中国梅花鹿全基因组初步组装、分析及单核苷酸多态性研究
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摘要
新一代高通量测序技术的诞生和快速发展使对一个物种的基因组进行细致全貌的分析成为可能。本文利用SOLiD（Applied Biosciences）测序平台和全基因组鸟枪法测序策略对一只中国梅花鹿（东北亚种，Cervus nippon hortulorum)进行了全基因组测序，东北梅花鹿亚种是中国鹿产业中最重要的鹿种之一。
对梅花鹿基因组原始测序数据进行初步的质量评估后，共产生约1.9×109个50bp双末端配对读段，评估基因组测序深度约32倍，构建了插入长度1kbp和2kbp两个测序库。本文组合了当前可利用的基因组组装策略，包括全局从头组装，参考局部向导组装，也利用了鹿与牛基因组之间的保守序列进行共线性局部组装，尽最大限度地组装了梅花鹿基因组。产生约4百万长度大于100bp个重叠群（contigs），包含碱基总量1.83Gbp，N50值为695bp，最大重叠群长度10.80kbp。梅花鹿基因组质量评估发现约0.3%的重叠群存在组装错误，进一步更正了组装错误。最后利用双末端配对信息对重叠群定位和定向，产生约1.9百万个基因组序列框架（scaffolds），N50值为21.6kbp，最大长度249kbp，包含碱基总量2.6Gbp，约1.8百万个缺口（gap）。
本文通过各种生物信息学数据处理方法对组装后的梅花鹿基因组作了进一步的分析，主要结果和结论如下：
1.测序偏倚导致梅花鹿基因组不同区域覆盖率相差较大，基因组区域GC含量越高，其覆盖率越低。梅花鹿基因组覆盖牛基因组约62%（相似性85%以上），覆盖鹿转录组约62%（相似性90%以上）。
2.从鹿、牛和羊的微卫星引物数据集中筛选了1,534个在梅花鹿基因组上保守的微卫星引物，占收集微卫星总数的61%。
3.鹿、牛基因组功能区SNP变异与Indel变异比非功能区更趋保守，基因组水平上的SNP变异与Indel变异有强的正相关性，鹿、牛与人、黑猩猩的基因组SNP变异数据比较结果支持分子钟理论。
4.在组装的梅花鹿基因组中筛选了2.7百万个SNP杂合位点，平均每678bp包含1个SNP位点。梅花鹿个体常染色体基因组、外显子区和编码区的SNP杂合率分别为0.152%、0.087%和0.082%，梅花鹿基因组表现高度杂合现象暗示中国梅花鹿在长期的人工饲养和驯化过程，具有不同遗传背景的梅花鹿发生了血缘交换。
5.本研究产生的6,367个SNP位点非常适合中等密度的SNP分型芯片的定制，并能在种属间，包括梅花鹿、马鹿和赤鹿等鹿种，进行检测分型等相关研究，证明了开发高密度的鹿全基因组SNP分型芯片具有可行性。
6.梅花鹿线粒体基因组的组装进一步证实了Numts序列在脊椎动物和无脊椎动物核基因组中广泛存在，同时也暗示梅花鹿核基因组中存在大量的Numts序列，其数量相当于1,867个线粒体基因组。
The advent and rapid development of next generation sequencing technology have enabled us toanalyse the whole-genome of any species comprehensively. In this study, we sequenced thewhole-genome of an adult male Chinese sika deer (Cervus nippon hortulorum), one of the mostimportant species for the Chinese deer industry, using a whole-genome shotgun sequencing approachand SOLiD (Applied Biosciences) sequencing technology platform.
Following the preliminary analysis of the raw sequencing data, we obtained1.92billion of the50bp paired-end reads equivalent to32x coverage of the sika deer genome. Two separate librarieswere made, one with1kbp inserts and the other with2kbp inserts. For the sika deer genomeassembling we combined a variety of currently available techniques. This included global de novoassembly, reference-guided local assembly and conserved synteny local assembly. Furthermore, weutilized the conserved synteny between sika deer and cattle genome. We generated4.15millioncontigs of100bp size or longer, comprising a total of1.83billion base pairs of assembled sequence.Half number of the contigs are longer than695bp (N50), the maximum contig length is10.80kbp. Thequality of these assembled contigs was checked and about0.3%contigs are misassembled. Thesemisassembled contigs were then corrected before the subsequent analyses were carried out. We furtherutilized the paired-end information to generate1.94million scaffolds with an N50of21.6kbp, amaximum length of249kbp. The assembled genome has1.8million gaps.
Next, we analyzed the assembled sika deer genome by a verity of bioinformatics approaches andtools. The main results and conclusion are as follows.
1. The sequencing bias in the different regions of the assembled sika deer genome led to anapparently different coverage. The higher the GC content in different genome regions, the lowerthe region coverage. The assembled sika deer genome covers about62%of the reference cattlegenome (the identity is above85%), and covers about62%of the deer transcriptome sequence (theidentity is above90%).
2. Amongst the collected datasets of the microsatellite primers of deer, cattle and sheep, the1,534microsatellite primers,61%in total, were screened as candidates in the sika deer genome becausethey are conservative between the sika deer and the cattle and sheep.
3. The variations between the deer and the cattle genome are more conservative in the functionalregions than in the non-functional regions. There is a strong positive correlation between the SNPvariations and Indel variations among the different genome regions. The SNPs between humanand chimpanzee are compared with those between cattle and deer, the results validated once againthe theory of molecular clock.
4. Within this sequenced and assembled genome, the2.7million SNPs were detected, which isequivalent to one SNP of every678bp. The SNP heterozygous rates were0.152%,0.087%and0.082%in the autosomal genome, exon and coding regions, respectively. The high SNPheterozygous rates in the sika deer genome implies that the sika deer belongs to the different genetic background that had produced the gene flowing in the long-term domestication andartificial breeding processes.
5. This study produced the6,367SNP sites that are suitable for the development of medium densityof genotype SNP chips. This type of chip if developed can be applied to different deer species,including sika deer, red deer and wapiti. In addition, it proved the feasibility about thedevelopment of high density whole genome SNP genotype chip.
