82 Song C, Wang C, Zhang C, et al. Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics, 2010, 11: 431？？
[2]
83 Liang C, Zhang X, Zou J, et al. Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis. PLoS One, 2010, 5: e10698？？
[3]
84 Yao J, Wang Y, Wang W, et al. Solexa sequencing analysis of chicken pre-adipocyte microRNAs. Biosci Biotechnol Biochem, 2011, 75:54-61？？
[4]
85 Xie W, Feng Q, Yu H, et al. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci USA, 2010, 107: 10578-10583？？
[5]
86 Li G, Li Y, Li X, et al. MicroRNA identity and abundance in developing swine adipose tissue as determined by Solexa sequencing. J Cell Biochem, 2011, 112: 1318-1328？？
[6]
87 Fu Y, Shi Z, Wu M, et al. Identification and differential expression of microRNAs during metamorphosis of the Japanese flounder (Paralichthys olivaceus). PLoS One, 2011, 6: e22957？？
[7]
88 Huang Q X, Cheng X Y, Mao Z C, et al. MicroRNA discovery and analysis of pinewood nematode Bursaphelenchus xylophilus by deep sequencing. PLoS One, 2011, 5: e13271
[8]
89 Xu M J, Liu Q, Nisbet A J, et al. Identification and characterization of microRNAs in Clonorchis sinensis of human health significance. BMC Genomics, 2010, 11: 521？？
[9]
90 Wei Z, Liu X, Feng T, et al. Novel and conserved micrornas in Dalian purple urchin (Strongylocentrotus nudus) identified by next generation sequencing. Int J Biol Sci, 2011, 7: 180-192
[10]
91 German M A, Pillay M, Jeong D H, et al. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol, 2008, 26: 941-946？？
[11]
92 Zhou M, Gu L, Li P, et al. Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica). Front Biol,2010, 5: 24
[12]
93 Frommer M, McDonald L E, Millar D S, et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA, 1992, 89: 1827-1831？？
[13]
94 Xiang H, Zhu J, Chen Q, et al. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol, 2011,28: 516-520
[14]
95 Meissner A, Gnirke A, Bell G W, et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res, 2005, 33: 5868-5877？？
[15]
96 Hirst M, Marra M A, Next generation sequencing based approaches to epigenomics. Brief Funct Genomics, 2011, 9: 455-465？？
[16]
97 Li Q, Li N, Hu X, et al. Genome-wide mapping of DNA methylation in chicken. PLoS One, 2011, 6: e19428？？
[17]
98 Wang X, Elling A A, Li X, et al. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell, 2009, 21: 1053-1069？？
[18]
1 Ansorge W J. Next-generation DNA sequencing techniques. N Biotechnol, 2009, 25: 195-203？？
[19]
2 Glenn T C. Field guide to next-generation DNA sequencers. Mol Ecol Resour, 2011, 11: 759-769？？
[20]
3 Hillier L W, Marth G T, Quinlan A R, et al. Whole-genome sequencing and variant discovery in C. elegans. Nat Methods, 2008, 5:183-188？？
[21]
4 TAGI. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 2000, 408: 796-815？？
[22]
5 Check E. Mouse genome: the real deal. Nature, 2002, 420: 457？？
[23]
6 Waterston R H, Lindblad-Toh K, Birney E, et al. Initial sequencing and comparative analysis of the mouse genome. Nature, 2002, 420:520-562？？
[24]
7 Yu J, Hu S, Wang J, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 2002, 296: 79-92？？
[25]
8 Li R, Fan W, Tian G, et al. The sequence and de novo assembly of the giant panda genome. Nature, 2010, 463: 311-317？？
[26]
9 Huang S, Li R, Zhang Z, et al. The genome of the cucumber, Cucumis sativus L. Nat Genet, 2009, 41: 1275-1281？？
[27]
10 Werren J H, Richards S, Desjardins C A, et al. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science, 2010, 327: 343-348？？
[28]
11 Velasco R, Zharkikh A, Affourtit J, et al. The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet, 2010, 42: 833-839？？
[29]
12 Bonasio R, Zhang G, Ye C, et al. Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator. Science, 2010, 329:1068-1071？？
[30]
13 Dalloul R A, Long J A, Zimin A V, et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol, 2010, 8: e1000475？？
[31]
14 Kim M Y, Lee S, Van K, et al. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci USA, 2010, 107: 22032-22037？？
[32]
15 Shulaev V, Sargent D J, Crowhurst R N, et al. The genome of woodland strawberry (Fragaria vesca). Nat Genet, 2011, 43: 109-116？？
[33]
16 Argout X, Salse J, Aury J M, et al. The genome of Theobroma cacao. Nat Genet, 2011, 43: 101-108？？
[34]
17 Smith C D, Zimin A, Holt C, et al. Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc Natl Acad Sci USA, 2011, 108: 5673-5678？？
