Next generation sequencing in animal science - a review

• Autorzy: Dunislawska A. , Lachmanska J. , Slawinska A. , Siwek M.
• Języki publikacji: EN

Abstrakty

EN

Next-generation sequencing (NGS), also known as high-throughput sequencing, is a novel method widely used in animal science and veterinary research. Introduction of NGS was a great breakthrough that has revolutionized the world of molecular biology techniques and animal genetics. An unquestionable advantage of NGS is connected with the almost unlimited insight into genetic information it provides. This review discusses the most important applications and achievements in animal genomics thanks to detailed sequence information. Here we present the history of sequencing and its further development. Applications of the NGS technique in whole genome sequencing, whole exorne sequencing, targeted sequencing of DNA fragments and RNA sequencing in animal research are discussed.

Słowa kluczowe

EN

animal genome; genome; sequencing; animal science; veterinary research; animal genetics; molecular biology; DNA sequencing

• Wydawca: -
• Czasopismo: Animal Science Papers and Reports
• Rocznik: 2017
• Tom: 35
• Numer: 3
• Opis fizyczny: p.205-224,ref.

Twórcy

autor

Dunislawska A.

• Department of Animal Biochemistry and Biotechnology, University of Science and Technology, Mazowiecka 28, 85-084 Bydgoszcz, Poland

autor

Lachmanska J.

• Department of Animal Biochemistry and Biotechnology, University of Science and Technology, Mazowiecka 28, 85-084 Bydgoszcz, Poland

autor

Slawinska A.

• Department of Animal Biochemistry and Biotechnology, University of Science and Technology, Mazowiecka 28, 85-084 Bydgoszcz, Poland

autor

Siwek M.

• Department of Animal Biochemistry and Biotechnology, University of Science and Technology, Mazowiecka 28, 85-084 Bydgoszcz, Poland