6. We further confirmed the claim that the Numts sequence are widespread in vertebrates andinvertebrates nuclear genome, which is in accordance with the assembled sika deer mitochondrialgenome. This implies that there are numerous Numt sequences in the sika deer nuclear genomealmost equivalent to1,867mitochondrial genomes
对梅花鹿基因组原始测序数据进行初步的质量评估后，共产生约1.9×109个50bp双末端配对读段，评估基因组测序深度约32倍，构建了插入长度1kbp和2kbp两个测序库。本文组合了当前可利用的基因组组装策略，包括全局从头组装，参考局部向导组装，也利用了鹿与牛基因组之间的保守序列进行共线性局部组装，尽最大限度地组装了梅花鹿基因组。产生约4百万长度大于100bp个重叠群（contigs），包含碱基总量1.83Gbp，N50值为695bp，最大重叠群长度10.80kbp。梅花鹿基因组质量评估发现约0.3%的重叠群存在组装错误，进一步更正了组装错误。最后利用双末端配对信息对重叠群定位和定向，产生约1.9百万个基因组序列框架（scaffolds），N50值为21.6kbp，最大长度249kbp，包含碱基总量2.6Gbp，约1.8百万个缺口（gap）。
本文通过各种生物信息学数据处理方法对组装后的梅花鹿基因组作了进一步的分析，主要结果和结论如下：
1.测序偏倚导致梅花鹿基因组不同区域覆盖率相差较大，基因组区域GC含量越高，其覆盖率越低。梅花鹿基因组覆盖牛基因组约62%（相似性85%以上），覆盖鹿转录组约62%（相似性90%以上）。
2.从鹿、牛和羊的微卫星引物数据集中筛选了1,534个在梅花鹿基因组上保守的微卫星引物，占收集微卫星总数的61%。
3.鹿、牛基因组功能区SNP变异与Indel变异比非功能区更趋保守，基因组水平上的SNP变异与Indel变异有强的正相关性，鹿、牛与人、黑猩猩的基因组SNP变异数据比较结果支持分子钟理论。
4.在组装的梅花鹿基因组中筛选了2.7百万个SNP杂合位点，平均每678bp包含1个SNP位点。梅花鹿个体常染色体基因组、外显子区和编码区的SNP杂合率分别为0.152%、0.087%和0.082%，梅花鹿基因组表现高度杂合现象暗示中国梅花鹿在长期的人工饲养和驯化过程，具有不同遗传背景的梅花鹿发生了血缘交换。
5.本研究产生的6,367个SNP位点非常适合中等密度的SNP分型芯片的定制，并能在种属间，包括梅花鹿、马鹿和赤鹿等鹿种，进行检测分型等相关研究，证明了开发高密度的鹿全基因组SNP分型芯片具有可行性。
6.梅花鹿线粒体基因组的组装进一步证实了Numts序列在脊椎动物和无脊椎动物核基因组中广泛存在，同时也暗示梅花鹿核基因组中存在大量的Numts序列，其数量相当于1,867个线粒体基因组。
The advent and rapid development of next generation sequencing technology have enabled us toanalyse the whole-genome of any species comprehensively. In this study, we sequenced thewhole-genome of an adult male Chinese sika deer (Cervus nippon hortulorum), one of the mostimportant species for the Chinese deer industry, using a whole-genome shotgun sequencing approachand SOLiD (Applied Biosciences) sequencing technology platform.
Following the preliminary analysis of the raw sequencing data, we obtained1.92billion of the50bp paired-end reads equivalent to32x coverage of the sika deer genome. Two separate librarieswere made, one with1kbp inserts and the other with2kbp inserts. For the sika deer genomeassembling we combined a variety of currently available techniques. This included global de novoassembly, reference-guided local assembly and conserved synteny local assembly. Furthermore, weutilized the conserved synteny between sika deer and cattle genome. We generated4.15millioncontigs of100bp size or longer, comprising a total of1.83billion base pairs of assembled sequence.Half number of the contigs are longer than695bp (N50), the maximum contig length is10.80kbp. Thequality of these assembled contigs was checked and about0.3%contigs are misassembled. Thesemisassembled contigs were then corrected before the subsequent analyses were carried out. We furtherutilized the paired-end information to generate1.94million scaffolds with an N50of21.6kbp, amaximum length of249kbp. The assembled genome has1.8million gaps.
Next, we analyzed the assembled sika deer genome by a verity of bioinformatics approaches andtools. The main results and conclusion are as follows.
1. The sequencing bias in the different regions of the assembled sika deer genome led to anapparently different coverage. The higher the GC content in different genome regions, the lowerthe region coverage. The assembled sika deer genome covers about62%of the reference cattlegenome (the identity is above85%), and covers about62%of the deer transcriptome sequence (theidentity is above90%).
2. Amongst the collected datasets of the microsatellite primers of deer, cattle and sheep, the1,534microsatellite primers,61%in total, were screened as candidates in the sika deer genome becausethey are conservative between the sika deer and the cattle and sheep.
3. The variations between the deer and the cattle genome are more conservative in the functionalregions than in the non-functional regions. There is a strong positive correlation between the SNPvariations and Indel variations among the different genome regions. The SNPs between humanand chimpanzee are compared with those between cattle and deer, the results validated once againthe theory of molecular clock.
4. Within this sequenced and assembled genome, the2.7million SNPs were detected, which isequivalent to one SNP of every678bp. The SNP heterozygous rates were0.152%,0.087%and0.082%in the autosomal genome, exon and coding regions, respectively. The high SNPheterozygous rates in the sika deer genome implies that the sika deer belongs to the different genetic background that had produced the gene flowing in the long-term domestication andartificial breeding processes.
5. This study produced the6,367SNP sites that are suitable for the development of medium densityof genotype SNP chips. This type of chip if developed can be applied to different deer species,including sika deer, red deer and wapiti. In addition, it proved the feasibility about thedevelopment of high density whole genome SNP genotype chip.
6. We further confirmed the claim that the Numts sequence are widespread in vertebrates andinvertebrates nuclear genome, which is in accordance with the assembled sika deer mitochondrialgenome. This implies that there are numerous Numt sequences in the sika deer nuclear genomealmost equivalent to1,867mitochondrial genomes
引文
1.陈祥贵,胡军,杨潇.人类蛋白编码基因局部GC水平相关性分析.遗传,2008(9):1169-1174.
2.韩建文,张学军.全基因组关联研究现状.遗传,2011(1):25-35.
3.何余湧,李完波,张志燕等.利用全基因组高通量SNP标记定位二花脸×沙子岭家系中的断奶体重QTL.中国农业科学,2011(22):4694-4699.
4.李春义,王文英.鹿茸成分研究探讨.特产研究,1990(4):19-22.
5.李明,王小明,盛和林等.四种鹿属动物的线粒体DNA差异和系统进化关系研究.动物学报,1999(1):99-105.
6.李义,吴国栋,左瑾等.应用单核苷酸多态性技术筛查2型糖尿病易感基因.中国医学科学院学报,2005(3).
7.刘海,杨光,魏辅文等.中国大陆梅花鹿mtDNA控制区序列变异及种群遗传结构分析.动物学报,2003(1).
8.吕晓平,魏辅文,李明等.中国梅花鹿(Cervus nippon)遗传多样性及与日本梅花鹿间的系统关系.科学通报,2006(3):292-298.
9.盛和林.中国鹿科动物.生物学通报,1992(5):4-7.
10.唐立群,肖层林,王伟平. SNP分子标记的研究及其应用进展.中国农学通报,2012(12):154-158.
