Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S: Genetic structure and diversity in Oryza sativa L. Genetics. 2005, 169: 1631-1638. 10.1534/genetics.104.035642.
Article
PubMed
CAS
PubMed Central
Google Scholar
Huang X, Kurata N, Wei X, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, et al: A map of rice genome variation reveals the origin of cultivated rice. Nature. 2012, 490: 497-501. 10.1038/nature11532.
Article
PubMed
CAS
Google Scholar
Zhao KY, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD, McCouch SR: Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. Plos One. 2010, 5: e10780-10.1371/journal.pone.0010780.
Article
PubMed
PubMed Central
Google Scholar
Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, Zhao K, Brisbin A, Parker HG, vonHoldt BM, Cargill M, Auton A, Reynolds A, Elkahloun AG, Castelhano M, Mosher DS, Sutter NB, Johnson GS, Novembre J, Hubisz MJ, Siepel A, Wayne RK, Bustamante CD, Ostrander EA: A simple genetic architecture underlies morphological variation in dogs. PLoS Biol. 2010, 8: e1000451-10.1371/journal.pbio.1000451.
Article
PubMed
PubMed Central
Google Scholar
Weir BS, Cardon LR, Anderson AD, Nielsen DM, Hill WG: Measures of human population structure show heterogeneity among genomic regions. Genome Res. 2005, 15: 1468-1476. 10.1101/gr.4398405.
Article
PubMed
CAS
PubMed Central
Google Scholar
Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez GJ, Buckler E, Doebley J: A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci U S A. 2002, 99: 6080-6084. 10.1073/pnas.052125199.
Article
PubMed
CAS
PubMed Central
Google Scholar
Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR: Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun. 2011, 2: 467-10.1038/ncomms1467.
Article
PubMed
PubMed Central
Google Scholar
Ma J, Bennetzen JL: Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A. 2004, 101: 12404-12410. 10.1073/pnas.0403715101.
Article
PubMed
CAS
PubMed Central
Google Scholar
Cheng CY, Motohashi R, Tsuchimoto S, Fukuta Y, Ohtsubo H, Ohtsubo E: Polyphyletic origin of cultivated rice: Based on the interspersion pattern of SINEs. Mol Biol Evol. 2003, 20: 67-75. 10.1093/molbev/msg004.
Article
PubMed
CAS
Google Scholar
Kovach MJ, Sweeney MT, McCouch SR: New insights into the history of rice domestication. Trends Genet. 2007, 23: 578-587. 10.1016/j.tig.2007.08.012.
Article
PubMed
CAS
Google Scholar
Roy SC: A preliminary classification of the wild rices of the Central Province and Berar. Agric J India. 1921, 16: 365-380.
Google Scholar
Second G: Origin of the genic diversity of cultivated rice (Oryza-spp) - study of the polymorphism scored at 40 isoenzyme loci. Jpn J Genet. 1982, 57: 25-57. 10.1266/jjg.57.25.
Article
Google Scholar
Second G: Molecular markers in rice systematics and the evaluation of genetic resources. Biotechnol Agric For. 1991, 14: 468-494.
Google Scholar
Ding J, Araki H, Wang Q, Zhang P, Yang S, Chen JQ, Tian D: Highly asymmetric rice genomes. BMC Genomics. 2007, 8: 154-10.1186/1471-2164-8-154.
Article
PubMed
PubMed Central
Google Scholar
Liu XH, Lu TT, Yu SL, Li Y, Huang YC, Huang T, Zhang L, Zhu JJ, Zhao Q, Fan DL, Mu J, Shangguan YY, Feng Q, Guan JP, Ying K, Zhang Y, Lin ZX, Sun ZX, Qian Q, Lu YP, Han B: A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies. Plant Mol Biol. 2007, 65: 403-415. 10.1007/s11103-007-9174-7.
Article
PubMed
CAS
Google Scholar
Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH: An SNP resource for rice genetics and breeding based on subspecies Indica and Japonica genome alignments. Genome Res. 2004, 14: 1812-1819. 10.1101/gr.2479404.
Article
PubMed
CAS
PubMed Central
Google Scholar
Huang XH, Lu GJ, Zhao Q, Liu XH, Han B: Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice. Plant Physiol. 2008, 148: 25-40. 10.1104/pp.108.121491.
Article
PubMed
CAS
PubMed Central
Google Scholar
Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M: Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet. 2008, 40: 1023-1028. 10.1038/ng.169.
