Agronomy Science, przyrodniczy lublin, czasopisma up, czasopisma uniwersytet przyrodniczy lublin
Przejdź do głównego menu Przejdź do sekcji głównej Przejdź do stopki
Agronomy Science Baner text

Tom 73 Nr 4 (2018)

Artykuły

Metody redukcji złożoności genomu w protokołach tworzenia bibliotek do sekwencjonowania

DOI: https://doi.org/10.24326/asx.2018.4.9
Przesłane: 10 stycznia 2019
Opublikowane: 19-12-2018

Abstrakt

Od czasu opublikowania pełnej sekwencji genomu Arabidopsis thaliana w 2000 r. [AGI Initiative 2000] rozpoczął się okres dynamicznej eksploracji genomów. W ostatniej dekadzie, wraz z rewolucją w technologii sekwencjonowania nowej generacji, lawinowo wzrosła ilość doniesień naukowych opartych na analizie sekwencji. Nowe, szybkie, wysokoprzepustowe i relatywnie tanie technologie sekwencjonowania kwasów nukleinowych stały się dostępne i powszechne, otwierając możliwość szerokiego wykorzystania narzędzi molekularnych w nauce i praktyce hodowlanej. Te nowe metody obejmują sekwencjonowanie pełnogenomowe oraz wiele metod sekwencjonowania redukowanej frakcji genomu (RRS, ang. reduced representation sequencing). Wielość dostępnych metod, zróżnicowanych pod względem przystępności i kosztów, generujących różne rodzaje danych wynikowych, dedykowanych różnym celom badawczym
i aplikacyjnym, może sprawić trudność przy wyborze najlepszego wariantu [Poland et al. 2012]. Celem niniejszego opracowania jest przybliżenie czytelnikowi możliwości i zastosowania wybranych protokołów konstrukcji bibliotek do sekwencjonowania zredukowanej frakcji genomu.