11.田埂,苏夜阳.从“人类”基因组计划到“千人”基因组计划.生命世界,2011(8):54-57.
12.王继文.动物线粒体假基因的识别及其在进化生物学中的应用.动物学杂志,2004(3):103-108.
13.王继文,许恒勇.动物线粒体假基因的特征及产生机制.安徽农业科学,2005(3):496-498.
14.岳桂东,高强,罗龙海等.高通量测序技术在动植物研究领域中的应用.中国科学:生命科学,2012(2):107-124.
15.王兴春,杨致荣,王敏等.高通量测序技术及其应用.中国生物工程杂志,2012(1):109-114.
16.燕燕.国际千人基因组计划首阶段成功完成:深圳特区报[Z].2010.
17.赵辉,李启寨,李俊等.相邻碱基组分与产生SNP的转换或颠换在植物基因组中的研究.中国科学C辑:生命科学,2006(1):1-8.
18.周晓光,任鲁风,李运涛等.下一代测序技术:技术回顾与展望.中国科学:生命科学,2010(1):23-37.
19.邹新慧,葛颂.基因树冲突与系统发育基因组学研究.植物分类学报,2008(6):795-807.
20.邹喻苹,葛颂.新一代分子标记——SNPs及其应用.生物多样性,2003(5):370-382.
21. Adams M.D., Celniker S.E., Holt R.A., et al. The genome sequence of Drosophila melanogaster.Science,2000,287(5461):2185-2195.
22. Archibald A.L., Bolund L., Churcher C., et al. Pig genome sequence--analysis and publicationstrategy. BMC Genomics,2010,11:438.
23. Archibald A.L., Cockett N.E., Dalrymple B.P., et al. The sheep genome reference sequence: awork in progress. Anim Genet,2010,41(5):449-453.
24. Bai Y., Sartor M., Cavalcoli J. Current Status and Future Perspectives for Sequencing LivestockGenomes. Journal of Animal Science and Biotechnology,2012,3(1):8-12.
25. Basti G., Perrone A.L. A fast hybrid block-sorting algorithm for lossless interferometric datacompression[Z].2003:5103,92.
26. Batzoglou S., Jaffe D.B., Stanley K., et al. ARACHNE: a whole-genome shotgun assembler.Genome Res,2002,12(1):177-189.
27. Bentley D.R. Whole-genome re-sequencing. Curr Opin Genet Dev,2006,16(6):545-552.
28. Boetzer M., Henkel C.V., Jansen H.J., et al. Scaffolding pre-assembled contigs using SSPACE.Bioinformatics,2011,27(4):578-579.
29. Brooks S.A., Gabreski N., Miller D., et al. Whole-genome SNP association in the horse:identification of a deletion in myosin Va responsible for Lavender Foal Syndrome. PLoS Genet,2010,6(4):e1000909.
30. Burgoyne P.S. Genetic homology and crossing over in the X and Y chromosomes of Mammals.Hum Genet,1982,61(2):85-90.
31. Burt D.W. Chicken genome: current status and future opportunities. Genome Res,2005,15(12):1692-1698.
32. Butler J., MacCallum I., Kleber M., et al. ALLPATHS: de novo assembly of whole-genomeshotgun microreads. Genome Res,2008,18(5):810-820.
33. Carninci P., Sandelin A., Lenhard B., et al. Genome-wide analysis of mammalian promoterarchitecture and evolution. Nat Genet,2006,38(6):626-635.
34. Chaisson M.J., Pevzner P.A. Short read fragment assembly of bacterial genomes. Genome Res,2008,18(2):324-330.
35. Chen Y., Souaiaia T., Chen T. PerM: efficient mapping of short sequencing reads with periodic fullsensitive spaced seeds. Bioinformatics,2009,25(19):2514-2521.
36. Dalca A.V., Brudno M. Genome variation discovery with high-throughput sequencing data. BriefBioinform,2010,11(1):3-14.
37. Dayarian A., Michael T.P., Sengupta A.M. SOPRA: Scaffolding algorithm for paired reads viastatistical optimization. BMC Bioinformatics,2010,11:345.
38. de Roos A.P., Schrooten C., Mullaart E., et al. Breeding value estimation for fat percentage usingdense markers on Bos taurus autosome14. J Dairy Sci,2007,90(10):4821-4829.
39. Decker J.E., Pires J.C., Conant G.C., et al. Resolving the evolution of extant and extinct ruminantswith high-throughput phylogenomics. Proc Natl Acad Sci U S A,2009,106(44):18644-18649.
40. Delcher A.L., Kasif S., Fleischmann R.D., et al. Alignment of whole genomes. Nucleic Acids Res,1999,27(11):2369-2376.
41. Dohm J.C., Lottaz C., Borodina T., et al. Substantial biases in ultra-short read data sets fromhigh-throughput DNA sequencing. Nucleic Acids Res,2008,36(16):e105.
42. Dressman D., Yan H., Traverso G., et al. Transforming single DNA molecules into fluorescentmagnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci U S A,2003,100(15):8817-8822.
43. Elsik C.G., Tellam R.L., Worley K.C., et al. The genome sequence of taurine cattle: a window toruminant biology and evolution. Science,2009,324(5926):522-528.
44. Ewing B., Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities.Genome Res,1998,8(3):186-194.
45. Fan J.B., Gunderson K.L., Bibikova M., et al. Illumina universal bead arrays. Methods Enzymol,2006,410:57-73.
46. Fedurco M., Romieu A., Williams S., et al. BTA, a novel reagent for DNA attachment on glass andefficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res,2006,34(3):e22.
47. Feng Q., Moran J.V., Kazazian H.J., et al. Human L1retrotransposon encodes a conservedendonuclease required for retrotransposition. Cell,1996,87(5):905-916.
48. Flicek P., Birney E. Sense from sequence reads: methods for alignment and assembly. NatMethods,2009,6(11Suppl):S6-S12.
49. Florea L., Souvorov A., Kalbfleisch T.S., et al. Genome assembly has a major impact on genecontent: a comparison of annotation in two Bos taurus assemblies. PLoS One,2011,6(6):e21400.
50. Gilbert C., Ropiquet A., Hassanin A. Mitochondrial and nuclear phylogenies of Cervidae(Mammalia, Ruminantia): Systematics, morphology, and biogeography. Mol Phylogenet Evol,2006,40(1):101-117.
51. Goloboff P.A. Analyzing large data sets in reasonable times: solutions for composite optima.Cladistics,1999,15(4):415-428.
52. Gonzalez-Recio O., Gianola D., Rosa G.J., et al. Genome-assisted prediction of a quantitative traitmeasured in parents and progeny: application to food conversion rate in chickens. Genet Sel Evol,2009,41:3.
53. Green E.D. Strategies for the systematic sequencing of complex genomes. Nat Rev Genet,2001,2(8):573-583.
54. Groenen M.A., Megens H.J., Zare Y., et al. The development and characterization of a60K SNPchip for chicken. BMC Genomics,2011,12(1):274.