Article
PubMed
CAS
Google Scholar
Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, Padhukasahasram B, Bustamante C, Yoshimura A, Doi K, McCouch S: Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genet. 2007, 3: e133-10.1371/journal.pgen.0030133.
Article
Google Scholar
Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, Padhukasahasram B, Bustamante C, Yoshimura A, Doi K, McCouch S: Evolutionary history of GS3, a gene conferring grain length in rice. Genetics. 2009, 182: 1323-1334. 10.1534/genetics.109.103002.
Article
PubMed
CAS
PubMed Central
Google Scholar
Tan L, Li X, Liu F, Sun X, Li C, Zhu Z, Fu Y, Cai H, Wang X, Xie D, Sun C: Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet. 2008, 40: 1360-1364. 10.1038/ng.197.
Article
PubMed
CAS
Google Scholar
Harushima Y, Nakagahra M, Yano M, Sasaki T, Kurata N: Diverse variation of reproductive barriers in three intraspecific rice crosses. Genetics. 2002, 160: 313-322.
PubMed
PubMed Central
Google Scholar
Lin SY, Ikehashi H, Yanagihara S, Kawashima A: Segregation distortion via male gametes in hybrids between Indica and Japonica or wide-compatibility varieties of rice (Oryza-sativa L). Theor Appl Genet. 1992, 84: 812-818.
PubMed
CAS
Google Scholar
Oka HI: Functions and genetic base of reproductive barriers. Origin of Cultivated Rice. 1988, Tokyo/Elsevier Science/Japan Scientific Societies Press, Amsterdam, 181-209.
Google Scholar
Sano Y: Constraints in using wild relatives in breeding: lack of basic knowledge on crop gene pools. Int Crop Sci. 1993, 1: 437-443.
Google Scholar
Ammiraju JSS, Song XA, Luo MZ, Sisneros N, Angelova A, Kudrna D, Kim H, Yu Y, Goicoechea JL, Lorieux M, Kurata N, Brar D, Ware D, Jackson S, Wing RA: The Oryza BAC resource: a genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives. Breeding Sci. 2010, 60: 536-543. 10.1270/jsbbs.60.536.
Article
Google Scholar
International Rice Genome Sequencing Project: The map-based sequence of the rice genome. Nature. 2005, 436: 793-800. 10.1038/nature03895.
Article
Google Scholar
Gao ZY, Zhao SC, He WM, Guo LB, Peng YL, Wang JJ, Guo XS, Zhang XM, Rao YC, Zhang C, Dong GJ, Zheng FY, Lu CX, Hu J, Zhou Q, Liu HJ, Wu HY, Xu J, Ni PX, Zeng DL, Liu DH, Tian P, Gong LH, Ye C, Zhang GH, Wang J, Tian FK, Xue DW, Liao Y, Zhu L, et al: Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences. Proc Natl Acad Sci U S A. 2013, 110: 14492-14497. 10.1073/pnas.1306579110.
Article
PubMed
CAS
PubMed Central
Google Scholar
Yu J, Wang J, Lin W, Li SG, Li H, Zhou J, Ni PX, Dong W, Hu SN, Zeng CQ, Zhang JG, Zhang Y, Li RQ, Xu ZY, Li ST, Li XR, Zheng HK, Cong LJ, Lin L, Yin JN, Geng JN, Li GY, Shi JP, Liu J, Lv H, Li J, Wang J, Deng YJ, Ran LH, Shi XL, et al: The Genomes of Oryza sativa: A history of duplications. PLoS Biol. 2005, 3: 266-281. 10.1371/journal.pbio.0030038.
Article
CAS
Google Scholar
Huang XH, Wei XH, Sang T, Zhao QA, Feng Q, Zhao Y, Li CY, Zhu CR, Lu TT, Zhang ZW, Li M, Fan DL, Guo YL, Wang A, Wang L, Deng LW, Li WJ, Lu YQ, Weng QJ, Liu KY, Huang T, Zhou TY, Jing YF, Li W, Lin Z, Buckler ES, Qian QA, Zhang QF, Li JY, Han B: Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010, 42: 961–U76-10.1038/ng.695.
Article
Google Scholar
McCouch SR, Zhao KY, Wright M, Tung CW, Ebana K, Thomson M, Reynolds A, Wang D, DeClerck G, Ali ML, McClung A, Eizenga G, Bustamante C: Development of genome-wide SNP assays for rice. Breeding Sci. 2010, 60: 524-535. 10.1270/jsbbs.60.524.
