S, Williams M, Feldblyum T, Schubert K, Beachy R, Fraser CM, Quackenbush J. Enrichment of gene-coding sequences in maize by genome filtration. Science, 2003,302(5653):2118-2120. | [14] | Palmer LE, Rabinowicz PD O'Shaughnessy AL, Balija VS, Nascimento LU, Dike S, de la Bastide M, Martienssen RA, McCombie WR. Maize genome sequencing by methylation filtration. Science, 2003,302(5653):2115-2117. | [15] | George RD McVicker G, Diederich R, Ng SB, MacKenzie AP, Swanson WJ, Shendure J, Thomas JH. Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. Genome Res, 2011,21(10):1686-1694. | [16] | Potato Genome Sequencing C, Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti SK, Patil VU, Skryabin KG, Kuznetsov BB, Ravin NV, Kolganova TV, Beletsky AV, Mardanov AV, Di Genova A, Bolser DM, Martin DM, Li G, Yang Y, Kuang H, Hu Q, Xiong X, Bishop GJ, Sagredo B, Mejia N, Zagorski W, Gromadka R, Gawor J, Szczesny P, Huang S, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Zhang Y, Xie B, Du Y, Qu D, Bonierbale M, Ghislain M, Herrera Mdel R, Giuliano G, Pietrella M, Perrotta G, Facella P, O'Brien K, Feingold SE, Barreiro LE, Massa GA, Diambra L, Whitty BR, Vaillancourt B, Lin H, Massa AN, Geoffroy M, Lundback S, DellaPenna D, Buell CR, Sharma SK, Marshall DF, Waugh R, Bryan GJ, Destefanis M, Nagy I, Milbourne D, Thomson SJ, Fiers M, Jacobs JM, Nielsen KL, Sonderkaer M, Iovene M, Torres GA, Jiang J, Veilleux RE, Bachem CW, de Boer J, Borm T, Kloosterman B, van Eck H, Datema E, Hekkert B, Goverse A, van Ham RC, Visser RG . Genome sequence and analysis of the tuber crop potato. Nature, 2011,475(7355):189-195. | [17] | Yang H, Chen X, Wong WH . Completely phased genome sequencing through chromosome sorting. Proc Natl Acad Sci USA, 2011,108(1):12-17. | [18] | Fan HC, Wang J, Potanina A, Quake SR . Whole-genome molecular haplotyping of single cells. Nat Biotechnol, 2011,29(1):51-57. | [19] | Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E, Margulies EH . A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Res, 2010,20(2):249-256. | [20] | Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, Hekele A , DeRisi JL . The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing. PLoS One, 2008,3(10):e3495. | [21] | Hiatt JB, Patwardhan RP, Turner EH, Lee C, Shendure J . Parallel, tag-directed assembly of locally derived short sequence reads. Nat Methods, 2010,7(2):119-122. | [22] | Rhoads A, Au KF . PacBio sequencing and its applications. Genom Prot Bioinf, 2015,13(5):278-289. | [23] | Jain M, Olsen HE, Paten B, Akeson M . The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol, 2016,17(1):239. | [24] | Staňková H, Hastie AR, Chan S, Vrána J, Tulpová Z, Kubaláková M, Visendi P, Hayashi S, Luo M, Batley J, Edwards D, Doleel J, imková H . BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnol J, 2016,14(7):1523-1531. | [25] | Chen P, Jing X, Liao B, Zhu Y, Xu J, Liu R, Zhao Y, Li X . BioNano genome map resource for Oryza sativa ssp. japonica and indica and its application in rice genome sequence correction and gap filling. Mol Plant, 2017,10(6):895-898. | [26] | Belton JM McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods, 2012,58(3):268-276. | [27] | Paulsen J, Liyakat Ali TM, Collas P . Computational 3D genome modeling using Chrom3D. Nat Protoc, 2018,13(5):1137-1152. | [28] | Zerbino DR, Birney E . Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res, 2008,18(5):821-829. | [29] | Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G . Aggressive assembly of pyrosequencing reads with mates. Bioinformatics, 2008,24(24):2818-2824. | [30] | Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM . Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res, 2017,27(5):722-736. | [31] | Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB . High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA, 2011,108(4):1513-1518. | [32] | Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM . Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol, 2015,33(6):623-630. | [33] | Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol, 2012,19(5):455-477. | [34] | Ye C, Hill CM, Wu S, Ruan J, Ma ZS . DBG2OLC: efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies. Sci Rep, 2016,6:31900. | [35] | Zimin AV, Marcais G, Puiu D, Roberts M, Salzberg SL, Yorke JA . The MaSuRCA genome assembler. Bioinformatics, 2013,29(21):2669-2677. | [36] | Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marcais G, Puiu D, Roberts M Wegrzyn JL, de Jong PJ, Neale DB, Salzberg SL, Yorke JA, Langley CH. Sequencing and assembly of the 22-gb loblolly pine genome. Genetics, 2014,196(3):875-890. | [37] | Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marcais G, Yorke JA, Dvorak J, Salzberg SL . Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm. Genome Res, 2017,27(5):787-792. | [38] | Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu S-M, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam T-W, Wang J . SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience, 2012,1(1):18. | [39] | Marcais G, Yorke JA, Zimin A . QuorUM: an error corrector for illumina reads. PLoS One, 2015,10(6):e0130821. | [40] | Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL . Versatile and open software for comparing large genomes. Genome Biol, 2004,5(2):R12. | [41] | Li H . Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics, 2016,32(14):2103-2110. | [42] | Xiao CL, Chen Y, Xie SQ, Chen KN, Wang Y, Han Y, Luo F, Xie Z . MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nat Methods, 2017,14(11):1072-1074. | [43] | Schmidt MH-W, Vogel A, Denton A, Istace B Wormit A, van de Geest H, Bolger ME, Alseekh S, Mass J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury J-M, Fernie AR, Zamir D, Bolger AM, Usadel B. Reconstructing the gigabase plant genome of Solanum pennellii using nanopore sequencing. bioRxiv, 2017, doi: 10.1101/129148. | [44] | Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods, 2016,13(12):1050-1054. | [45] | Roach MJ, Schmidt SA, Borneman AR . Purge haplotigs: synteny reduction for third-gen diploid genome assemblies. bioRxiv, 2018, doi: 10.1101/286252. | [46] | de Lannoy CV, de Ridder D, Risse J . A sequencer coming of age: de novo genome assembly using MinION reads. bioRxiv, 2017, doi: 10.1101/142711. | [47] | Jones SJ, Haulena M, Taylor GA, Chan S, Bilobram S, Warren RL, Hammond SA, Mungall KL, Choo C, Kirk H, Pandoh P, Ally A, Dhalla N, Tam AKY, Troussard A, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Jones SJM. The genome of the northern sea otter ( Enhydra lutris kenyoni) .Genes ( Basel), 2017, 8(12): genes8120379. | [48] | Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, Wang JY, Lin YC, Xu Q, Chen LJ, Yoshida K, Fujiwara S, Wang ZW, Zhang YQ, Mitsuda N, Wang M, Liu GH, Pecoraro L, Huang HX, Xiao XJ, Lin M, Wu XY, Wu WL, Chen YY, Chang SB, Sakamoto S, Ohme-Takagi M, Yagi M, Zeng SJ, Shen CY, Yeh CM, Luo YB, Tsai WC Van de Peer Y, Liu ZJ. The Apostasia genome and the evolution of orchids. Nature, 2017,549(7672):379-383. | [49] | Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL . De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017,356(6333):92-95. | [50] | Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H, Chen NJ, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen M, Wang G, Xie L, Sovero V, Sha S, Huang W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull RE, Bennetzen JL, Wang J, Zhang S . The genome of the pear ( Pyrus bretschneideri Rehd.). Genome Res, 2013,23(2):396-408. | [51] | Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W . Scaffolding pre-assembled contigs using SSPACE. Bioinformatics, 2011,27(4):578-579. | [52] | Delcher AL, Phillippy A, Carlton J, Salzberg SL . Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res, 2002,30(11):2478-2483. | [53] | Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ . Basic local alignment search tool. J Mol Biol, 1990,215(3):403-410. | [54] | Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X, Qi H, Xiong Z, Que H, Xie Y, Holland PW, Paps J, Zhu Y, Wu F, Chen Y, Wang J, Peng C, Meng J, Yang L, Liu J, Wen B, Zhang N, Huang Z, Zhu Q, Feng Y, Mount A, Hedgecock D, Xu Z, Liu Y, Domazet-Loso T, Du Y, Sun X, Zhang S, Liu B, Cheng P, Jiang X, Li J, Fan D, Wang W, Fu W, Wang T, Wang B, Zhang J, Peng Z, Li Y, Li N, Wang J, Chen M, He Y, Tan F, Song X, Zheng Q, Huang R, Yang H, Du X, Chen L, Yang M, Gaffney PM, Wang S, Luo L, She Z, Ming Y, Huang W, Zhang S, Huang B, Zhang Y, Qu T, Ni P, Miao G, Wang J, Wang Q, Steinberg CE, Wang H, Li N, Qian L, Zhang G, Li Y, Yang H, Liu X, Wang J, Yin Y, Wang J . The oyster genome reveals stress adaptation and complexity of shell formation. Nature, 2012,490(7418):49-54. | [55] | Wuyun TN, Wang L, Liu H, Wang X, Zhang L, Bennetzen JL, Li T, Yang L, Liu P, Du L, Wang L, Huang M, Qing J, Zhu L, Bao W, Li H, Du Q, Zhu J, Yang H, Yang S, Liu H, Yue H, Hu J, Yu G, Tian Y, Liang F, Hu J, Wang D, Gao R, Li D, Du H . The hardy rubber tree genome provides insights into the evolution of polyisoprene biosynthesis. Mol Plant, 2018,11(3):429-442. | [56] | English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA . Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One, 2012,7(11):e47768. | [57] | Appels R, Eversole K, Feuillet C, Keller B, Rogers J, Stein N, Pozniak CJ, Stein N, Choulet F, Distelfeld A, Eversole K, Poland J, Rogers J, Ronen G, Sharpe AG, Pozniak C, Ronen G, Stein N, Barad O, Baruch K, Choulet F, Keeble-Gagnère G, Mascher M, Sharpe AG, Ben-Zvi G, Josselin A-A, Stein N, Mascher M, Himmelbach A, Choulet F, Keeble-Gagnère G, Mascher M, Rogers J, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Josselin A-A, Koh C, Muehlbauer G, Pasam RK, Paux E, Pozniak CJ, Rigault P, Sharpe AG, Tibbits J, Tiwari V, Choulet F, Keeble-Gagnère G, Mascher M, Josselin A-A, Rogers J, Spannagl M, Choulet F, Lang D, Gundlach H, Haberer G, Keeble-Gagnère G, Mayer KFX, Ormanbekova D, Paux E, Prade V, Šimková H, Wicker T, Choulet F, Spannagl M, Swarbreck D, Rimbert H, Felder M, Guilhot N, Gundlach H, Haberer G, Kaithakottil G, Keilwagen J, Lang D, Leroy P, Lux T, Mayer KFX, Twardziok S, Venturini L, Appels R, Rimbert H, Choulet F, Juhász A, Keeble-Gagnère G, Choulet F, Spannagl M, Lang D, Abrouk M, Haberer G, Keeble-Gagnère G, Mayer KFX, Wicker T, Choulet F, Wicker T, Gundlach H, Lang D, Spannagl M, Lang D, Spannagl M, Appels R, Fischer I, Uauy C, Borrill P, Ramirez-Gonzalez RH, Appels R, Arnaud D, Chalabi S, Chalhoub B, Choulet F, Cory A, Datla R, Davey MW, Hayden M, Jacobs J, Lang D, Robinson SJ, Spannagl M, Steuernagel B, Tibbits J, Tiwari V, van Ex F, Wulff BBH, Pozniak CJ, Robinson SJ, Sharpe AG, Cory A, Benhamed M, Paux E, Bendahmane A, Concia L, Latrasse D, Rogers J, Jacobs J, Alaux M, Appels R, Bartoš J, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, Letellier T, Olsen O-A, Šimková H, Singh K, Valárik M, van der Vossen E, Vautrin S, Weining S, Korol A, Frenkel Z, Fahima T, Glikson V, Raats D, Rogers J, Tiwari V, Gill B, Paux E, Poland J, Doležel J, Číhalíková J, Šimková H, Toegelová H, Vrána J, Sourdille P, Darrier B, Appels R, Spannagl M, Lang D, Fischer I, Ormanbekova D, Prade V, Barabaschi D, Cattivelli L, Hernandez P, Galvez S, Budak