55. Havlak P., Chen R., Durbin K.J., et al. The Atlas genome assembly system. Genome Res,2004,14(4):721-732.
56. Hillier LW M.W.B.E. Sequence and comparative analysis of the chicken genome provide uniqueperspectives on vertebrate evolution. Nature,2004,432(432):695-716.
57. Homer N., Merriman B., Nelson S.F. BFAST: an alignment tool for large scale genomeresequencing. PLoS One,2009,4(11):e7767.
58. Huang X., Wang J., Aluru S., et al. PCAP: a whole-genome assembly program. Genome Res,2003,13(9):2164-2170.
59. Itai A., Papadimitriou C.H., Szwarcfiter A.L. Hamilton Paths in Grid Graphs. SIAM J. Comput.,1982,11(4):676-686.
60. Jaenisch R., Wilmut I. Developmental biology. Don't clone humans!. Science,2001,291(5513):2552.
61. Jarne P., Lagoda P.J. Microsatellites, from molecules to populations and back. Trends Ecol Evol,1996,11(10):424-429.
62. Kamimura N., Ishii S., Ma L.D., et al. Three separate mitochondrial DNA sequences arecontiguous in human genomic DNA. J Mol Biol,1989,210(4):703-707.
63. Kashi Y., King D., Soller M. Simple sequence repeats as a source of quantitative genetic variation.Trends Genet,1997,13(2):74-78.
64. Kimura M. Evolutionary rate at the molecular level. Nature,1968,217(5129):624-626.
65. Kurtz S., Phillippy A., Delcher A.L., et al. Versatile and open software for comparing largegenomes. Genome Biol,2004,5(2):R12.
66. Kuwayama R., Ozawa T. Phylogenetic relationships among european red deer, wapiti, and sikadeer inferred from mitochondrial DNA sequences. Mol Phylogenet Evol,2000,15(1):115-123.
67. Lander E.S. The new genomics: global views of biology. Science,1996,274(5287):536-539.
68. Lander E.S., Linton L.M., Birren B., et al. Initial sequencing and analysis of the human genome.Nature,2001,409(6822):860-921.
69. Langmead B., Trapnell C., Pop M., et al. Ultrafast and memory-efficient alignment of short DNAsequences to the human genome. Genome Biol,2009,10(3):R25.
70. Lee H., Tang H. Next-generation sequencing technologies and fragment assembly algorithms.Methods Mol Biol,2012,855:155-174.
71. Li C., Yang F., Sheppard A. Adult stem cells and mammalian epimorphic regeneration-insightsfrom studying annual renewal of deer antlers. Curr Stem Cell Res Ther,2009,4(3):237-251.
72. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics,2009,25(14):1754-1760.
73. Li H., Handsaker B., Wysoker A., et al. The Sequence Alignment/Map format and SAMtools.Bioinformatics,2009,25(16):2078-2079.
74. Li H., Ruan J., Durbin R. Mapping short DNA sequencing reads and calling variants usingmapping quality scores. Genome Res,2008,18(11):1851-1858.
75. Li R., Fan W., Tian G., et al. The sequence and de novo assembly of the giant panda genome.Nature,2010,463(7279):311-317.
76. Li R., Li Y., Kristiansen K., et al. SOAP: short oligonucleotide alignment program. Bioinformatics,2008,24(5):713-714.
77. Li R., Yu C., Li Y., et al. SOAP2: an improved ultrafast tool for short read alignment.Bioinformatics,2009,25(15):1966-1967.
78. Li R., Zhu H., Ruan J., et al. De novo assembly of human genomes with massively parallel shortread sequencing. Genome Res,2010,20(2):265-272.
79. Li W., Zhang P., Fellers J.P., et al. Sequence composition, organization, and evolution of the coreTriticeae genome. Plant J,2004,40(4):500-511.
80. Li Y., Vinckenbosch N., Tian G., et al. Resequencing of200human exomes identifies an excess oflow-frequency non-synonymous coding variants. Nat Genet,2010,42(11):969-972.
81. Lin H., Zhang Z., Zhang M.Q., et al. ZOOM! Zillions of oligos mapped. Bioinformatics,2008,24(21):2431-2437.
82. Liu Y., Qin X., Song X.Z., et al. Bos taurus genome assembly. BMC Genomics,2009,10:180.
83. Lopez J.V., Yuhki N., Masuda R., et al. Numt, a recent transfer and tandem amplification ofmitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol,1994,39(2):174-190.
84. Ludt C.J., Schroeder W., Rottmann O., et al. Mitochondrial DNA phylogeography of red deer(Cervus elaphus). Mol Phylogenet Evol,2004,31(3):1064-1083.
85. Ma B., Tromp J., Li M. PatternHunter: faster and more sensitive homology search. Bioinformatics,2002,18(3):440-445.
86. Marra M.A., Kucaba T.A., Dietrich N.L., et al. High throughput fingerprint analysis of large-insertclones. Genome Res,1997,7(11):1072-1084.
87. Matukumalli L.K., Lawley C.T., Schnabel R.D., et al. Development and characterization of a highdensity SNP genotyping assay for cattle. PLoS One,2009,4(4):e5350.
88. McCarthy E.M., McDonald J.F. Long terminal repeat retrotransposons of Mus musculus. GenomeBiol,2004,5(3):R14.
89. Messing J., Crea R., Seeburg P.H. A system for shotgun DNA sequencing. Nucleic Acids Res,1981,9(2):309-321.
90. Mikkelsen T.S., Hillier L.W., Eichler E.E., et al. Initial sequence of the chimpanzee genome andcomparison with the human genome. Nature,2005,437(7055):69-87.
91. Milne I., Bayer M., Cardle L., et al. Tablet--next generation sequence assembly visualization.Bioinformatics,2010,26(3):401-402.
92. Myers A., Holmans P., Marshall H., et al. Susceptibility locus for Alzheimer's disease onchromosome10. Science,2000,290(5500):2304-2305.
93. Needleman S.B., Wunsch C.D. A general method applicable to the search for similarities in theamino acid sequence of two proteins. J Mol Biol,1970,48(3):443-453.
94. Olson M.V. The maps. Clone by clone by clone. Nature,2001,409(6822):816-818.
95. Osoegawa K., Woon P.Y., Zhao B., et al. An improved approach for construction of bacterialartificial chromosome libraries. Genomics,1998,52(1):1-8.
96. Pavlicek A., Hrda S., Flegr J. Free-Tree--freeware program for construction of phylogenetic treeson the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Application inthe RAPD analysis of genus Frenkelia. Folia Biol (Praha),1999,45(3):97-99.
97. Pevzner P.A., Tang H., Waterman M.S. An Eulerian path approach to DNA fragment assembly.Proc Natl Acad Sci U S A,2001,98(17):9748-9753.