Bibliografia

  1. AGI Initiative, 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 (6814), 796–815.
  2. Al-Beyroutiová M., Sabo M., Sleziak P., Dušinský R., Birčák E., Hauptvogel P., Kilian A., Švec M., 2016. Evolutionary relationships in the genus Secale revealed by DArTseq DNA polymorphism. Plant Syst. Evol. 302, 1083–1091.
  3. Altshuler D., Pollara V. J., Cowles C. R., Van Etten W. J., Baldwin J., Linton L., Lander E. S., 2000. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407 (6803), 513–516.
  4. Andolfatto P., Davison D., Erezyilmaz D., Hu T. T., Mast J., Sunayama-Morita T., Stern D. L., 2011. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res. 21 (4), 610–617.
  5. Andrews K. R., Good J. M., Miller M. R., Luikart G., Hohenlohe P. A., 2016. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat. Rev. Genet. 17(2), 81–92.
  6. Arafa R. A., Rakha M. T., Soliman N. E. K., Moussa O. M., Kamel S. M., Shirasawa K., 2017. Rapid identification of candidate genes for resistance to tomato late blight disease using next-generation sequencing technologies. PLOS One 12(12), e0189951.
  7. Baird N.A., Etter P.D., Atwood T.S., Currey M.C., Shiver A.L., 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLOS One 3(10), e3376.
  8. Barilli E., Cobos M.J., Carrillo E., Kilian A., Carling J., Rubiales D., 2018. A high-density integrated DArTseq SNP-based genetic map of Pisum fulvum and identification of QTLs controlling Rust Resistance. Front Plant Sci. 9, 167.
  9. Bennetzen J.L., Schrick K., Springer P.S., Brown W.E., SanMiguel P., 1994. Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome 37, 565–576.
  10. Bergey Ch.M., Pozzi L., Disotell T.R., Burrell A.S., 2013. A new method of genome-wide marker development and genotyping holds great promise for molecular primatology. Int. J. Primatol. 34, 303–314.
  11. Brunner A.L., Johnson D.S., Kim S.W., Valouev A., Reddy T.E., Neff N.F., Anton E., Medina C., Nguyen L., Chiao E., Oyolu C.B., Schroth G.P., Absher D.M., Baker J.C., Myers R.M., 2009. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 19 (6), 1044–1056.
  12. Bybee S.M., Bracken-Grissom H., Haynes B.D., Hermansen R.A., Byers R.L., Clement M.J., Udall J.A., Wilcox E.R., Crandall K.A., 2011. Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics. Genome Biol Evol. 3, 1312–1323.
  13. Cheng Y., Wang J., Shao J., Chen Q., Mo F., Ma L., Han X., Zhang J., Chen C., Zhang C., Lin S., Yu J., Zheng S., Lin S.C., Lin B., 2010. Identification of novel SNPs by next-generation sequencing of the genomic region containing the APC gene in colorectal cancer patients in China. OMICS 14(3), 315–325.
  14. Collard B. C. Y., Mackill D. J., 2008. Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philosophical transactions of the Royal Society of London. Series B, Biological Sciences 363 (1491), 557–572.
  15. Courtois B., Audebert A., Dardou A., Roques S., Ghneim-Herrera T., Droc G., Frouin J., Rouan L., Gozé E., Kilian A., Ahmadi N., Dingkuhn M., 2013. Genome-wide association mapping of root traits in a japonica rice panel. PLOS One 8(11), e78037.
  16. von Cruz M., Kilian A., Dierig D.A., 2013. Development of DArT marker platforms and genetic diversity assessment of the U.S. collection of the new oil seed crop Lesquerella and related Species. PLOS One 8(5), e64062.
  17. DaCosta J.M., Sorenson M.D., 2014. Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol. PLOS One 9(9), e106713.
  18. Davey J.W., Hohenlohe P.A., Etter P.D., Boone J.Q., Catchen J.M., Blaxter M.L., 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. 12(7), 499–510.
  19. Davik J., Sargent D.J., Brurberg M.B., Lien S., Kent M., Alsheikh M., 2015. A ddRAD based linkage map of the cultivated strawberry, Fragaria × ananassa. PLOS One 10(9), e0137746.
  20. Dracatos P.M., Haghdoust R., Singh D., Park R.F., 2017. Genetic analysis and molecular mapping of resistance to Puccinia striiformis f. sp. pseudo-hordei in common wheat. Plant Pathol. 66, 285–292.
  21. Dracatos P.M., Zhang P., Park R.F., McIntosh R.A., Wellings C.R., 2016. Complementary resistance genes in wheat selection ‘Avocet R’ confer resistance to stripe rust. Theor. Appl. Genet. 129, 65–76.
