請用此 Handle URI 來引用此文件：
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/67877完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 蔡怡陞(Isheng Jason Tsai) | |
| dc.contributor.author | Dang Liu | en |
| dc.contributor.author | 劉當 | zh_TW |
| dc.date.accessioned | 2021-06-17T01:55:32Z | - |
| dc.date.available | 2020-08-29 | |
| dc.date.copyright | 2017-08-29 | |
| dc.date.issued | 2017 | |
| dc.date.submitted | 2017-07-21 | |
| dc.identifier.citation | References 1. Touchman J. Comparative Genomics. Nat Educ Knowl. 2010;3: 13. doi:10.1007/978-3-642-37146-2 2. Ureta-Vidal A, Ettwiller L, Birney E. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat Rev Genet. 2003;4: 251–262. doi:10.1038/nrg1043 3. Penny D. Darwin’s theory of descent with modification, versus the biblical tree of life. PLoS Biol. 2011;9. doi:10.1371/journal.pbio.1001096 4. Koonin E V. Orthologs, Paralogs, and Evolutionary Genomics. Annu Rev Genet. 2005;39: 309–338. doi:10.1146/annurev.genet.39.073003.114725 5. Chen F, Mackey AJ, Vermunt JK, Roos DS. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One. 2007;2. doi:10.1371/journal.pone.0000383 6. Gabaldón T, Koonin E V. Functional and evolutionary implications of gene orthology. Nat Rev Genet. Nature Publishing Group; 2013;14: 360–366. doi:10.1038/nrg3456 7. Yang Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24: 1586–1591. doi:10.1093/molbev/msm088 8. Langille M, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes J, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31: 814–21. doi:10.1038/nbt.2676 9. Petrov AS, Bernier CR, Gulen B, Waterbury CC, Hershkovits E, Hsiao C, et al. Secondary structures of rRNAs from all three domains of life. PLoS One. 2014;9. doi:10.1371/journal.pone.0088222 10. Doolittle WF, Logsdon JM. Archaeal genomics: do archaea have a mixed heritage? Curr Biol. 1998;8: R209–R211. doi:10.1016/S0960-9822(98)70127-7 11. Huynen MA, Bork P. Measuring genome evolution. Proc Natl Acad Sci. 1998;95: 5849–5856. doi:10.1073/pnas.95.11.5849 12. Snel B, Bork P, Huynen M a. Genome phylogeny based on gene content. Nat Genet. 1999;21: 108–110. doi:10.1038/5052 13. Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, Nichol S, Tracey A, et al. Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. Nat Genet. Nature Publishing Group; 2014;46: 693–700. doi:10.1038/ng.3010 14. Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, et al. The genomic basis of parasitism in the Strongyloides clade of nematodes. Nat Genet. Nature Publishing Group; 2016;48: 1–11. doi:10.1038/ng.3495 15. Felsenstein J. PHYLIP - Phylogeny inference package - v3.2. Cladistics. 1989. pp. 164–166. doi:10.1111/j.1096-0031.1989.tb00562.x 16. De Bie T, Cristianini N, Demuth JP, Hahn MW. CAFE: a computational tool for the study of gene family evolution. Bioinformatics. 2006;22: 1269–71. doi:10.1093/bioinformatics/btl097 17. Renwick JH. The mapping of human chromosome. Annu Rev Genet. 1971;5: 81–120. 18. Nadeau JH. Maps of linkage and synteny homologies between mouse and man. Trends Genet. 1989; 1–5. 19. Vergara IA, Chen N. Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster. BMC Genomics. 2010;11: 516. doi:10.1186/1471-2164-11-516 20. Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M. Screening synteny blocks in pairwise genome comparisons through integer programming. 2011; 1–11. 21. Ehrlich J, Sankoff D, Nadeau JH. Synteny conservation and chromosome rearrangements during mammalian evolution. Genetics. 1997;147: 289–296. doi:10.1159/000322358 22. Schmidt R. Synteny - Recent Advances and Future Prospects. Curr Opin Plant Biol. 2000;3: 97–102. 23. Vandepoele K, Saeys Y, Simillion C, Raes J, Van de Peer Y. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res. 2002;12: 1792–1801. doi:10.1101/gr.400202 24. Coghlan A, Eichler EE, Oliver SG, Paterson AH, Stein L. Chromosome evolution in eukaryotes: A multi-kingdom perspective. Trends Genet. 2005;21: 673–682. doi:10.1016/j.tig.2005.09.009 25. Molinari NA, Petrov DA, Price HJ, Smith JD, Gold JR, Vassiliadis C, et al. Synteny and Collinearity in Plant Genomes. Science (80- ). 