Bibliografia

• 1. AHMADIAN A., GHARIZA DEH B., GUSTAFSSON A. C., STĚRKY F., NYRĚN P., UHLĚN M., LUNDEBERG J., 2000 - Single - Nucleotide Polymorphism Analysis by Pyrosequencing. Analytical Biochemistry 280, 103 - 110.
• 2. ALFÖLDI J., LINDBLAD-TOFI K., 2013 - Comparative genomics as a tool to understand evolution and disease. Genome Research 23, 1063 - 1068.
• 3. ALTMÜLLER J., BUDDE B. S., NÜRNBERG P., 2014 - Enrichment of target sequences for next- generation sequencing applications in research and diagnostics. Biological Chemistry 395, 231 - 237.
• 4. ALWINE J. C., KEMP D. J., STARK G. R., 1977 - Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl - paper and hybridization with DNA probes. Proceedings of the National Academy of Sciences 74, 5350 - 5354.
• 5. ARCHIBALD A. L., COCKETT N. E., DALRYMPLE B. P., FARAUT T., KIJAS J. W., MADDOX J. F., MCEWAN J. C., HUTTON ODDY V., RAADSMA H. W., WADE C., WANG J., WANG W., WANG J., 2010 - The sheep genome reference sequence: a work in progress. Animat Genetics 41, 449 - 453.
• 6. BERRY D. P., BERMINGHAM M. L., GOOD M., MORE S. J., 2011 - Genetics of animal health and disease in cattle. Irish Veterinary Journal 64, 5.
• 7. BROECKX B. J., COOPMAN F., VERHOEVEN G., BOSMANS T., GIELEN I., DINGEMANSE W., SAUNDERS J. H., DEFORCE D., VAN NIEUWERBURGH E, 2015 - An heuristic filtering tool to identify phenotype - associated genetic variants applied to human intellectual disability and canine coat colors. BMC Bioinformatics 16, 391.
• 8. BRYANT J., CHEWAPREECHAC., BENTLEY S. D., 2012 - Developing insights into the mechanisms of evolution of bacterial pathogens from whole - genome sequences. Future Microbiology 7, 1283 - 1296.
• 9. CÁNOVAS A., RINCÓN G., BEVILACQUA C., ISLAS-TREJO A., BRENAUT P., HOVEY R. C., BOUTINAUD M., MORGENTHALER C., VAN KLOMPENBERG M. K., MARTIN P., MEDRANO J. F., 2014 - Comparison of five different RNA sources to examine the lactating bovine mammary gland transcriptome using RNA-Sequencing. Scientific Reports 4, 5297.
• 10. CAPUCO A.V., BINELLI M., TUCKER H. A., 2011 - Neither bovine somatotropin nor growth hormone - releasing factor alters expression of thyroid hormone receptors in liver and mammary tissues. Journal of Dairy Science 94, 4915 - 4921.
• 11. CHALLIS G. L., 2014 - Exploitation of the Streptomyces coelicolor A3 (2) genome sequence for discovery of new natural products and biosynthetic pathways. Journal of Industrial Microbiology & Biotechnology 41, 219 - 232.
• 12. CHO Y. S., HU L., HOU H., LEE H., XU J., KWON S., OH S., KIM H. M., JHO S., KIM S., SHIN Y. A., KIM B. C., KIM H., KIM C. U., LOU S. J., JOHNSON W. E., KOEPFLI K. P., SCHMIDT-KÜNTZEL A., TURNER J. A., MARKER L., HARPER C., MILLER S. M., JACOBS W., BERTOLA L. D., KIM T. H., LEE S., ZHOU Q., JUNG H. J., XU X., GADHVI P., XU P., XIONG Y., LUO Y., PAN S., SHIN Y. A., GOU C., CHU X., ZHANG J., LIU S., HE J., CHEN Y., YANG L., YANG Y., HE J., LIU S., WANG J., KIM C. H., KWAK H., KIM J. S., HWANG S., KO J., KIM C. B., KIM S., BAYARLKHAGVA D., PAEK W. K., KIM S. J., O’BRIEN S. J., WANG J., BHAK J., 2013 - The tiger genome and comparative analysis with lion and snow leopard genomes. Nature Communications 4.
• 13. COLEMAN S. J., ZENG Z., WANG K., LUO S., KHREBTUKOVA I., MIENALTOWSKI M. J., SCHROTH G. P., LIU J., MACLEOD J. N., 2010 - Structural annotation of equine protein coding genes determined by mRNA sequencing. Animal Genetics 41, 121 - 130.
• 14. COLLINS J. E., WHITE S., SEARLE S. M., STEMPLE D. L., 2012 - Incorporating RNA-seq data into the zebrafish Ensembl genebuild. Genome Research 22, 2067 - 2078.
• 15. SEQUENCING CONSORTIUM S. ELEGANS, 1998 - Genome sequence of the nematode C. elegans: a platform for investigating bilogy. Science 282, 2012 - 2018.