Article
Google Scholar
McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Ratsch G, Buell CR, Leung H, Leach JE: Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A. 2009, 106: 12273-12278. 10.1073/pnas.0900992106.
Article
PubMed
CAS
PubMed Central
Google Scholar
Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ: Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature. 2006, 442: 705-708. 10.1038/nature04920.
Article
PubMed
CAS
Google Scholar
Huang XH, Feng Q, Qian Q, Zhao Q, Wang L, Wang AH, Guan JP, Fan DL, Weng QJ, Huang T, Dong GJ, Sang T, Han B: High-throughput genotyping by whole-genome resequencing. Genome Res. 2009, 19: 1068-1076. 10.1101/gr.089516.108.
Article
PubMed
CAS
PubMed Central
Google Scholar
Xu X, Liu X, Ge S, Jensen JD, Hu FY, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, Li JX, He WM, Zhang GJ, Zheng XM, Zhang FM, Li YR, Yu C, Kristiansen K, Zhang XQ, Wang J, Wright M, McCouch S, Nielsen R, Wang J, Wang W: Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol. 2012, 30: 105–U57-
Google Scholar
Li JY, Wang J, Zeigler RS: The 3,000 rice genomes project: new opportunities and challenges for future rice research. Gigascience. 2014, 3: 8-10.1186/2047-217X-3-8.
Article
PubMed
PubMed Central
Google Scholar
Han B, Xue YB: Genome-wide intraspecific DNA-sequence variations in rice. Curr Opin Plant Biol. 2003, 6: 134-138. 10.1016/S1369-5266(03)00004-9.
Article
PubMed
CAS
Google Scholar
Zuccolo A, Sebastian A, Talag J, Yu Y, Kim H, Collura K, Kudrna D, Wing RA: Transposable element distribution, abundance and role in genome size variation in the genus Oryza. BMC Evol Biol. 2007, 7: 152-10.1186/1471-2148-7-152.
Article
PubMed
PubMed Central
Google Scholar
Yu P, Wang CH, Xu Q, Feng Y, Yuan XP, Yu HY, Wang YP, Tang SX, Wei XH: Detection of copy number variations in rice using array-based comparative genomic hybridization. BMC Genomics. 2011, 12: 372-10.1186/1471-2164-12-372.
Article
PubMed
CAS
PubMed Central
Google Scholar
Famoso AN, Zhao K, Clark RT, Tung CW, Wright MH, Bustamante C, Kochian LV, McCouch SR: Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genet. 2011, 7: e1002221-10.1371/journal.pgen.1002221.
Article
PubMed
CAS
PubMed Central
Google Scholar
Gamuyao R, Chin JH, Pariasca-Tanaka J, Pesaresi P, Catausan S, Dalid C, Slamet-Loedin I, Tecson-Mendoza EM, Wissuwa M, Heuer S: The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature. 2012, 488: 535-10.1038/nature11346.
Article
PubMed
CAS
Google Scholar
Uga Y, Sugimoto K, Ogawa S, Rane J, Ishitani M, Hara N, Kitomi Y, Inukai Y, Ono K, Kanno N, Inoue H, Takehisa H, Motoyama R, Nagamura Y, Wu J, Matsumoto T, Takai T, Okuno K, Yano M: Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nat Genet. 2013, 45: 1097-1102. 10.1038/ng.2725.
Article
PubMed
CAS
Google Scholar
Liakat Ali M, McClung AM, Jia MH, Kimball JA, McCouch SR, Susan R, Georgia CE: A rice diversity panel evaluated for genetic and agro-morphological diversity between subpopulations and its geographic distribution. Crop Sci. 2011, 51: 2021-2035. 10.2135/cropsci2010.11.0641.
Article
Google Scholar
Garris AJ, McCouch SR, Kresovich S: Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics. 2003, 165: 759-769.
PubMed
PubMed Central
Google Scholar
Hattori Y, Nagai K, Furukawa S, Song XJ, Kawano R, Sakakibara H, Wu J, Matsumoto T, Yoshimura A, Kitano H, Matsuoka M, Mori H, Ashikari M: The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature. 2009, 460: 1026-1030. 10.1038/nature08258.
Article
PubMed
CAS
Google Scholar
Bernier J, Kumar A, Venuprasad R, Spaner D, Verulkar S, Mandal N, Sinha P, Peeraju P, Dongre P, Mahto RN, Atlin G: Characterization of the effect of a QTL for drought resistance in rice, qtl12.1, over a range of environments in the Philippines and eastern India. Euphytica. 2009, 166: 207-217. 10.1007/s10681-008-9826-y.