2008; 486–489. 26. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003;423: 241–254. doi:10.1038/nature01644 27. Jovelin R, Krizus A, Taghizada B, Gray JC, Phillips PC, Claycomb JM, et al. Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis. RNA. 2016;22: 968–78. doi:10.1261/rna.055392.115 28. Dupont P-Y, Cox MP. Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi. G3 (Bethesda). 2017;7: g3.116.038448. doi:10.1534/g3.116.038448 29. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, et al. Reply: A unified classification system for eukaryotic transposable elements should reflect their phylogeny. Nat Rev Genet. 2009;10: 276–276. doi:10.1038/nrg2165-c4 30. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. The sequence of the human genome. Science (80- ). 2001;291: 1304–1351. doi:10.1126/science.1058040 31. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, et al. Life with 6000 Genes. Science (80- ). 1996;274: 546–567. doi:10.1126/science.274.5287.546 32. Perna NT, Plunkett 3rd G, Burland V, Mau B, Glasner JD, Rose DJ, et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature. 2001;409: 529–533. doi:10.1038/35054089 33. C. elegans Sequencing Consortium TC elegans S, Fleischmann RD, Bult CJ, Goffeau A, Coulson AR, Coulson A, et al. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science. 1998;282: 2012–8. doi:10.1126/science.282.5396.2012 34. Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408: 796–815. doi:10.1038/35048692 35. Adams MD. The Genome Sequence of Drosophila melanogaster. Science (80- ). 2000;287: 2185–2195. doi:10.1126/science.287.5461.2185 36. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, et al. Comparative genomics of the eukaryotes. Science. 2000;287: 2204–15. doi:8396 [pii] 37. Sommer RJ. The future of evo–devo: model systems and evolutionary theory. Nat Rev Genet. 2009; doi:10.1038/nrg2567 38. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002;420: 520–562. doi:10.1038/nature01262 39. Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 2003;1: E45. doi:10.1371/journal.pbio.0000045 40. Genome Sequencing Consortium IC. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2005;433: 777–777. doi:10.1038/nature03394 41. and Analysis Consortium TCS. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005;437: 69–87. doi:10.1038/nature04072 42. Soltis DE, Soltis PS. Polyploidy: Recurrent formation and genome evolution. Trends in Ecology and Evolution. 1999. pp. 348–352. doi:10.1016/S0169-5347(99)01638-9 43. Millar AA, Waterhouse PM. Plant and animal microRNAs: Similarities and differences. Functional and Integrative Genomics. 2005. pp. 129–135. doi:10.1007/s10142-005-0145-2 44. Feng S, Jacobsen SE, Reik W. Epigenetic reprogramming in plant and animal development. Sci (New York, NY). 2010;330: 622–627. doi:10.1126/science.1190614 45. Blaxter ML, De Ley P, Garey JR, Liu LX, Scheldeman P, Vierstraete A, et al. A molecular evolutionary framework for the phylum Nematoda. Nature. 1998;392: 71–75. doi:10.1038/32160 46. “Caenorhabditis.” In: WordSense.eu Online Dictionary [Internet]. [cited 22 May 2017]. Available: http://www.wordsense.eu/Caenorhabditis/ 47. Kiontke KC, Félix M-A, Ailion M, Rockman M V, Braendle C, Pénigault J-B, et al. A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits. BMC Evol Biol. 2011;11: 339. doi:10.1186/1471-2148-11-339 48. Cutter AD. Caenorhabditis evolution in the wild. BioEssays. 2015;37: 983–995. doi:10.1002/bies.201500053 49. Kiontke K. Ecology of Caenorhabditis species. WormBook. 2006; 1–14. doi:10.1895/wormbook.1.37.1 50. Brenner S. The genetics of Caenorhabditis elegans. Genetics. 1974;77: 71–94. doi:10.1002/cbic.200300625 51. Ellis H. Genetic control of programmed cell death in the nematode C. elegans. Cell. 1986;44: 817–829. doi:10.1016/0092-8674(86)90004-8 52. Miura M, Zhu H, Rotello R, Hartwieg EA, Yuan J. Induction of apoptosis in fibroblasts by IL-1β-converting enzyme, a mammalian homolog of the C. elegans cell death gene ced-3. Cell. 1993;75: 653–660. doi:10.1016/0092-8674(93)90486-A 53. Klass MR. Aging in the nematode Caenorhabditis elegans: Major biological and environmental factors influencing life span. Mech Ageing Dev. 1977;6: 413–429. doi:10.1016/0047-6374(77)90043-4 54. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993;75: 843–854. doi:10.1016/0092-8674(93)90529-Y 55. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 1998;391: 806–811. doi:10.1038/35888 56. Rocheleau CE, Downs WD, Lin R, Wittmann C, Bei Y, Cha YH, et al. Wnt signaling and an APC-related gene specify endoderm in early C. elegans embryos. Cell. 1997;90: 707–716. doi:10.1016/S0092-8674(00)80531-0 57. Wolkow CA, Kimura KD, Lee M-S, Ruvkun G. Regulation of C. elegans Life-Span by Insulinlike Signaling in the Nervous System. Science (80- ). 2000;290: 147 LP-150. doi:10.1126/science.290.5489.147 58. Serafini T, Kennedy TE, Gaiko MJ, Mirzayan C, Jessell TM, Tessier-Lavigne M. The netrins define a family of axon outgrowth-promoting proteins homologous to C. elegans UNC-6. Cell. 1994;78: 409–424. doi:10.1016/0092-8674(94)90420-0 59. Maricq A V., Peckol E, Driscoll M, Bargmann CI. Mechanosensory signalling in C. elegans mediated by the GLR-1 glutamate receptor. Nature. 1995;378: 78–81. doi:10.1038/378078a0 60. Guo S, Kemphues KJ. par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell. 1995;81: 611–620. doi:10.1016/0092-8674(95)90082-9 61. Hodgkin J. Sex determination in the nematode C. elegans: Analysis of tra-3 suppressors and characterization of fem genes. Genetics. 1986;114: 15–52. 62. Schedl T, Kimble J. fog-2, a germ-line-specific sex determination gene required for hermaphrodite spermatogenesis in Caenorhabditis elegans. Genetics. 1988;119: 43–61. 63. Corsi AK. A Transparent window into biology: A primer on Caenorhabditis elegans. WormBook. 2015; 1–31. doi:10.1895/wormbook.1.177.1 64. Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M, et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature. 2003;421: 231–237. doi:10.1038/nature01278 65. Kim SK. A Gene Expression Map for Caenorhabditis elegans. Science (80- ). 2001;293: 2087–2092. doi:10.1126/science.1061603 66. Sternberg PW, Waterston RH, Spieth J, Eddy S, Wilson RK. Genome Sequence of Additional Caenorhabditis species : Enhancing the Utility of C . elegans as a Model Organism. Addit Caenorhabditis Genomes. 2003; 1–13. 67. Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, et al. Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science (80- ). 2010;330: 1775–1787. doi:10.1126/science.1196914 68. Culetto E. A role for Caenorhabditis elegans in understanding the function and interactions of human disease genes. Hum Mol Genet. 2000;9: 869–877. doi:10.1093/hmg/9.6.869 69. Kirouac M, Sternberg PW. cis-Regulatory control of three cell fate-specific genes in vulval organogenesis of Caenorhabditis elegans and C. briggsae. Dev Biol. 2003;257: 85–103. doi:10.1016/S0012-1606(03)00032-0 70. Lim LP, Lim LP, Lau NC, Lau NC, Weinstein EG, Weinstein EG, et al. The microRNAs of C. elegans. Genes Dev. 2003; 991–1008. doi:10.1101/gad.1074403.regulating 71. Cutter AD, Dey A, Murray RL. Evolution of the Caenorhabditis elegans genome. Mol Biol Evol. 2009;26: 1199–1234. doi:10.1093/molbev/msp048 72. Ross JA, Koboldt DC, Staisch JE, Chamberlin HM, Gupta BP, Miller RD, et al. Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination. PLoS Genet. 2011;7. doi:10.1371/journal.pgen.1002174 73. Thomas CG, Wang W, Jovelin R, Ghosh R, Lomasko T, Trinh Q, et al. Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis. Genome Res. 2015;125: 667–678. doi:10.1101/gr.187237.114 74. Kelly WG, Schaner CE, Dernburg AF, Lee M-H, Kim SK, Villeneuve AM, et al. X-chromosome silencing in the germline of C. elegans. Development. 2002;129: 479–92. 