98. Pereira S., Baker A. Low number of mitochondrial pseudogenes in the chicken (Gallus gallus)nuclear genome: implications for molecular inference of population history and phylogenetics.BMC Evolutionary Biology,2004,4(1):1.
99. Pfeifer G.P., Steigerwald S.D., Mueller P.R., et al. Genomic sequencing and methylation analysisby ligation mediated PCR. Science,1989,246(4931):810-813.
100. Polziehn R.O., Strobeck C. Phylogeny of wapiti, red deer, sika deer, and other North Americancervids as determined from mitochondrial DNA. Mol Phylogenet Evol,1998,10(2):249-258.
101. Pop M., Kosack D. Using the TIGR assembler in shotgun sequencing projects. Methods Mol Biol,2004,255:279-294.
102. Ramos A.M., Crooijmans R.P., Affara N.A., et al. Design of a high density SNP genotyping assayin the pig using SNPs identified and characterized by next generation sequencing technology.PLoS One,2009,4(8):e6524.
103. Robertson G., Hirst M., Bainbridge M., et al. Genome-wide profiles of STAT1DNA associationusing chromatin immunoprecipitation and massively parallel sequencing. Nat Methods,2007,4(8):651-657.
104. Rostoks N., Mudie S., Cardle L., et al. Genome-wide SNP discovery and linkage analysis in barleybased on genes responsive to abiotic stress. Mol Genet Genomics,2005,274(5):515-527.
105. Rumble S.M., Lacroute P., Dalca A.V., et al. SHRiMP: accurate mapping of short color-spacereads. PLoS Comput Biol,2009,5(5):e1000386.
106. Sachidanandam R., Weissman D., Schmidt S.C., et al. A map of human genome sequence variationcontaining1.42million single nucleotide polymorphisms. Nature,2001,409(6822):928-933.
107. Sanger F., Coulson A.R., Hong G.F., et al. Nucleotide sequence of bacteriophage lambda DNA. JMol Biol,1982,162(4):729-773.
108. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain-terminating inhibitors.1977.Biotechnology,1992,24:104-108.
109. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain-terminating inhibitors. Proc NatlAcad Sci U S A,1977,74(12):5463-5467.
110. Schatz M.C., Delcher A.L., Salzberg S.L. Assembly of large genomes using second-generationsequencing. Genome Res,2010,20(9):1165-1173.
111. Seo T.S., Bai X., Kim D.H., et al. Four-color DNA sequencing by synthesis on a chip usingphotocleavable fluorescent nucleotides. Proc Natl Acad Sci U S A,2005,102(17):5926-5931.
112. Seabury C.M., Bhattarai E.K., Taylor J.F., et al. Genome-wide polymorphism and comparative analysesin the white-tailed deer (Odocoileus virginianus): a model for conservation genomics. PLoS One,2011,6(1):e15811.
113. Simpson J.T., Wong K., Jackman S.D., et al. ABySS: a parallel assembler for short read sequencedata. Genome Res,2009,19(6):1117-1123.
114. Singer M.F. SINEs and LINEs: highly repeated short and long interspersed sequences inmammalian genomes. Cell,1982,28(3):433-434.
115. Slate J., Coltman D.W., Goodman S.J., et al. Bovine microsatellite loci are highly conserved in reddeer (Cervus elaphus), sika deer (Cervus nippon) and Soay sheep (Ovis aries). Anim Genet,1998,29(4):307-315.
116. Slate J., Van Stijn T.C., Anderson R.M., et al. A deer (subfamily Cervinae) genetic linkage mapand the evolution of ruminant genomes. Genetics,2002,160(4):1587-1597.
117. Smith T.F., Waterman M.S. Identification of common molecular subsequences. J Mol Biol,1981,147(1):195-197.
118. Soderlund C., Longden I., Mott R. FPC: a system for building contigs from restrictionfingerprinted clones. Comput Appl Biosci,1997,13(5):523-535.
119. Souaiaia T., Frazier Z., Chen T. ComB: SNP calling and mapping analysis for color and nucleotidespace platforms. J Comput Biol,2011,18(6):795-807.
120. Tatusova T.A., Madden T.L. BLAST2Sequences, a new tool for comparing protein andnucleotide sequences. FEMS Microbiol Lett,1999,174(2):247-250.
121. Tourmen Y., Baris O., Dessen P., et al. Structure and chromosomal distribution of humanmitochondrial pseudogenes. Genomics,2002,80(1):71-77.
122. Trapnell C., Salzberg S.L. How to map billions of short reads onto genomes. Nat Biotechnol,2009,27(5):455-457.
123. Van Tassell C.P., Smith T.P., Matukumalli L.K., et al. SNP discovery and allele frequencyestimation by deep sequencing of reduced representation libraries. Nat Methods,2008,5(3):247-252.
124. VanRaden P.M., Van Tassell C.P., Wiggans G.R., et al. Invited review: reliability of genomicpredictions for North American Holstein bulls. J Dairy Sci,2009,92(1):16-24.
125. Venkatesh B., Gilligan P., Brenner S. Fugu: a compact vertebrate reference genome. FEBS Lett,2000,476(1-2):3-7.
126. Venter J.C., Adams M.D., Myers E.W., et al. The sequence of the human genome. Science,2001,291(5507):1304-1351.
127. Wade C.M., Giulotto E., Sigurdsson S., et al. Genome sequence, comparative analysis, andpopulation genetics of the domestic horse. Science,2009,326(5954):865-867.
128. Wang J., Wang W., Li R., et al. The diploid genome sequence of an Asian individual. Nature,2008,456(7218):60-65.
129. Wetterbom A., Sevov M., Cavelier L., et al. Comparative genomic analysis of human andchimpanzee indicates a key role for indels in primate evolution. J Mol Evol,2006,63(5):682-690.
130. Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs.Genome Res,2008,18(5):821-829.
131. Zhang D.X., Hewitt G.M. Nuclear integrations: challenges for mitochondrial DNA markers.Trends Ecol Evol,1996,11(6):247-251.
132. Zimin A.V., Delcher A.L., Florea L., et al. A whole-genome assembly of the domestic cow, Bostaurus. Genome Biol,2009,10(4):R42.
2.韩建文,张学军.全基因组关联研究现状.遗传,2011(1):25-35.
3.何余湧,李完波,张志燕等.利用全基因组高通量SNP标记定位二花脸×沙子岭家系中的断奶体重QTL.中国农业科学,2011(22):4694-4699.
4.李春义,王文英.鹿茸成分研究探讨.特产研究,1990(4):19-22.
5.李明,王小明,盛和林等.四种鹿属动物的线粒体DNA差异和系统进化关系研究.动物学报,1999(1):99-105.
6.李义,吴国栋,左瑾等.应用单核苷酸多态性技术筛查2型糖尿病易感基因.中国医学科学院学报,2005(3).