Article
Google Scholar
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 U S A. 2011, 108: 1513-1518. 10.1073/pnas.1017351108.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, et al: Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013, 2: 10-10.1186/2047-217X-2-10.
Article
PubMed
PubMed Central
Google Scholar
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S: Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011, 21: 2224-2241. 10.1101/gr.126599.111.
Article
PubMed
CAS
PubMed Central
Google Scholar
Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marcais G, Pop M, Yorke JA: GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res. 2012, 22: 557-567. 10.1101/gr.131383.111.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T: Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice. 2013, 6: 4-10.1186/1939-8433-6-4.
Article
PubMed
Google Scholar
Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ, Ware D, Shiu SH, Childs KL, Sun Y, Jiang N, Yandell M: MAKER-P: A tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol. 2014, 164: 513-524. 10.1104/pp.113.230144.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lipman DJ, Souvorov A, Koonin EV, Panchenko AR, Tatusova TA: The relationship of protein conservation and sequence length. BMC Evol Biol. 2002, 2: 20-10.1186/1471-2148-2-20.
Article
PubMed
PubMed Central
Google Scholar
Capra JA, Pollard KS, Singh M: Novel genes exhibit distinct patterns of function acquisition and network integration. Genome Biol. 2010, 11: R127-10.1186/gb-2010-11-12-r127.
Article
PubMed
CAS
PubMed Central
Google Scholar
Cai JJ, Petrov DA: Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol. 2010, 2: 393-409. 10.1093/gbe/evq019.
Article
PubMed
PubMed Central
Google Scholar
Yanagihara S, Mccouch SR, Ishikawa K, Ogi Y, Maruyama K, Ikehashi H: Molecular analysis of the inheritance of the S-5 locus, conferring wide compatibility in Indica-Japonica hybrids of rice (Oryza-sativa L). Theor Appl Genet. 1995, 90: 182-188. 10.1007/BF00222200.
Article
PubMed
CAS
Google Scholar
Chen JJ, Ding JH, Ouyang YD, Du HY, Yang JY, Cheng K, Zhao J, Qiu SQ, Zhang XL, Yao JL, Liu KD, Wang L, Xu CG, Li XH, Xue YB, Xia M, Ji Q, Lu JF, Xu ML, Zhang QF: A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica-japonica hybrids in rice. Proc Natl Acad Sci U S A. 2008, 105: 11436-11441. 10.1073/pnas.0804761105.
Article
PubMed
CAS
PubMed Central
Google Scholar
Yang J, Zhao X, Cheng K, Du H, Ouyang Y, Chen J, Qiu S, Huang J, Jiang Y, Jiang L, Ding J, Wang J, Xu C, Li X, Zhang Q: A killer-protector system regulates both hybrid sterility and segregation distortion in rice. Science. 2012, 337: 1336-1340. 10.1126/science.1223702.
Article
PubMed
CAS
Google Scholar
He GM, Luo XJ, Tian F, Li KG, Zhu ZF, Su W, Qian XY, Fu YC, Wang XK, Sun CQ, Yang JS: Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice. Genome Res. 2006, 16: 618-626. 10.1101/gr.4814006.
Article
PubMed
CAS
PubMed Central
Google Scholar
Wissuwa M, Wegner J, Ae N, Yano M: Substitution mapping of Pup1: a major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil. Theor Appl Genet. 2002, 105: 890-897. 10.1007/s00122-002-1051-9.
Article
PubMed
CAS
Google Scholar
Wissuwa M, Yano M, Ae N: Mapping of QTLs for phosphorus-deficiency tolerance in rice (Oryza sativa L.). Theor Appl Genet. 1998, 97: 777-783. 10.1007/s001220050955.
Article
CAS
Google Scholar
Chin JH, Gamuyao R, Dalid C, Bustamam M, Prasetiyono J, Moeljopawiro S, Wissuwa M, Heuer S: Developing rice with high yield under phosphorus deficiency: Pup1 sequence to application. Plant Physiol. 2011, 156: 1202-1216. 10.1104/pp.111.175471.
Article
PubMed
CAS
PubMed Central
Google Scholar
Eizenga GCAM, Bryant RJ, Yeater KM, McClung AM, McCouch SR: Registration of the rice diversity panel 1 for genomewide association studies. J Plant Reg. 2013, 8: 109-116. 10.3198/jpr2013.03.0013crmp.