75. Sluder AE, Mathews SW, Hough D, Yin VP, Maina C V. The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes. Genome Res. 1999;9: 103–120. doi:10.1101/gr.9.2.103 76. Ward S, Burke DJ, Sulston JE, Coulson AR, Albertson DG, Ammons D, et al. Genomic organization of major sperm protein genes and pseudogenes in the nematode Caenorhabditis elegans. J Mol Biol. 1988;199: 1–13. doi:10.1016/0022-2836(88)90374-9 77. Miller MA, Cutter AD, Yamamoto I, Ward S, Greenstein D. Clustered organization of reproductive genes in the C. elegans genome. Curr Biol. 2004;14: 1284–1290. doi:10.1016/j.cub.2004.07.025 78. Allen MA, Hillier LW, Waterston RH, Blumenthal T. A global analysis of C. elegans trans-splicing. Genome Res. 2011;21: 255–264. doi:10.1101/gr.113811.110.The 79. Reinke V, Cutter AD. Germline expression influences operon organization in the Caenorhabditis elegans genome. Genetics. 2009;181: 1219–1228. doi:10.1534/genetics.108.099283 80. Roy SW, Fedorov A, Gilbert W. Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc Natl Acad Sci. 2003;100: 7158–7162. doi:10.1073/pnas.1232297100 81. Coulombe-Huntington J, Majewski J. Characterization of intron loss events in mammals. Genome Res. 2007;17: 23–32. doi:10.1101/gr.5703406 82. Coulombe-Huntington J, Majewski J. Intron loss and gain in Drosophila. Mol Biol Evol. 2007;24: 2842–2850. doi:10.1093/molbev/msm235 83. Kiontke K, Gavin NP, Raynes Y, Roehrig C, Piano F, Fitch DHA. Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Proc Natl Acad Sci. 2004;101: 9003–9008. doi:10.1073/pnas.0403094101 84. Cutter AD. Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. Mol Biol Evol. 2008;25: 778–786. doi:10.1093/molbev/msn024 85. Coghlan A, Wolfe KH. Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res. 2002;12: 857–867. doi:10.1101/gr.172702 86. Félix MA, Braendle C, Cutter AD. A streamlined system for species diagnosis in caenorhabditis (Nematoda: Rhabditidae) with name designations for 15 distinct biological species. PLoS One. 2014;9. doi:10.1371/journal.pone.0094723 87. Society G. Genes to Genomes. 2015;38: 1–5. 88. Fierst JL, Willis JH, Thomas CG, Wang W, Reynolds RM, Ahearne TE, et al. Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes. PLoS Genet. 2015;11: 1–25. doi:10.1371/journal.pgen.1005323 89. Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, et al. WormBase 2016: Expanding to enable helminth genomic research. Nucleic Acids Res. 2016;44: D774–D780. doi:10.1093/nar/gkv1217 90. Dieterich C, Clifton SW, Schuster LN, Chinwalla A, Delehaunty K, Dinkelacker I, et al. The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. Nat Genet. 2008;40: 1193–1198. doi:10.1038/ng.227 91. Andrews S. FastQC: A quality control tool for high throughput sequence data. Babraham Bioinforma. 2010; http://www.bioinformatics.babraham.ac.uk/projects/. doi:citeulike-article-id:11583827 92. Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30: 2114–2120. doi:10.1093/bioinformatics/btu170 93. Leggett RM, Clavijo BJ, Clissold L, Clark MD, Caccamo M. NextClip: An analysis and read preparation tool for nextera long mate pair libraries. Bioinformatics. 2014;30: 566–568. doi:10.1093/bioinformatics/btt702 94. Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res. 2014;24: 1384–1395. doi:10.1101/gr.170720.113 95. Zimin A V., Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013;29: 2669–2677. doi:10.1093/bioinformatics/btt476 96. Wences AH, Schatz MC. Metassembler: merging and optimizing de novo genome assemblies. Genome Biol. Genome Biology; 2015;16: 207. doi:10.1186/s13059-015-0764-4 97. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, et al. Versatile and open software for comparing large genomes. Genome Biol. 2004;5: R12. doi:10.1186/gb-2004-5-2-r12 98. Boetzer M, Pirovano W. Toward almost closed genomes with GapFiller. Genome Biol. 2012;13: R56. doi:10.1186/gb-2012-13-6-r56 99. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9. doi:10.1371/journal.pone.0112963 100. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12: 357–360. doi:10.1038/nmeth.3317 101. Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003. pp. 215–225. doi:10.1093/bioinformatics/btg1080 102. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7: 562–578. doi:10.1038/nprot.2012.016 103. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva E V. BUSCO : assessing genome assembly and annotation completeness with single-copy orthologs. Genome Anal. 2015;31: 9–10. doi:10.1093/bioinformatics/btv351 104. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. Genome Biology; 2015;16: 157. doi:10.1186/s13059-015-0721-2 105. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol. 2013;30: 772–780. doi:10.1093/molbev/mst010 106. Stamatakis A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30: 1312–1313. doi:10.1093/bioinformatics/btu033 107. Benson G. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res. 1999;27: 573–580. doi:10.1093/nar/27.2.573 108. Quinlan AR, Hall IM. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26: 841–842. doi:10.1093/bioinformatics/btq033 109. Abascal F, Zardoya R, Telford MJ. TranslatorX: Multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res. 2010;38: 1–7. doi:10.1093/nar/gkq291 110. Sun X, Yang Q, Xia X. An improved implementation of effective number of codons (Nc). Mol Biol Evol. 2013;30: 191–196. doi:10.1093/molbev/mss201 111. Bauer DF. Constructing Confidence Rank Sets Using Statistics. J Am Stat Assoc. 1972;67: 687–690. doi:10.2307/2284469 112. Hollander M, Wolfe D. Nonparametric Statistical Methods. A volume in the Wiley Series in Probability and Mathematical Statistics. 1973. 113. Haas BJ, Delcher AL, Wortman JR, Salzberg SL. DAGchainer: A tool for mining segmental genome duplications and synteny. Bioinformatics. 2004;20: 3643–3646. doi:10.1093/bioinformatics/bth397 114. Mistry J, Bateman A, Finn RD. Predicting active site residue annotations in the Pfam database. BMC Bioinformatics. 2007;8: 298. doi:10.1186/1471-2105-8-298 115. Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, et al. The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res. 2015;43: W580–W584. doi:10.1093/nar/gkv279 116. Alexa A, Rahnenfuhrer J. topGO: Enrichment Analysis for Gene Ontology. In: R package version 2.26.0. [Internet]. 2016. Available: http://bioconductor.org/packages/release/bioc/html/topGO.html 117. Wang J, Chen P-J, Wang GJ, Keller L. Chromosome size differences may affect meiosis and genome size. Science. 2010;329: 293. doi:10.1126/science.1190130 118. Dee R. Denver, Krystalynne Morris ML WKT. High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature. 2004;430: 679–682. doi:10.1038/nature02721.1. 119. Barnes TM, Kohara Y, Coulson A, Hekimi S. Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans. Genetics. 1995;141: 159–179. 120. Rockman M V., Kruglyak L. Recombinational landscape and population genomics of caenorhabditis elegans. PLoS Genet. 2009;5. doi:10.1371/journal.pgen.1000419 121. Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet. Nature Publishing Group; 2011;12: 363–76. doi:10.1038/nrg2958 122. Clifford R, Lee MH, Nayak S, Ohmachi M, Giorgini F, Schedl T. FOG-2, a novel F-box containing protein, associates with the GLD-1 RNA binding protein and directs male sex determination in the C. elegans hermaphrodite germline. Development. 2000;127: 5265–5276. 123. Kipreos ET, Pagano M. The F-box protein family. Genome Biol. 2000;1(5): 3002.1-3002.7. doi:10.1186/gb-2006-7-2-206 124. Bargmann CI. Chemosensation in C. elegans. WormBook. 2006; 1–29. doi:10.1895/wormbook.1.123.1 125. Kiontke KC, Félix M-A, Ailion M, Rockman M V, Braendle C, Pénigault J-B, et al. A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits. BMC Evol Biol. 2011;11: 339. doi:10.1186/1471-2148-11-339 126. Thomas JH, Robertson HM. The Caenorhabditis chemoreceptor gene families. BMC Biol. 2008;6: 42. doi:10.1186/1741-7007-6-42 127. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: A software Environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13: 2498–2504. doi:10.1101/gr.1239303 128. Kolde R. Package `pheatmap’. Bioconductor. 2012; 1–6. 129. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: an information esthetic for comparative genomics. Genome Res. 2009;19: 1639–1645. doi:10.1101/gr.092759.109 130. Mitreva M, Blaxter ML, Bird DM, McCarter JP. Comparative genomics of nematodes. Trends in Genetics. 