7.刘海,杨光,魏辅文等.中国大陆梅花鹿mtDNA控制区序列变异及种群遗传结构分析.动物学报,2003(1).
8.吕晓平,魏辅文,李明等.中国梅花鹿(Cervus nippon)遗传多样性及与日本梅花鹿间的系统关系.科学通报,2006(3):292-298.
9.盛和林.中国鹿科动物.生物学通报,1992(5):4-7.
10.唐立群,肖层林,王伟平. SNP分子标记的研究及其应用进展.中国农学通报,2012(12):154-158.
11.田埂,苏夜阳.从“人类”基因组计划到“千人”基因组计划.生命世界,2011(8):54-57.
12.王继文.动物线粒体假基因的识别及其在进化生物学中的应用.动物学杂志,2004(3):103-108.
13.王继文,许恒勇.动物线粒体假基因的特征及产生机制.安徽农业科学,2005(3):496-498.
14.岳桂东,高强,罗龙海等.高通量测序技术在动植物研究领域中的应用.中国科学:生命科学,2012(2):107-124.
15.王兴春,杨致荣,王敏等.高通量测序技术及其应用.中国生物工程杂志,2012(1):109-114.
16.燕燕.国际千人基因组计划首阶段成功完成:深圳特区报[Z].2010.
17.赵辉,李启寨,李俊等.相邻碱基组分与产生SNP的转换或颠换在植物基因组中的研究.中国科学C辑:生命科学,2006(1):1-8.
18.周晓光,任鲁风,李运涛等.下一代测序技术:技术回顾与展望.中国科学:生命科学,2010(1):23-37.
19.邹新慧,葛颂.基因树冲突与系统发育基因组学研究.植物分类学报,2008(6):795-807.
20.邹喻苹,葛颂.新一代分子标记——SNPs及其应用.生物多样性,2003(5):370-382.
21. Adams M.D., Celniker S.E., Holt R.A., et al. The genome sequence of Drosophila melanogaster.Science,2000,287(5461):2185-2195.
22. Archibald A.L., Bolund L., Churcher C., et al. Pig genome sequence--analysis and publicationstrategy. BMC Genomics,2010,11:438.
23. Archibald A.L., Cockett N.E., Dalrymple B.P., et al. The sheep genome reference sequence: awork in progress. Anim Genet,2010,41(5):449-453.
24. Bai Y., Sartor M., Cavalcoli J. Current Status and Future Perspectives for Sequencing LivestockGenomes. Journal of Animal Science and Biotechnology,2012,3(1):8-12.
25. Basti G., Perrone A.L. A fast hybrid block-sorting algorithm for lossless interferometric datacompression[Z].2003:5103,92.
26. Batzoglou S., Jaffe D.B., Stanley K., et al. ARACHNE: a whole-genome shotgun assembler.Genome Res,2002,12(1):177-189.
27. Bentley D.R. Whole-genome re-sequencing. Curr Opin Genet Dev,2006,16(6):545-552.
28. Boetzer M., Henkel C.V., Jansen H.J., et al. Scaffolding pre-assembled contigs using SSPACE.Bioinformatics,2011,27(4):578-579.
29. Brooks S.A., Gabreski N., Miller D., et al. Whole-genome SNP association in the horse:identification of a deletion in myosin Va responsible for Lavender Foal Syndrome. PLoS Genet,2010,6(4):e1000909.
30. Burgoyne P.S. Genetic homology and crossing over in the X and Y chromosomes of Mammals.Hum Genet,1982,61(2):85-90.
31. Burt D.W. Chicken genome: current status and future opportunities. Genome Res,2005,15(12):1692-1698.
32. Butler J., MacCallum I., Kleber M., et al. ALLPATHS: de novo assembly of whole-genomeshotgun microreads. Genome Res,2008,18(5):810-820.
33. Carninci P., Sandelin A., Lenhard B., et al. Genome-wide analysis of mammalian promoterarchitecture and evolution. Nat Genet,2006,38(6):626-635.
34. Chaisson M.J., Pevzner P.A. Short read fragment assembly of bacterial genomes. Genome Res,2008,18(2):324-330.
35. Chen Y., Souaiaia T., Chen T. PerM: efficient mapping of short sequencing reads with periodic fullsensitive spaced seeds. Bioinformatics,2009,25(19):2514-2521.
36. Dalca A.V., Brudno M. Genome variation discovery with high-throughput sequencing data. BriefBioinform,2010,11(1):3-14.
37. Dayarian A., Michael T.P., Sengupta A.M. SOPRA: Scaffolding algorithm for paired reads viastatistical optimization. BMC Bioinformatics,2010,11:345.
38. de Roos A.P., Schrooten C., Mullaart E., et al. Breeding value estimation for fat percentage usingdense markers on Bos taurus autosome14. J Dairy Sci,2007,90(10):4821-4829.
39. Decker J.E., Pires J.C., Conant G.C., et al. Resolving the evolution of extant and extinct ruminantswith high-throughput phylogenomics. Proc Natl Acad Sci U S A,2009,106(44):18644-18649.
40. Delcher A.L., Kasif S., Fleischmann R.D., et al. Alignment of whole genomes. Nucleic Acids Res,1999,27(11):2369-2376.
41. Dohm J.C., Lottaz C., Borodina T., et al. Substantial biases in ultra-short read data sets fromhigh-throughput DNA sequencing. Nucleic Acids Res,2008,36(16):e105.
42. Dressman D., Yan H., Traverso G., et al. Transforming single DNA molecules into fluorescentmagnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci U S A,2003,100(15):8817-8822.
43. Elsik C.G., Tellam R.L., Worley K.C., et al. The genome sequence of taurine cattle: a window toruminant biology and evolution. Science,2009,324(5926):522-528.
44. Ewing B., Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities.Genome Res,1998,8(3):186-194.
45. Fan J.B., Gunderson K.L., Bibikova M., et al. Illumina universal bead arrays. Methods Enzymol,2006,410:57-73.
46. Fedurco M., Romieu A., Williams S., et al. BTA, a novel reagent for DNA attachment on glass andefficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res,2006,34(3):e22.
47. Feng Q., Moran J.V., Kazazian H.J., et al. Human L1retrotransposon encodes a conservedendonuclease required for retrotransposition. Cell,1996,87(5):905-916.
48. Flicek P., Birney E. Sense from sequence reads: methods for alignment and assembly. NatMethods,2009,6(11Suppl):S6-S12.
49. Florea L., Souvorov A., Kalbfleisch T.S., et al. Genome assembly has a major impact on genecontent: a comparison of annotation in two Bos taurus assemblies. PLoS One,2011,6(6):e21400.
50. Gilbert C., Ropiquet A., Hassanin A. Mitochondrial and nuclear phylogenies of Cervidae(Mammalia, Ruminantia): Systematics, morphology, and biogeography. Mol Phylogenet Evol,2006,40(1):101-117.