[35]
18 Smith C R, Smith C D, Robertson H M, et al. Draft genome of the red harvester ant Pogonomyrmex barbatus. Proc Natl Acad Sci USA,2011, 108: 5667-5672？？
[36]
19 Wurm Y, Wang J, Riba-Grognuz O, et al. The genome of the fire ant Solenopsis invicta. Proc Natl Acad Sci USA, 2011, 108: 5679-5684？？
[37]
20 Sato S, Hirakawa H, Isobe S, et al. Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Res, 2011, 18: 65-76？？
[38]
21 Suen G, Teiling C, Li L, et al. The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet, 2011, 7: e1002007？？
[39]
22 Nygaard S, Zhang G, Schiott M, et al. The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Res, 2011, 21: 1339-1348？？
[40]
23 Al-Dous E K, George B, Al-Mahmoud M E, et al. De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol, 2011, 29: 521-527？？
[41]
24 Xu X, Pan S, Cheng S, et al. Genome sequence and analysis of the tuber crop potato. Nature, 2011, 475: 189-195？？
[42]
25 Fang X, Zhang Y, Zhang R, et al. Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque. Genome Biol, 2011, 12: R63
[43]
26 Shinzato C, Shoguchi E, Kawashima T, et al. Using the Acropora digitifera genome to understand coral responses to environmental change. Nature, 2011, 476: 320-323？？
[44]
27 Castoe T A, de Koning A J, Hall K T, et al. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biol, 2011, 12: 406？？
[45]
28 Star B, Nederbragt A J, Jentoft S, et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature, 2011, 477: 207-210？？
[46]
29 Renfree M B, Papenfuss A T, Deakin J E, et al. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol, 2011, 12: R81？？
[47]
30 Wang X, Wang H, Wang J, et al. The genome of the mesopolyploid crop species Brassica rapa. Nat Genet, 2011, 43: 1035-1039？？
[48]
31 Kim E B, Fang X, Fushan A A, et al. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature, 2011,479: 223-227？？
[49]
32 Yan G, Zhang G, Fang X, et al. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol, 2011, 29: 1019-1023？？
[50]
33 van Bakel H, Stout J M, Cote A G, et al. The draft genome and transcriptome of Cannabis sativa. Genome Biol, 2011, 12: R102？？
[51]
34 Varshney R K, Chen W, Li Y, et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol, 2012, 30: 83-89
[52]
35 Ebeling M, Kung E, See A, et al. Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment. Genome Res, 2011, 21: 1746-1756？？
[53]
36 Jex A R, Liu S, Li B, et al. Ascaris suum draft genome. Nature, 2011, 479: 529-533？？
[54]
37 Zhan S, Merlin C, Boore J L, et al. The monarch butterfly genome yields insights into long-distance migration. Cell, 2011, 147: 1171-1185？？
[55]
38 Young N D, Debelle F, Oldroyd G E, et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature, 2011, 480: 520-524
[56]
39 Lai J, Li R, Xu X, et al. Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet, 2010, 42: 1027-1030？？
[57]
40 Zheng L Y, Guo X S, He B, et al. Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol,2011, 12: R114？？
[58]
41 Xia Q, Guo Y, Zhang Z, et al. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science, 2009, 326: 433-436？？
[59]
42 Lam H M, Xu X, Liu X, et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet, 2010, 42: 1053-1059？？
[60]
43 Huang X, Feng Q, Qian Q, et al. High-throughput genotyping by whole-genome resequencing. Genome Res, 2009, 19: 1068-1076？？
[61]
44 Huang X, Wei X, Sang T, et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet, 2010, 42: 961-967？？
[62]
46 Sarin S, Prabhu S, O’Meara M M, et al. Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nat Methods,2008, 5: 865-867？？
[63]
47 Cuperus J T, Montgomery T A, Fahlgren N, et al. Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing. Proc Natl Acad Sci USA, 2010, 107: 466-471？？
[64]
48 Ashelford K, Eriksson M E, Allen C M, et al. Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis. Genome Biol, 2011, 12: R28
[65]
49 Fairfield H, Gilbert G J, Barter M, et al. Mutation discovery in mice by whole exome sequencing. Genome Biol, 2011, 12: R86？？ 50 Haun W J, Hyten D L, Xu W W, et al. The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiol, 2011, 155: 645-655？？
[66]
51 Bolon Y T, Haun W J, Xu W W, et al. Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. Plant Physiol, 2011, 156: 240-253？？
[67]
52 Cosart T, Beja-Pereira A, Chen S, et al. Exome-wide DNA capture and next generation sequencing in domestic and wild species. BMC Genomics, 2011, 12: 347？？