• 16. DASTJERDI A., ROBERT C., WATSON M., 2014 - Low coverage sequencing of two Asian elephant (Elephas maximus) genomes. GigaScience 3, 12.
• 17. DAVIS B. W., OSTRANDER E. A., 2014 - Domestic dogs and cancer research: A breed - based genomics approach. ILAR Journal 55, 59 - 68.
• 18. DEKKERS J. C. M., 2012 - Application of genomics tools to animal breeding. Current Genomics 13, 207 - 212.
• 19. DELSENY M., HAN B., HSING Y. I., 2010 - High throughput DNA sequencing: the new sequencing revolution. Plant Science 179, 407 - 422.
• 20. DIAZ-SANCHEZ S., HANNING I., PENDLETON S., D’SOUZE D., 2013 - Next - generation sequencing: the future of molecular genetics in poultry production and food safety. Poultry Science 92, 562 - 572.
• 21. DRIVER A. M., PEŃAGARICANO F., HUANG W., AHMAD K. R., HACKBART K. S., WILTBANK M. C., KHATIB H., 2012 - RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo-and in vitro-derived bovine blastocysts. BMC Genomics 13, 118.
• 22. EDEA Z., DADI H., KIM S. W., DESSIE T., LEE T., KIM H., KIM J. J., KIM K. S., 2013 - Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers. Frontiers in Genetics 4, 35.
• 23. ESTEVE-CODINA A., KOFLER R., PALMIERI N., BUSSOTTI G., NOTREDAME C., PÉREZ-ENCISO M., 2011 - Exploring the gonad transcriptome of two extreme male pigs with RNA-seq. BMC Genomics 12, 552.
• 24. FLEISCHMANN R. D., ADAMS M. D., WHITE O., CLAYTON R. A., KIRKNESS E. F., KERLAVAGE A. R., BULT C. J., TOMB J. F., DOUGHERTY B. A., MERRICK J. M., et ah, 1995 - Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496 - 512.
• 25. FRASER C. M., GOCAYNE J. D., WHITE O., ADAMS M. D., 1995 -The minimal gene complement of Mycoplasma genitalium. Science 270, 397 - 403.
• 26. GALIBERT F., ALEXANDRAS D., BAUR A., BOLES E., CHALWATZIS N., CHUAT J. C., COSTER F., CZIEPLUCH C., DE HAAN M., DOMDEY H., DURAND P., ENTIAN K. D., GATIUS M., GOFFEAU A., GRIVELL L. A., HENNEMANN A., HERBERT C. J., HEUMANN K., HILGER F., HOLLENBERG C. P., HUANG M. E., JACQ C., JAUNIAUX J. C., KATSOULOU C., KARPFINGER-HARTL L., et ah, 1996 - Complete nucleotide sequencing of Saccharomyces cerevisiae chromosome X. The EMBO Journal 15, 2031 - 2049.
• 27. GARRALDA E., PAZ K., LÓPEZ-CASAS P. P., JONES S., KATZ A., KANN L. M., LÓPEZ- RIOS F., SARNO F., AL-SHAHROUR F., VASQUEZ D., BRUCKHEIMER E., ANGIUOLI S.V., CALLES A., DIAZ L. A., VELCULESCU V. E., VALENCIA A., SIDRANSKY D., HIDALGO M., 2014 - Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment. Clinical Cancer Research 20, 2476 - 2484.
• 28. GARZA D. R., DUTILH B. E., 2015 - From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems. Cellular and Molecular Life Sciences 72, 4287 - 4308.
• 29. GOMEZ-ESCRIBANO J. P., CASTRO J. F., RAZMILIC V., CHANDRA G., ANDREWS B., ASENJO J. A., BIBB M. J., 2015 - The Streptomyces leeuwenhoekii genome: de novo sequencing and assembly in single contigs of the chromosome, circular plasmid pSLE1 and linear plasmid pSLE2. BMC Genomics 16, 485.
• 30. GROENEN M. A. M., ARCHIBALD A. L., UENISHI H., TUGGLE C. K., TAKEUCHI Y., ROTHSCHILD M.,F., et ah, 2012 -Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491, 393 - 398.
• 31. HEATHER J. M., CHAIN B., 2016 - The sequence of sequencers: The history of sequencing DNA. Genomics 107, 1 - 8.
• 32. HELYAR S. J., LIMBORG M. T., BEKKEVOLD D., BABBUCCI M., VAN HOUDT J., MAES G. E., BARGELLONI L., NIELSEN R. O., TAYLOR M. I., OGDEN R., CARI ANI A., CARVALHO G. R., FISH POP TRACE CONSORTIUM, PANITZ F., 2012 - SNP discovery using next generation transcriptomic sequencing in Atlantic herring (Clupea harengus). PLoS One 7, e42089.
• 33. HEMMER-HANSEN J., THERKILDSEN N. O., PUJOLAR J. M., 2014 - Population genomics of marine fishes: next-generation prospects and challenges. The Biological Bulletin 227, 117 - 132.
