References for Section A
1.
Gross BL, Zhao Z: Archaeological and genetic insights into the origins of domesticated rice. 2014, 111(17):6190-6197.
2.
Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang
FJN: Genomic variation in 3,010 diverse accessions of Asian cultivated rice. 2018, 557(7703):43.
3.
lchitani K, Okumoto Y, Tanisaka T: Photoperiod sensitivity gene of se-1 locus found in photoperiod insensitive rice cultivars
of the northern limit region of rice cultivation. Breeding science 1997, 47:8.
4.
Kim SL, Choi M, Jung KH, An G: Analysis of the early-flowering mechanisms and generation of T-DNA tagging lines in
Kitaake, a model rice cultivar. J Exp Bot 2013, 64(14):4169-4182.
5.
Kunihiro Y, Ebe Y, Wada S, Shinbashi N, Honma A, Sasaki T, Sasaki K, Numao Y, Morimura
K, Tan No H: The new rice variety Kita-ake. Bulletin of Hokkaido prefectural agricultural experiment stations 1989, 59:4.
6.
Wang L, Zheng J, Luo Y, Xu T, Zhang Q, Zhang L, Xu M, Wan J, Wang MB, Zhang CJPbj:
Construction of a genomewide RNA i mutant library in rice. 2013, 11(8):997-1005.
7.
Gao H, Zheng XM, Fei G, Chen J, Jin M, Ren Y, Wu W, Zhou K, Sheng P, Zhou F et al: Ehd4 encodes a novel and Oryza-genus-specific regulator of photoperiodic flowering
in rice. PLoS Genet 2013, 9(2):e1003281.
8.
Li G, Jain R, Chern M, Pham NT, Martin JA, Wei T, Schackwitz WS, Lipzen AM, Duong
PQ, Jones KC et al: The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional
Genomic Studies. Plant Cell 2017, 29(6):1218-1231.
9.
Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu
LH et al: A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 1995, 270(5243):1804-1806.
10.
Gao H, Jin M, Zheng X-M, Chen J, Yuan D, Xin Y, Wang M, Huang D, Zhang Z, Zhou KJPotNAoS:
Days to heading 7, a major quantitative locus determining photoperiod sensitivity
and regional adaptation in rice. 2014, 111(46):16337-16342.
11.
Ronald PC, Beutler B: Plant and animal sensors of conserved microbial signatures. Science 2010, 330(6007):1061-1064.
12.
Liu Y, Wu H, Chen H, Liu Y, He J, Kang H, Sun Z, Pan G, Wang Q, Hu JJNb: A gene cluster encoding lectin receptor kinases confers broad-spectrum and durable
insect resistance in rice. 2015, 33(3):301.
13.
Zhou X, Liao H, Chern M, Yin J, Chen Y, Wang J, Zhu X, Chen Z, Yuan C, Zhao WJPotNAoS:
Loss of function of a rice TPR-domain RNA-binding protein confers broad-spectrum disease
resistance. 2018:201705927.
14.
Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, Zilberman
D: Imprinted expression of genes and small RNA is associated with localized hypomethylation
of the maternal genome in rice endosperm. Proc Natl Acad Sci U S A 2013, 110(19):7934-7939.
15.
Li T, Liu B, Spalding MH, Weeks DP, Yang B: High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 2012, 30(5):390-392.
16.
Xie K, Minkenberg B, Yang Y: Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing
system. Proc Natl Acad Sci U S A 2015, 112(11):3570-3575.
17.
Jung K-H, An G, Ronald PC: Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nature Reviews Genetics 2008, 9:91.
18.
Kent WJ: BLAT--the BLAST-like alignment tool. Genome Res 2002, 12(4):656-664.
19.
Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna
D, Ammiraju JS et al: The genome sequence of African rice (Oryza glaberrima) and evidence for independent
domestication. Nat Genet 2014, 46(9):982-988.
20.
Guyot R, Keller BJG: Ancestral genome duplication in rice. 2004, 47(3):610-614.