2005. pp. 573–581. doi:10.1016/j.tig.2005.08.003 131. Coghlan A. Nematode genome evolution. WormBook. 2005; 1–15. doi:10.1895/wormbook.1.15.1 132. Eichler EE. Structural Dynamics of Eukaryotic Chromosome Evolution. Science (80- ). 2003;301: 793–797. doi:10.1126/science.1086132 133. Liu D, Hunt M, Tsai IJ. Inferring synteny between genome assemblies : a systematic evaluation. bioRxiv. 2017; doi:http://dx.doi.org/10.1101/149989 134. Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, et al. Long-read sequence assembly of the gorilla genome. Science. 2016;352: aae0344. doi:10.1126/science.aae0344 135. Lien S, Koop BF, Sandve SR, Miller JR, Matthew P, Leong JS, et al. The Atlantic salmon genome provides insights into rediploidization. Nature. 2016;533: 200–205. doi:10.1038/nature17164 136. Iorizzo M, Ellison S, Senalik D, Zeng P, Satapoomin P, Huang J, et al. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nat Genet. 2016;advance on: 657–666. doi:10.1038/ng.3565 137. Jarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B, Borm TJA, et al. The genome of Chenopodium quinoa. Nature. 2017; 1–6. doi:10.1038/nature21370 138. Ma L, Chen Z, Huang DW, Kutty G, Ishihara M, Wang H, et al. Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts. Nat Commun. Nature Publishing Group; 2016;7: 10740. doi:10.1038/ncomms10740 139. de Man TJB, Stajich JE, Kubicek CP, Teiling C, Chenthamara K, Atanasova L, et al. Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture. Proc Natl Acad Sci. 2016;113: 3567–3572. doi:10.1073/pnas.1518501113 140. Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, et al. The genome of Onchocerca volvulus, agent of river blindness. Nat Microbiol. 2016;2: 16216. doi:10.1038/nmicrobiol.2016.216 141. Chen X, Tompa M. Comparative assessment of methods for aligning multiple genome sequences. Nat Biotechnol. Nature Publishing Group; 2010;28: 567–572. doi:10.1038/nbt.1637 142. Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet. 2012;46: 36–46. doi:10.1038/nrg3164 143. Uricaru R, Michotey C, Chiapello H, Rivals E. YOC, A new strategy for pairwise alignment of collinear genomes. BMC Bioinformatics. 2015;16: 111. doi:10.1186/s12859-015-0530-3 144. Ghiurcuta CG, Moret BME. Evaluating synteny for improved comparative studies. Bioinformatics. 2014;30: 9–18. doi:10.1093/bioinformatics/btu259 145. Zhang G, Li B, Li C, Gilbert MTP, Jarvis ED, Wang J. Comparative genomic data of the Avian Phylogenomics Project. Gigascience. 2014;3: 26. doi:10.1186/2047-217X-3-26 146. Wong S, Wolfe KH. Birth of a metabolic gene cluster in yeast by adaptive gene relocation. Nat Genet. 2005;37: 777–782. doi:10.1038/ng1584 147. Lemons D, McGinnis W. Genomic evolution of Hox gene clusters. Science (80- ). 2006/09/30. 2006;313: 1918–1922. doi:10.1126/science.1132040 148. Ruelens P, de Maagd RA, Proost S, Theißen G, Geuten K, Kaufmann K. FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes. Nat Commun. 2013;4: 2280. doi:10.1038/ncomms3280 149. Kemkemer C, Kohn M, Cooper DN, Froenicke L, Högel J, Hameister H, et al. Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution. BMC Evol Biol. 2009;9: 84. doi:10.1186/1471-2148-9-84 150. Murat F, Armero A, Pont C, Klopp C, Salse J. Reconstructing the genome of the most recent common ancestor of flowering plants. Nat Genet. Nature Publishing Group; 2017;49: 490–496. doi:10.1038/ng.3813 151. Denton JF, Lugo-Martinez J, Tucker AE, Schrider DR, Warren WC, Hahn MW. Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies. PLoS Comput Biol. 2014;10. doi:10.1371/journal.pcbi.1003998 152. Batzoglou S. The many faces of sequence alignment. Brief Bioinform. 2005;6: 6–22. doi:10.1093/bib/6.1.6 153. Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, et al. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40: 1–14. doi:10.1093/nar/gkr1293 154. Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van De Peer Y, et al. i-ADHoRe 3.0-fast and sensitive detection of genomic homology in extremely large data sets. Nucleic Acids Res. 2012;40: 1–11. doi:10.1093/nar/gkr955 155. Drillon G, Carbone A, Fischer G. SynChro: A fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes. PLoS One. 2014;9: 1–8. doi:10.1371/journal.pone.0092621 156. Bhutkar A, Russo S, Smith TF, Gelbart WM. Techniques for multi-genome synteny analysis to overcome assembly limitations. Genome Inform. 2006;17: 152–161. 157. Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. Nature Publishing Group; 2016;17: 333–351. doi:10.1038/nrg.2016.49 158. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. Genome Biology; 2015;16: 157. doi:10.1186/s13059-015-0721-2 159. Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, et al. ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biol. 2015;16: 3. doi:10.1186/s13059-014-0573-1 160. Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 2014;15: 524. doi:10.1186/s13059-014-0524-x 161. Viney ME. The biology and genomics of Strongyloides. Med Microbiol Immunol. 2006;195: 49–54. doi:10.1007/s00430-006-0013-2 162. Ward JD. Rendering the intractable more tractable: Tools from caenorhabditis elegans ripe for import into parasitic nematodes. Genetics. 2015. pp. 1279–1294. doi:10.1534/genetics.115.182717 163. Armengol L, Marquès-Bonet T, Cheung J, Khaja R, González JR, Scherer SW, et al. Murine segmental duplications are hot spots for chromosome and gene evolution. Genomics. 2005;86: 692–700. doi:10.1016/j.ygeno.2005.08.008 164. Davidson RM, Gowda M, Moghe G, Lin H, Vaillancourt B, Shiu SH, et al. Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. Plant J. 2012;71: 492–502. doi:10.1111/j.1365-313X.2012.05005.x 165. Lovell P V, Wirthlin M, Wilhelm L, Minx P, Lazar NH, Carbone L, et al. Conserved syntenic clusters of protein coding genes are missing in birds. Genome Biol. 2014; 1–27. doi:10.1186/s13059-014-0565-1 166. Baldauf J, Marcon C, Paschold A, Hochholdinger F. Nonsyntenic genes drive tissue-specific dynamics of differential, nonadditive and allelic expression patterns in maize hybrids. Plant Physiol. 2016;171: pp.00262.2016. doi:10.1104/pp.16.00262 167. Assefa S, Keane TM, Otto TD, Newbold C, Berriman M. ABACAS: Algorithm-based automatic contiguation of assembled sequences. Bioinformatics. 2009;25: 1968–1969. doi:10.1093/bioinformatics/btp347 168. Husemann P, Stoye J. r2cat: Synteny plots and comparative assembly. Bioinformatics. 2009;26: 570–571. doi:10.1093/bioinformatics/btp690 169. Thompson PC, Zarlenga DS, Liu M-Y, Rosenthal BM. Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged over 7 million years. Parasitology. 2017; 1–14. doi:10.1017/S0031182017000348 170. Chain PSG, Grafham D V, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, et al. Genome Project Standards in a New Era of Sequencing. Science. 2009;326: 4–5. doi:10.1126/science.1180614 171. Ruby EG. Symbiotic conversations are revealed under genetic interrogation. Nat Rev Microbiol. 2008;6: 752–762. doi:10.1038/nrmicro1958 | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/67877 | - |
| dc.description.abstract | 隱桿線蟲屬（Caenorhabditis）以廣為生物研究應用的模式生物“秀麗隱桿線蟲（C. elegans）”聞名。相較於其豐富的遺傳暨分生研究知識背景，科學家對於C. elegans演化方面的認知相對來得有限。主要的原因在於缺乏來自與許多不同親鄰物種比較研究後而得的精密演化架構。在本論文中，基於十一種隱桿線蟲屬物種基因體的可用性，比較基因體學可作為研究此主題的一個有效方法。本論文分為五章，首章與末章分別為背景介紹與結語，二到四章為研究主題的呈現。 在論文的第二章裡，我首先運用秀麗隱桿線蟲的姊妹物種——C. inopinata，與C. elegans做了一個染色體規模的基因體比較；由於姊妹物種所代表的親近演化親緣關係，再加上兩者都具有組裝完整的基因體，高解析度的基因體比較可以藉由顯現出兩者於基因族群以及基因同線性上的些微差異來探討兩者的物種獨特性。 而在第三章中，我想藉由現有的C. elegans完整基因體去將其他未完整組裝成染色體規模的隱桿線蟲基因體做分群歸納，試圖讓這些線蟲也能以染色體規模的方式被研究。通過我篩選條件的序列片段能剛好被分成六群象徵著隱桿線蟲屬基因體共有的六條染色體；然而，未通過篩選條件的序列片段並不佔少數，進一步的分析發現這些情形多數是因為其基因體組裝的過於破碎而不完整或過度組裝。 於是在第四章，我藉由比較基因體學中一塊重要的下游分析——基因同線性分析，來系統性地探討基因體組裝長度上的完整性對於其下游比較分析的影響；最後，針對比較基因體學分析的資料穩定性與正確性而言，我在此提出了一個基因體組裝長度完整性評估統計值N50至少要達1Mb的基本需求，而此需求條件會依據物種的基因密度而進一步有所調整。 | zh_TW |