Article
Google Scholar
Bin Rahman AN, Zhang J: Rayada specialty: the forgotten resource of elite features of rice. Rice. 2013, 6: 41-10.1186/1939-8433-6-41.
Article
PubMed
PubMed Central
Google Scholar
Roberts RJ, Carneiro MO, Schatz MC: The advantages of SMRT sequencing. Genome Biol. 2013, 14: 405-10.1186/gb-2013-14-6-405.
Article
PubMed
Google Scholar
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, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012, 1: 18-10.1186/2047-217X-1-18.
Article
PubMed
PubMed Central
Google Scholar
Simpson JT, Durbin R: Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 2012, 22: 549-556. 10.1101/gr.126953.111.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kelley DR, Schatz MC, Salzberg SL: Quake: quality-aware detection and correction of sequencing errors. Genome Biol. 2010, 11: R116-10.1186/gb-2010-11-11-r116.
Article
PubMed
CAS
PubMed Central
Google Scholar
Smit AFA, Hubley R, Green P: RepeatMaster Open-3.0. 1996–2010. http://www.repeatmasker.org,
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sanchez Alvarado A, Yandell M: MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008, 18: 188-196. 10.1101/gr.6743907.
Article
PubMed
CAS
PubMed Central
Google Scholar
Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, et al: The iPlant Collaborative: cyberinfrastructure for plant biology. Front Plant Sci. 2011, 2: 34-10.3389/fpls.2011.00034.
Article
PubMed
PubMed Central
Google Scholar
Holt C, Yandell M: MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC bioinformatics. 2011, 12: 491-10.1186/1471-2105-12-491.
Article
PubMed
PubMed Central
Google Scholar
Salamov AA, Solovyev VV: Ab initio gene finding in Drosophila genomic DNA. Genome Res. 2000, 10: 516-522. 10.1101/gr.10.4.516.
Article
PubMed
CAS
PubMed Central
Google Scholar
Korf I: Gene finding in novel genomes. BMC bioinformatics. 2004, 5: 59-10.1186/1471-2105-5-59.
Article
PubMed
PubMed Central
Google Scholar
Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S: InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014, 30: 1236-1240. 10.1093/bioinformatics/btu031.
Article
PubMed
CAS
PubMed Central
Google Scholar
Oliver SL, Lenards AJ, Barthelson RA, Merchant N, McKay SJ: Using the iPlant collaborative discovery environment. Curr Protoc Bioinformatics. 2013, Chapter 1: Unit1 22-
PubMed
Google Scholar
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: R12-10.1186/gb-2004-5-2-r12.
Article
PubMed
PubMed Central
Google Scholar
Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010, 26: 841-842. 10.1093/bioinformatics/btq033.
Article
PubMed
CAS
PubMed Central
Google Scholar
Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M: Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Brief Bioinform. 2013, 14: 213-224. 10.1093/bib/bbr074.
Article
PubMed
CAS
PubMed Central
Google Scholar
Marcais G, Kingsford C: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011, 27: 764-770. 10.1093/bioinformatics/btr011.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kurtz S, Narechania A, Stein JC, Ware D: A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics. 2008, 9: 517-10.1186/1471-2164-9-517.
Article
PubMed
PubMed Central
Google Scholar
Phillippy AM, Schatz MC, Pop M: Genome assembly forensics: finding the elusive mis-assembly. Genome Biol. 2008, 9: R55-10.1186/gb-2008-9-3-r55.
Article
PubMed
PubMed Central
Google Scholar
Reyes J, Gomez-Romero L, Ibarra-Soria X, Palacios-Flores K, Arriola LR, Wences A, Garcia D, Boege M, Davila G, Flores M, Palacios R: Context-dependent individualization of nucleotides and virtual genomic hybridization allow the precise location of human SNPs. Proc Natl Acad Sci U S A. 2011, 108: 15294-15299. 10.1073/pnas.1112567108.
Article
PubMed
CAS
PubMed Central
Google Scholar
New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica. [http://schatzlab.cshl.edu/data/rice]
ALLPATHS-LG. [http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12]
MUMmer. [http://mummer.sourceforge.net]
AMOS. [http://amos.sourceforge.net]
Jellyfish. [http://www.genome.umd.edu/jellyfish.html]
BEDTools. [https://github.com/arq5x/bedtools2]