H, Steuernagel B, Jones JDG, Witek K, Wulff BBH, Yu G, Small I, Melonek J, Zhou R, Juhász A, Belova T, Appels R, Olsen O-A, Kanyuka K, King R, Nilsen K, Walkowiak S, Pozniak CJ, Cuthbert R, Datla R, Knox R, Wiebe K, Xiang D, Rohde A, Golds T, Doležel J, Čížková J, Tibbits J, Budak H, Akpinar BA, Biyiklioglu S, Muehlbauer G, Poland J, Gao L, Gutierrez-Gonzalez J, N’Daiye A, Doležel J, Šimková H, Číhalíková J, Kubaláková M, Šafář J, Vrána J, Berges H, Bellec A, Vautrin S, Alaux M, Alfama F, Adam-Blondon A-F, Flores R, Guerche C, Letellier T, Loaec M, Quesneville H, Pozniak CJ, Sharpe AG, Walkowiak S, Budak H, Condie J, Ens J, Koh C, Maclachlan R, Tan Y, Wicker T, Choulet F, Paux E, Alberti A, Aury J-M, Balfourier F, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P, Gill B, Kaur G, Luo M, Sehgal S, Singh K, Chhuneja P, Gupta OP, Jindal S, Kaur P, Malik P, Sharma P, Yadav B, Singh NK, Khurana J, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar RS, Rogers J, Jacobs J, Alaux M, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, van der Vossen E, Vautrin S, Gill B, Kaur G, Luo M, Sehgal S, Bartoš J, Holušová K, Plíhal O, Clark MD, Heavens D, Kettleborough G, Wright J, Valárik M, Abrouk M, Balcárková B, Holušová K, Hu Y, Luo M, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu J, Appels R, Hayden M, Keeble-Gagnère G, Rigault P, Tibbits J, Olsen O-A, Belova T, Cattonaro F, Jiumeng M, Kugler K, Mayer KFX, Pfeifer M, Sandve S, Xun X, Zhan B, Šimková H, Abrouk M, Batley J, Bayer PE, Edwards D, Hayashi S, Toegelová H, Tulpová Z, Visendi P, Weining S, Cui L, Du X, Feng K, Nie X, Tong W, Wang L, Borrill P, Gundlach H, Galvez S, Kaithakottil G, Lang D, Lux T, Mascher M, Ormanbekova D, Prade V, Ramirez-Gonzalez RH, Spannagl M, Stein N, Uauy C, Venturini L, Stein N, Appels R, Eversole K, Rogers J, Borrill P, Cattivelli L, Choulet F, Hernandez P, Kanyuka K, Lang D, Mascher M, Nilsen K, Paux E, Pozniak CJ, Ramirez-Gonzalez RH, Šimková H, Small I, Spannagl M, Swarbreck D, Uauy C. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 2018, 361(6403): science. aar7191. | [58] | Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Goméz JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN Sinha N, van Ham RCHJ, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JKC, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR. The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics, 2014,46:1034. | [59] | Schmidt MH, Vogel A, Denton AK, Istace B Wormit A, van de Geest H, Bolger ME, Alseekh S, Mass J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B. De novo assembly of a new Solanum pennellii accession using nanopore sequencing. Plant Cell, 2017,29(10):2336-2348. | [60] | Geng J, Chiu CH, Tang P, Chen Y, Shieh HR, Hu S, Chen YY . Complete genome and transcriptomes of Streptococcus parasanguinis FW213: phylogenic relations and potential virulence mechanisms. PLoS One, 2012,7(4):e34769. | [61] | Al-Mssallem IS, Hu S, Zhang X, Lin Q, Liu W, Tan J, Yu X, Liu J, Pan L, Zhang T, Yin Y, Xin C, Wu H, Zhang G, Ba Abdullah MM, Huang D, Fang Y, Alnakhli YO, Jia S, Yin A, Alhuzimi EM, Alsaihati BA, Al-Owayyed SA, Zhao D, Zhang S, Al-Otaibi NA, Sun G, Majrashi MA, Li F, Tala, Wang J Yun Q, Alnassar NA, Wang L, Yang M, Al-Jelaify RF, Liu K, Gao S, Chen K, Alkhaldi SR, Liu G, Zhang M, Guo H, Yu J. Genome sequence of the date palm Phoenix dactylifera L. Nat Commun, 2013,4:2274. | [62] | Wang S, Wang S, Luo Y, Xiao L, Luo X, Gao S, Dou Y, Zhang H, Guo A, Meng Q, Hou J, Zhang B, Zhang S, Yang M, Meng X, Mei H, Li H, He Z, Zhu X, Tan X, Zhu XQ, Yu J, Cai J, Zhu G, Hu S, Cai X . Comparative genomics reveals adaptive evolution of Asian tapeworm in switching to a new intermediate host. Nat Commun, 2016,7:12845. |
|