| dc.description.abstract | Caenorhabditis genus is known mainly for presence of a model species Caenorhabditis elegans, which is widely used in biological research. In contrast to abundant genetics and molecular biology knowledge accumulated in this model species, the evolutionary and ecological contents of C. elegans remain relatively unexplored. This inadequacy is due to lack of an explicit evolutionary framework made from comparing closely related species. In this thesis, with the availability of 11 Caenorhabditis species genomes, comparative genomics provides a useful way to investigate this topic. The thesis is divided into five chapters. The first and last chapters are Background and Conclusions, respectively. Chapter 2~4 are standalone topics but are related to each other. In Chapter 2, I have carried out comparative genomics analyses between C. elegans and its sister species C. inopinata. As a result of their closely related phylogenetic relationship and high quality genome assemblies, genome wide comparisons at high resolution in features such as gene families and synteny can be partitioned according to chromosomes and achieved for a deep evolutionary interpretation of their species uniqueness. In Chapter 3, the comparisons were carried out at larger scale that across several branches using 11 available Caenorhabditis species genomes. I have shown that selected scaffolds of each species can be assigned to six linkage groups representing six chromosomes. Inspecting the exceptions revealed a striking case of over-assembly as well as the issue of incomplete assembled genomes. In Chapter 4, to investigate the interplay between assembly contiguation and downstream analysis, I evaluated synteny in different contiguation assemblies of model nematodes in Caenorhabditis and Strongyloides. I have demonstrated that a minimum standard of N50 depending on species gene density is required for a robust downstream study such as synteny analysis in comparative genomics. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-17T01:55:32Z (GMT). No. of bitstreams: 1 ntu-106-R04b48004-1.pdf: 11807053 bytes, checksum: 8bff50c1f410536a7acf4f3da9b5bf62 (MD5) Previous issue date: 2017 | en |
| dc.description.tableofcontents | TABLE OF CONTENTS / 目錄 口試委員會審定書 i ACKNOWLEDGEMENT / 致謝 ii 中文摘要 iv ABSTRACT v TABLE OF CONTENTS / 目錄 vii LIST OF FIGURES ix LIST OF TABLES x CHAPTER 1. Background 1 1.1 Comparative genomics 1 1.2 Caenorhabditis species 4 CHAPTER 2. Caenorhabditis inopinata: the sister species of C. elegans 9 2.1 Introduction 9 2.2 Materials and Methods 10 2.3 Results 15 2.4 Discussions 20 CHAPTER 3. A chromosomal view of Caenorhabditis species 24 3.1 Introduction 24 3.2 Materials and Methods 25 3.3 Results 26 3.4 Discussions 29 CHAPTER 4. Systematically inferring synteny between genome assemblies 31 4.1 Introduction 31 4.2 Materials and Methods 33 4.3 Results 35 4.4 Discussions 41 CHAPTER 5. Conclusions 45 5.1 Comparative genomics of Caenorhabditis species benefits the knowledge of C. elegans evolutionary contents 45 5.2 Chromosome level genome comparisons provide deep insights of genome structure evolution 46 5.3 Standard assembly quality is required for the robustness of comparative genomics 46 Figures 48 Tables 74 References 94 | |
| dc.language.iso | en | |
| dc.subject | 秀麗隱桿線蟲 | zh_TW |
| dc.subject | 隱桿線蟲 | zh_TW |
| dc.subject | 演化 | zh_TW |
| dc.subject | 比較基因體學 | zh_TW |
| dc.subject | Comparative genomics | en |
| dc.subject | Caenorhabditis elegans | en |
| dc.subject | Evolution | en |
| dc.subject | Caenorhabditis nematodes | en |
| dc.title | 隱桿線蟲屬物種之比較基因體學 | zh_TW |
| dc.title | Comparative genomics of Caenorhabditis species | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 105-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 王忠信(John Wang),蔡懷寬,莊樹諄 | |
| dc.subject.keyword | 隱桿線蟲,秀麗隱桿線蟲,演化,比較基因體學, | zh_TW |
| dc.subject.keyword | Caenorhabditis nematodes,Caenorhabditis elegans,Evolution,Comparative genomics, | en |
| dc.relation.page | 106 | |
| dc.identifier.doi | 10.6342/NTU201701786 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2017-07-24 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 基因體與系統生物學學位學程 | zh_TW |
| 顯示於系所單位： | 基因體與系統生物學學位學程 | |
文件中的檔案：
| 檔案 | 大小 | 格式 | |
|---|---|---|---|
| ntu-106-1.pdf 未授權公開取用 | 11.53 MB | Adobe PDF |
系統中的文件，除了特別指名其著作權條款之外，均受到著作權保護，並且保留所有的權利。