51. Goloboff P.A. Analyzing large data sets in reasonable times: solutions for composite optima.Cladistics,1999,15(4):415-428.
52. Gonzalez-Recio O., Gianola D., Rosa G.J., et al. Genome-assisted prediction of a quantitative traitmeasured in parents and progeny: application to food conversion rate in chickens. Genet Sel Evol,2009,41:3.
53. Green E.D. Strategies for the systematic sequencing of complex genomes. Nat Rev Genet,2001,2(8):573-583.
54. Groenen M.A., Megens H.J., Zare Y., et al. The development and characterization of a60K SNPchip for chicken. BMC Genomics,2011,12(1):274.
55. Havlak P., Chen R., Durbin K.J., et al. The Atlas genome assembly system. Genome Res,2004,14(4):721-732.
56. Hillier LW M.W.B.E. Sequence and comparative analysis of the chicken genome provide uniqueperspectives on vertebrate evolution. Nature,2004,432(432):695-716.
57. Homer N., Merriman B., Nelson S.F. BFAST: an alignment tool for large scale genomeresequencing. PLoS One,2009,4(11):e7767.
58. Huang X., Wang J., Aluru S., et al. PCAP: a whole-genome assembly program. Genome Res,2003,13(9):2164-2170.
59. Itai A., Papadimitriou C.H., Szwarcfiter A.L. Hamilton Paths in Grid Graphs. SIAM J. Comput.,1982,11(4):676-686.
60. Jaenisch R., Wilmut I. Developmental biology. Don't clone humans!. Science,2001,291(5513):2552.
61. Jarne P., Lagoda P.J. Microsatellites, from molecules to populations and back. Trends Ecol Evol,1996,11(10):424-429.
62. Kamimura N., Ishii S., Ma L.D., et al. Three separate mitochondrial DNA sequences arecontiguous in human genomic DNA. J Mol Biol,1989,210(4):703-707.
63. Kashi Y., King D., Soller M. Simple sequence repeats as a source of quantitative genetic variation.Trends Genet,1997,13(2):74-78.
64. Kimura M. Evolutionary rate at the molecular level. Nature,1968,217(5129):624-626.
65. Kurtz S., Phillippy A., Delcher A.L., et al. Versatile and open software for comparing largegenomes. Genome Biol,2004,5(2):R12.
66. Kuwayama R., Ozawa T. Phylogenetic relationships among european red deer, wapiti, and sikadeer inferred from mitochondrial DNA sequences. Mol Phylogenet Evol,2000,15(1):115-123.
67. Lander E.S. The new genomics: global views of biology. Science,1996,274(5287):536-539.
68. Lander E.S., Linton L.M., Birren B., et al. Initial sequencing and analysis of the human genome.Nature,2001,409(6822):860-921.
69. Langmead B., Trapnell C., Pop M., et al. Ultrafast and memory-efficient alignment of short DNAsequences to the human genome. Genome Biol,2009,10(3):R25.
70. Lee H., Tang H. Next-generation sequencing technologies and fragment assembly algorithms.Methods Mol Biol,2012,855:155-174.
71. Li C., Yang F., Sheppard A. Adult stem cells and mammalian epimorphic regeneration-insightsfrom studying annual renewal of deer antlers. Curr Stem Cell Res Ther,2009,4(3):237-251.
72. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics,2009,25(14):1754-1760.
73. Li H., Handsaker B., Wysoker A., et al. The Sequence Alignment/Map format and SAMtools.Bioinformatics,2009,25(16):2078-2079.
74. Li H., Ruan J., Durbin R. Mapping short DNA sequencing reads and calling variants usingmapping quality scores. Genome Res,2008,18(11):1851-1858.
75. Li R., Fan W., Tian G., et al. The sequence and de novo assembly of the giant panda genome.Nature,2010,463(7279):311-317.
76. Li R., Li Y., Kristiansen K., et al. SOAP: short oligonucleotide alignment program. Bioinformatics,2008,24(5):713-714.
77. Li R., Yu C., Li Y., et al. SOAP2: an improved ultrafast tool for short read alignment.Bioinformatics,2009,25(15):1966-1967.
78. Li R., Zhu H., Ruan J., et al. De novo assembly of human genomes with massively parallel shortread sequencing. Genome Res,2010,20(2):265-272.
79. Li W., Zhang P., Fellers J.P., et al. Sequence composition, organization, and evolution of the coreTriticeae genome. Plant J,2004,40(4):500-511.
80. Li Y., Vinckenbosch N., Tian G., et al. Resequencing of200human exomes identifies an excess oflow-frequency non-synonymous coding variants. Nat Genet,2010,42(11):969-972.
81. Lin H., Zhang Z., Zhang M.Q., et al. ZOOM! Zillions of oligos mapped. Bioinformatics,2008,24(21):2431-2437.
82. Liu Y., Qin X., Song X.Z., et al. Bos taurus genome assembly. BMC Genomics,2009,10:180.
83. Lopez J.V., Yuhki N., Masuda R., et al. Numt, a recent transfer and tandem amplification ofmitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol,1994,39(2):174-190.
84. Ludt C.J., Schroeder W., Rottmann O., et al. Mitochondrial DNA phylogeography of red deer(Cervus elaphus). Mol Phylogenet Evol,2004,31(3):1064-1083.
85. Ma B., Tromp J., Li M. PatternHunter: faster and more sensitive homology search. Bioinformatics,2002,18(3):440-445.
86. Marra M.A., Kucaba T.A., Dietrich N.L., et al. High throughput fingerprint analysis of large-insertclones. Genome Res,1997,7(11):1072-1084.
87. Matukumalli L.K., Lawley C.T., Schnabel R.D., et al. Development and characterization of a highdensity SNP genotyping assay for cattle. PLoS One,2009,4(4):e5350.
88. McCarthy E.M., McDonald J.F. Long terminal repeat retrotransposons of Mus musculus. GenomeBiol,2004,5(3):R14.
89. Messing J., Crea R., Seeburg P.H. A system for shotgun DNA sequencing. Nucleic Acids Res,1981,9(2):309-321.
90. Mikkelsen T.S., Hillier L.W., Eichler E.E., et al. Initial sequence of the chimpanzee genome andcomparison with the human genome. Nature,2005,437(7055):69-87.
91. Milne I., Bayer M., Cardle L., et al. Tablet--next generation sequence assembly visualization.Bioinformatics,2010,26(3):401-402.
92. Myers A., Holmans P., Marshall H., et al. Susceptibility locus for Alzheimer's disease onchromosome10. Science,2000,290(5500):2304-2305.
93. Needleman S.B., Wunsch C.D. A general method applicable to the search for similarities in theamino acid sequence of two proteins. J Mol Biol,1970,48(3):443-453.