  22. Elshire R.J., Glaubitz J.C., Sun Q., Poland J.A., Kawamoto K., Buckler E.S., Mitchell S.E. 2011. A robust, Simple Genotyping-by-Sequencing (GBS) approach for high diversity species. PLOS One 6(5), e19379.
  23. Etter P.D., Bassham S., Hohenlohe P.A., Johnson E.A., Cresko W.A., 2011. SNP discovery and genotyping for evolutionary genetics using RAD sequencing. Methods Mol. Biol. 772, 157–178.
  24. Fan J.B., Chee M.S., Gunderson K.L., 2006. Highly parallel genomic assays. Nat. Rev. Genet. 7, 632–644.
  25. Gasc C., Peyretaillade E., Peyret P., 2016. Sequence capture by hybridization to explore modern and ancient genomic diversity in model and non-model organisms. Nucleic Acids Res. 44 (10), 4504–4518.
  26. Gore M.A., Chia J.M., Elshire R.J., Sun Q., Ersoz E.S., Hurwitz B.L., Peiffer J.A., McMullen M.D., Grills G.S., Ross-Ibarra J., Ware D.H., Buckler E.S., 2009. A first-generation haplotype map of maize. Science 326 (5956), 1115–1117.
  27. Guo-Qian Y., Chen Y.M., Wang J.P., Guo C., Li L.L., Li D.Z., Guo Z.H., 2016. Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants. Plant Methods 12, 39.
  28. Habyarimana E., Parisi B., Mandolino G., 2017. Genomic prediction for yields, processing and nutritional quality traits in cultivated potato (Solanum tuberosum L.). Plant Breed. 136, 245–252.
  29. He J., Zhao X., Laroche A., Lu Z.X., Liu H., Li Z., 2014. Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci. 5 (484), 1–6.
  30. Hedges D.J., Guettouche T., Yang S., Bademci G., Diaz A., Andersen A., Hulme W.F., Linker S., Mehta A., Edwards Y.J.K., Beecham G.W., Martin E.R., Pericak-Vance M.A., Zuchner S., Vance J.M., Gilbert J.R., 2011. Comparison of three targeted enrichment strategies on the SOLiD sequencing platform. PLOS One 6(4), e18595.
  31. Heslot N., Rutkoski J., Poland J., Jannink J.L., Sorrells M.E., 2013. Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity. PLOS One 8(9), e74612.
  32. Hillier L.W., Marth G.T., Quinlan A.R., Dooling D., Fewell G., Barnett D., Fox P., Glasscock J.I., Hickenbotham M., Huang W., Magrini V.J., Richt R.J., Sander S.N., Stewart D.A., Stromberg M., Tsung E.F., Wylie T., Schedl T., Wilson R.K., Mardis E.R., 2008. Whole-genome sequencing and variant discovery in C. elegans. Nat. Methods 5 (2), 183–188.
  33. Huang X., Wei X., Sang T., Zhao Q., Feng Q., Zhao Y., Jing W., Li W., Lin Z., Buckler E.S., Qian Q., Zhang Q-F., Li J., Han B., 2010. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961–967.
  34. Huang, X., Feng Q., Qian Q., Zhao Q., Wang L., Wang A., Guan J., Fan D., Weng Q., Huang T., Dong G., Sang T., Han B., 2009. High-throughput genotyping by whole-genome resequencing. Genome Res. 19(6), 1068–1076.
  35. Jaccoud D., Peng K., Feinstein D., Kilian A., 2001. Diversity Arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res. 29(4), 25.
  36. Kenta S., Hideki H., Sachiko I. 2016. Analytical workflow of double-digest Restriction site –associated DNA sequencing based on empirical and in silico optimization in tomato. DNA Res. 23(2), 145–153.
  37. Kiialainen A., Karlberg O., Ahlford A., Sigurdsson S., Lindblad-Toh K., Syvänen A.C., 2011. Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery. PLOS One 6(2), e16486.
  38. Konar A., Choudhury O., Bullis R., Fiedler L., Kruser J.M., Stephens M.T., Gailing O., Schlarbaum S., Coggeshall M.V., Staton M.E., Carlson J.E., Emrich S., Severson J.R., 2017. High-quality genetics mapping with ddRADseq in the non-model tree Quercus rubra. Genomics 18, 417.
  39. Kotowska M., Zakrzewska-Czerwińska J., 2010. Kurs szybkiego czytania DNA – nowoczesne techniki sekwencjonowania [Fast DNA reading course – modern sequencing techniques]. Biotechnologia 4(91), 24–38.
  40. Mardis E., McCombie W.R., 2017. Agarose gel size selection for DNA sequencing libraries. Cold Spring Harbor Protocols (8).
  41. Mascher M., Richmond T.A., Gerhardt D.J., Himmelbach A., Clissold L., Sampath D., Ayling S., Steuernagel B., Pfeifer M., D’Ascenzo M., Akhunov E.D., Hedley P.E., Gonzales A.M., Morrell P.L., Kilian B., Blattner F.R., Scholz U., Mayer K.FX., Flavell A.J., Muehlbauer G.J., Waugh R., Jeddeloh J.A., Stein N., 2013. Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J. 76(3), 494–505.