[68]
53 Wang H, Chattopadhyay A, Li Z, et al. Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Res, 2011, 20: 981-988
[69]
54 Van Tassell C P, Smith T P, Matukumalli L K, et al. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods, 2008, 5: 247-252？？
[70]
55 Kerstens H H, Crooijmans R P, Veenendaal A, et al. Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey. BMC Genomics, 2009, 10: 479？？
[71]
56 Wu X, Ren C, Joshi T, et al. SNP discovery by high-throughput sequencing in soybean. BMC Genomics, 2010, 11: 469？？
[72]
57 Baird N A, Etter P D, Atwood T S, et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One, 2008, 3: e3376？？
[73]
58 Hohenlohe P A, Bassham S, Etter P D, et al. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet, 2010, 6: e1000862？？
[74]
59 Emerson K J, Merz C R, Catchen J M, et al. Resolving postglacial phylogeography using high-throughput sequencing. Proc Natl Acad Sci USA, 2010, 107: 16196-16200？？
[75]
60 Baxter S W, Davey J W, Johnston J S, et al. Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS One, 2011, 6: e19315？？
[76]
61 Chutimanitsakun Y, Nipper R W, Cuesta-Marcos A, et al. Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics, 2011, 12: 4？？
[77]
62 Pfender W F, Saha M C, Johnson E A, et al. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet, 2011, 122: 1467-1480？？
[78]
63 Zhang G, Guo G, Hu X, et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res, 2010, 20: 646-654？？
[79]
64 Li P, Ponnala L, Gandotra N, et al. The developmental dynamics of the maize leaf transcriptome. Nat Genet, 2010, 42: 1060-1067？？
[80]
65 Graham I A, Besser K, Blumer S, et al. The genetic map of Artemisia annua L. identifies loci affecting yield of the antimalarial drug artemisinin. Science, 2010, 327: 328-331？？
[81]
66 Wang Z, Fang B, Chen J, et al. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genomics, 2010, 11: 726？？
[82]
67 Chen M X, Ai L, Xu M J, et al. Identification and characterization of microRNAs in Trichinella spiralis by comparison with Brugia malayi and Caenorhabditis elegans. Parasitol Res, 2011, 109: 553-558？？
[83]
68 Xiao S, Jia J, Mo D, et al. Understanding PRRSV infection in porcine lung based on genome-wide transcriptome response identified by deep sequencing. PLoS One, 2010, 5: e11377？？
[84]
69 Wang Q Q, Liu F, Chen X S, et al. Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant. Genomics, 2010, 96: 369-376？？
[85]
70 Wu J, Zhang Y, Zhang H, et al. Whole genome wide expression profiles of Vitis amurensis grape responding to downy mildew by using Solexa sequencing technology. BMC Plant Biol, 2010, 10: 234？？
[86]
71 Wang X W, Luan J B, Li J M, et al. De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics, 2010, 11: 400？？
[87]
72 Mu Y, Ding F, Cui P, et al. Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection. BMC Genomics, 2010, 11: 506？？
[88]
73 Hao D C, Ge G B, Xiao P G, et al. The first insight into the tissue specific taxus transcriptome via illumina second generation sequencing. PLoS One, 2011, 6: e21220？？
[89]
74 Tang Q, Ma X J, Mo C M, et al. An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis. BMC Genomics, 2011, 12: 343？？
[90]
75 Wei Y, Chen S, Yang P, et al. Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. Genome Biol, 2009, 10: R6？？
[91]
76 Li T, Li H, Zhang Y X, et al. Identification and analysis of seven HO-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica). Nucleic Acids Res, 2011, 39: 2821-2833？？
[92]
45 Yu H, Xie W, Wang J, et al. Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS One, 2011, 6: e17595？？
[93]
78 Wang L, Liu H, Li D, et al. Identification and characterization of maize microRNAs involved in the very early stage of seed germination. BMC Genomics, 2011, 12: 154？？
[94]
79 Zhao C Z, Xia H, Frazier T P, et al. Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol, 2010, 10: 3？？
[95]
80 Xin M, Wang Y, Yao Y, et al. Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.). BMC Plant Biol, 2010, 10: 123？？
[96]
81 Yang Y, Chen X, Chen J, et al. Differential miRNA expression in Rehmannia glutinosa plants subjected to continuous cropping. BMC Plant Biol, 2011, 11: 53？？
[97]
77 Kwak P B, Wang Q Q, Chen X S, et al. Enrichment of a set of microRNAs during the cotton fiber development. BMC Genomics, 2009, 10:457？？