21.
Zhang J, Chen L-L, Xing F, Kudrna DA, Yao W, Copetti D, Mu T, Li W, Song J-M, Xie
W et al: Extensive sequence divergence between the reference genomes of two elite <em>indica</em>
rice varieties Zhenshan 97 and Minghui 63. 2016, 113(35):E5163-E5171.
22.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SLJGb:
Versatile and open software for comparing large genomes. 2004, 5(2):R12.
23.
Matsumoto T, Wu J, Itoh T, Numa H, Antonio B, Sasaki T: The Nipponbare genome and the next-generation of rice genomics research in Japan. Rice (New York, NY) 2016, 9(1):33-33.
24.
Tang X, Liu G, Zhou J, Ren Q, You Q, Tian L, Xin X, Zhong Z, Liu B, Zheng XJGb: A large-scale whole-genome sequencing analysis reveals highly specific genome editing
by both Cas9 and Cpf1 (Cas12a) nucleases in rice. 2018, 19(1):84.
25.
Schwessinger B, Bahar O, Thomas N, Holton N, Nekrasov V, Ruan D, Canlas PE, Daudi
A, Petzold CJ, Singan VR et al: Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice
leads to ligand-dependent activation of defense responses. PLoS Pathog 2015, 11(3):e1004809.
26.
Zhao H, Yao W, Ouyang Y, Yang W, Wang G, Lian X, Xing Y, Chen L, Xie W: RiceVarMap: a comprehensive database of rice genomic variations. Nucleic Acids Res 2015, 43(Database issue):D1018-1022.
27.
Li G, Chern M, Jain R, Martin JA, Schackwitz WS, Jiang L, Vega-Sanchez ME, Lipzen
AM, Barry KW, Schmutz J et al: Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse
Mutations Induced by Fast-Neutron Irradiation. Mol Plant 2016, 9(7):1078-1081.
28.
Paradis E, Claude J, Strimmer K: APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 2004, 20(2):289-290.
29.
Bairoch A, Apweiler R: The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 2000, 28(1):45-48.
30.
Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T: A gene ontology inferred from molecular networks. Nat Biotechnol 2013, 31(1):38-45.
31.
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztanyi
Z, El-Gebali S, Fraser M et al: InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res 2017, 45(D1):D190-D199.
32.
Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K: KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017, 45(D1):D353-D361.
33.
Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, Schijlen E, van de Geest H,
Bianco L, Micheletti D, Velasco R et al: High-quality de novo assembly of the apple genome and methylome dynamics of early
fruit development. Nat Genet 2017, 49(7):1099-1106.
34.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra
MA: Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19(9):1639-1645.
35.
Flutre T, Duprat E, Feuillet C, Quesneville H: Considering transposable element diversification in de novo annotation approaches. PLoS One 2011, 6(1):e16526.
36.
Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A,
Maldonado LC, Roffler S et al: RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics 2015, 16:538.
37.
Nawrocki EP, Eddy SR: Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 2013, 29(22):2933-2935.
38.
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner
PP, Jones TA, Tate J et al: Rfam 12.0: updates to the RNA families database. Nucleic Acids Res 2015, 43(Database issue):D130-137.
39.
Schattner P, Brooks AN, Lowe TM: The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 2005, 33(Web Server issue):W686-689.
40.
Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM:
A program for annotating and predicting the effects of single nucleotide polymorphisms,
SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 2012, 6(2):80-92.
41.
Li G, Jain R, Chern M, Pham NT, Martin JA, Wei T, Schackwitz WS, Lipzen AM, Duong
PQ, Jones KCJTPC: The sequences of 1,504 mutants in the model rice variety Kitaake facilitate rapid
functional genomic studies. 2017:tpc. 00154.02017.
42.
Luo M, Wing RA: An Improved Method for Plant BAC Library Construction. In: Plant Functional Genomics. Edited by Grotewold E. Totowa, NJ: Humana Press; 2003: 3-19.