  42. Milczarski P., Hanek M., Tyrka M., Stojałowski S., 2016. The application of GBS markers for extending the dense genetic map of rye (Secale cereale L.) and the localization of the Rfc1 gene restoring male fertility in plants with the C source of sterility-inducing cytoplasm. J. Appl. Genet. 57, 439–451.
  43. Myllykangas S., Natsoulis G., Bell J.M., Ji H.P., 2011. Targeted sequencing library preparation by genomic DNA circularization. BMC Biotechnol. 11, 122.
  44. Ng S.B., Turner E.H., Robertson P.D., Flygare S.D., Bigham A.W., Lee C., Shaffer T., Wong M., Bhattacharjee A., Eichler E.E., Bamshad M., Nickerson D.A., Shendure J., 2009. Targeted capture and massively parallel sequencing of twelve human exomes. Nature 461 (7261), 272–276.
  45. Pachota K., Niedziela A., Orłowska R., Bednarek P.T., 2016. Nowoczesne metody genotypowania DArT i GBS w hodowli gatunków roślin użytkowych [Modern methods of DArT and GBS genotyping in the cultivation of utility plant species]. Biul. IHAR 279.
  46. Peterson B.K., Weber J.N., Kay E.H., Fisher H.S., Hoekstra H.E., 2012. Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLOS One 7(5), e37135.
  47. Poland J.A., Brown P.J., Sorreils M.E., Jannink J., 2012. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLOS One 7(2), e32253.
  48. Quail M.A., Smith M., Coupland P., Otto T.D., Harris S.R., Connor T.R., Bertoni A., Swerdlow H.P., Gu Y. 2012. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13, 341.
  49. Qiu X., Pang Y., Yuan Z., Xing D., Xu J., Dingkuhn M., Li Z., Ye G., 2015. Genome-wide association study of grain appearance and milling quality in a worldwide collection of indica rice germplasm. PLOS One 10(12), e0145577.
  50. Roldan-Ruiz I., Dendauw J., Van Bockstaele E., Depicker A., De Loose M., 2000. AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol. Breeding 6, 125–134.
  51. Sánchez-Sevilla J.F., Horvath A., Botella M.A., Gaston A., Folta K., Kilian A., Denoyes B., Amaya I., 2015. Diversity Arrays Technology (DArT) marker platforms for diversity analysis and linkage mapping in a complex crop, the octoploid cultivated strawberry (Fragaria × ananassa). PLOS One 10(12), e0144960.
  52. Sansaloni C., Petroli C., Jaccoud D., Carling J., Detering F., Grattapaglia D., Kilian A., 2011. Diversity Arrays Technology (DArT) and next-generation sequencing combined: genome- wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus. BMC Proceedings 5 (Suppl. 7), 54.
  53. Sonah H., Bastien M., Iquira E., Tardivel A., Légaré G., Boyle B., Normandeau E., Laroche J., Larose S., Jean M., Belzile F., 2013. PLOS One 8(1), e54603.
  54. Song K., Ren J., Zhai Z., Liu X., Deng M., Sun F., 2013. Alignment-free sequence comparison based on next-generation sequencing reads. J. Comput. Biol. 20(2), 64–79.
  55. Van Tassell, C.P., Smith T.P., Matukumalli L.K., Taylor J.F., Schnabel R.D., Lawley C.T., Haundenschild C.D., Moore S.S., Warren W.C., Sonstegard T.S., 2008. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat. Methods 5(3), 247–252.
  56. Tyrka M., Tyrka D., Wędzony M., 2015. Genetic map of Triticale integrating microsatellite, DArT and SNP markers. PLOS One 10(12), e0145714.
  57. Valdisser P.A.M.R., Pereira W.J., Filho J.E.A., Müller B.S.F., Coelho G.R.C, de Menezes I.P.P., Vianna J.P.G., Zucchi M.I., Lanna A.C., Coelho A.S.G., de Oliveira J.P., da Cunha Moraes A., Brondani C., Vianello R.P., 2017. In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping. BMC Genomics 18, 423.
  58. Wang S., Meyer E., McKay J.K., Matz M.V., 2012. 2b-RAD a simple and flexible method for genome-wide genotyping. Nat. Methods 9(8), 808–810.
  59. Wu Z., Wang B., Chen X., Wu J., King G.J., Xiao Y., Liu K., 2016. Evaluation of linkage disequilibrium pattern and association study on seed oil content in Brassica napus using ddRAD sequencing. PLOS One 11(1), 1–15.
  60. Xie, W., Feng Q., Yu H., Huang X., Zhao Q., Xing Y., Yu S., Han B., Zhang Q., 2010. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc. Natl. Acad. Sci. USA. 107(23), 10578–10583.
  61. https://www.diversityarrays.com/ [access 20.09.2018].
  62. https://www.illumina.com/systems/sequencing-platforms/miseq.html [access 20.09.2018].
  63. http://www.sagescience.com/wpcontent/uploads/2012/11/sage_wp_saygoodbyetomanualgels_0912_6.pdf [access 20.09.2018].

Downloads

Download data is not yet available.

Inne teksty tego samego autora