94. Olson M.V. The maps. Clone by clone by clone. Nature,2001,409(6822):816-818.
95. Osoegawa K., Woon P.Y., Zhao B., et al. An improved approach for construction of bacterialartificial chromosome libraries. Genomics,1998,52(1):1-8.
96. Pavlicek A., Hrda S., Flegr J. Free-Tree--freeware program for construction of phylogenetic treeson the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Application inthe RAPD analysis of genus Frenkelia. Folia Biol (Praha),1999,45(3):97-99.
97. Pevzner P.A., Tang H., Waterman M.S. An Eulerian path approach to DNA fragment assembly.Proc Natl Acad Sci U S A,2001,98(17):9748-9753.
98. Pereira S., Baker A. Low number of mitochondrial pseudogenes in the chicken (Gallus gallus)nuclear genome: implications for molecular inference of population history and phylogenetics.BMC Evolutionary Biology,2004,4(1):1.
99. Pfeifer G.P., Steigerwald S.D., Mueller P.R., et al. Genomic sequencing and methylation analysisby ligation mediated PCR. Science,1989,246(4931):810-813.
100. Polziehn R.O., Strobeck C. Phylogeny of wapiti, red deer, sika deer, and other North Americancervids as determined from mitochondrial DNA. Mol Phylogenet Evol,1998,10(2):249-258.
101. Pop M., Kosack D. Using the TIGR assembler in shotgun sequencing projects. Methods Mol Biol,2004,255:279-294.
102. Ramos A.M., Crooijmans R.P., Affara N.A., et al. Design of a high density SNP genotyping assayin the pig using SNPs identified and characterized by next generation sequencing technology.PLoS One,2009,4(8):e6524.
103. Robertson G., Hirst M., Bainbridge M., et al. Genome-wide profiles of STAT1DNA associationusing chromatin immunoprecipitation and massively parallel sequencing. Nat Methods,2007,4(8):651-657.
104. Rostoks N., Mudie S., Cardle L., et al. Genome-wide SNP discovery and linkage analysis in barleybased on genes responsive to abiotic stress. Mol Genet Genomics,2005,274(5):515-527.
105. Rumble S.M., Lacroute P., Dalca A.V., et al. SHRiMP: accurate mapping of short color-spacereads. PLoS Comput Biol,2009,5(5):e1000386.
106. Sachidanandam R., Weissman D., Schmidt S.C., et al. A map of human genome sequence variationcontaining1.42million single nucleotide polymorphisms. Nature,2001,409(6822):928-933.
107. Sanger F., Coulson A.R., Hong G.F., et al. Nucleotide sequence of bacteriophage lambda DNA. JMol Biol,1982,162(4):729-773.
108. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain-terminating inhibitors.1977.Biotechnology,1992,24:104-108.
109. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain-terminating inhibitors. Proc NatlAcad Sci U S A,1977,74(12):5463-5467.
110. Schatz M.C., Delcher A.L., Salzberg S.L. Assembly of large genomes using second-generationsequencing. Genome Res,2010,20(9):1165-1173.
111. Seo T.S., Bai X., Kim D.H., et al. Four-color DNA sequencing by synthesis on a chip usingphotocleavable fluorescent nucleotides. Proc Natl Acad Sci U S A,2005,102(17):5926-5931.
112. Seabury C.M., Bhattarai E.K., Taylor J.F., et al. Genome-wide polymorphism and comparative analysesin the white-tailed deer (Odocoileus virginianus): a model for conservation genomics. PLoS One,2011,6(1):e15811.
113. Simpson J.T., Wong K., Jackman S.D., et al. ABySS: a parallel assembler for short read sequencedata. Genome Res,2009,19(6):1117-1123.
114. Singer M.F. SINEs and LINEs: highly repeated short and long interspersed sequences inmammalian genomes. Cell,1982,28(3):433-434.
115. Slate J., Coltman D.W., Goodman S.J., et al. Bovine microsatellite loci are highly conserved in reddeer (Cervus elaphus), sika deer (Cervus nippon) and Soay sheep (Ovis aries). Anim Genet,1998,29(4):307-315.
116. Slate J., Van Stijn T.C., Anderson R.M., et al. A deer (subfamily Cervinae) genetic linkage mapand the evolution of ruminant genomes. Genetics,2002,160(4):1587-1597.
117. Smith T.F., Waterman M.S. Identification of common molecular subsequences. J Mol Biol,1981,147(1):195-197.
118. Soderlund C., Longden I., Mott R. FPC: a system for building contigs from restrictionfingerprinted clones. Comput Appl Biosci,1997,13(5):523-535.
119. Souaiaia T., Frazier Z., Chen T. ComB: SNP calling and mapping analysis for color and nucleotidespace platforms. J Comput Biol,2011,18(6):795-807.
120. Tatusova T.A., Madden T.L. BLAST2Sequences, a new tool for comparing protein andnucleotide sequences. FEMS Microbiol Lett,1999,174(2):247-250.
121. Tourmen Y., Baris O., Dessen P., et al. Structure and chromosomal distribution of humanmitochondrial pseudogenes. Genomics,2002,80(1):71-77.
122. Trapnell C., Salzberg S.L. How to map billions of short reads onto genomes. Nat Biotechnol,2009,27(5):455-457.
123. Van Tassell C.P., Smith T.P., Matukumalli L.K., et al. SNP discovery and allele frequencyestimation by deep sequencing of reduced representation libraries. Nat Methods,2008,5(3):247-252.
124. VanRaden P.M., Van Tassell C.P., Wiggans G.R., et al. Invited review: reliability of genomicpredictions for North American Holstein bulls. J Dairy Sci,2009,92(1):16-24.
125. Venkatesh B., Gilligan P., Brenner S. Fugu: a compact vertebrate reference genome. FEBS Lett,2000,476(1-2):3-7.
126. Venter J.C., Adams M.D., Myers E.W., et al. The sequence of the human genome. Science,2001,291(5507):1304-1351.
127. Wade C.M., Giulotto E., Sigurdsson S., et al. Genome sequence, comparative analysis, andpopulation genetics of the domestic horse. Science,2009,326(5954):865-867.
128. Wang J., Wang W., Li R., et al. The diploid genome sequence of an Asian individual. Nature,2008,456(7218):60-65.
129. Wetterbom A., Sevov M., Cavelier L., et al. Comparative genomic analysis of human andchimpanzee indicates a key role for indels in primate evolution. J Mol Evol,2006,63(5):682-690.
130. Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs.Genome Res,2008,18(5):821-829.
131. Zhang D.X., Hewitt G.M. Nuclear integrations: challenges for mitochondrial DNA markers.Trends Ecol Evol,1996,11(6):247-251.
132. Zimin A.V., Delcher A.L., Florea L., et al. A whole-genome assembly of the domestic cow, Bostaurus. Genome Biol,2009,10(4):R42.
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