• 34. HIATT J. B., PRITCHARD C. C., SALIPANTE S. J., O’ROAK B. J., SHENDURE J., 2013 - Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation. Genome Research 23, 843 - 854.
• 35. HILLIER L. W., MILLER W., BIRNEY E., WARREN W., HARDISON R. C., PONTING C. P., INTERNATIONAL CHICKEN GENOME SEQUENCING CONSORTIUM, et ah, 2004 - Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695 - 716.
• 36. HU Z. L., PARK C. A., WU X. L., REECY J. M., 2013 - Animal QTLdb: an improbed database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleid Acids Research 41, 871 - 879.
• 37. HUANG W., YANDELL B. S., KHATIB H., 2010 -Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development. BMC Genomics 11, 23.
• 38. IKEDA H., ISHIKAWA J., HANAMOTO A., SHINOSE M., KIKUCHI K., SHIBA T., SAKAKI Y., HATTORI M., OMURA S., 2003 - Complete genome sequence and comparatibe analysis of the industrial microorganism Streptomyces avermitilis. Nature Biotechnology 21, 526 - 531.
• 39. JIA H., GUO Y., ZHAO W., WANG K., 2014 - Long - range PCR in next - generation sequencing: comparison of six enzymes and evaluation on the MiSeq sequencer. Scientific Reports 4, 5737.
• 40. JIANG J., WANG J., WANG H., ZHANG Y., KANG H., FENG X., WANG J., YIN Z., BAO W., ZHANG Q., LIU J., 2014 - Global copy number analyses by next generation sequencing provide insight into pig genome variation. BMC Genomics 15, 593.
• 41. JIANG L., LIU X., YANG J., WANG H., JIANG J., LIU L., HE S., DING X., LIU J., ZHANG Q., 2014 - Targeted resequencing of G WAS loci reveals novel genetic variants for milk production traits. BMC Genomics 15, 1105.
• 42. JOHNSON R. N., HOBBS M., ELDR1DGE M. D. B., KING A. G., COLDAN D. J., WILKINGS M. R., et al., 2014 - The Koala Genome Consortium. Technical Reports of the Australian Museum 24, 91 - 92.
• 43. KOMORI H. K., LAMERE S. A., TORKAMANI A., HART G. T., KOTSOPOULOS S., WARNER J., SAMUELS M. L., OLSEN J., HEAD S. R., ORDOUKHANIAN P., LEE P. L., LINK D. R., SALOMON D. R., 2011 - Application of microdroplet PCR for larg-scale targeted bisulfate sequencing. Genome Research 21, 1738 - 1745.
• 44. LI R., FAN W., TIAN G., ZHU H., HE L., CAI J., et ah, 2010 - The sequence and de novo assembly of the giant panda genome. Nature 463, 311 - 317.
• 45. LI R. W., SCHROEDER S. G., 2012 - Cytoskeleton remodeling and alterations in smooth muscle contractility in the bovine jejunum during nematode infection. Functional & Integrative Genomics 12, 35 - 44.
• 46. LINDBLAD-TOH K., WADE C. M., MIKKELSEN T. S., KARLSSON E. K., JAFFE D. B., KAMAL M., et ah, 2005 - Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438, 803 - 819.
• 47. MA J., YANG J., ZHOU L., REN J., LIU X., ZHANG H., YANG B., ZHANG Z., MA H., XIE X., XING Y., GUO Y., HUANG L., 2014 - A splice mutation in the PHKG1 gene causes high glycogen content and low meat quality in pig skeletal muscle. PLoS Genetics 10, el004710.
• 48. MAMANOVA L., COFFEY A. J., SCOTT C. E., KOZAREWA I., TURNER E. H., KUMAR A., HOWARD E., SHENDURE J., TURNER D. J., 2010 - Target-enrichment strategies for next- generation sequencing. Nature Methods 7, 111 - 118.
• 49. MAMO S., MEHTA J. P., FORDE N., MCGETTIGAN P., LONERGAN P., 2012 - Conceptus- endometrium crosstalk during material recognition of pregnancy in cattle. Biology of Reproduction 87, 1 - 9.
• 50. MARDIS E. R., 2008a - The impact of next generation sequencing technology on genetics. Trends in Genetics 24, 133 - 141.
• 51. MARDIS E. R., 2008b - Next-Generation DNA Sequencing Methods. Annual Review of Genomics and Human Genetics 9, 387 - 402.
• 52. MARROQUIN J., 2007 - The Language of God: A Scientific Presents Evidence for Belif by Francis Collins. Proceedings (Baylor University Medical Centre) 20, 197 - 199.
• 53. MASSER D. R., STANFORD D. R., FREEMAN W. M., 2015 - Target DNA methylation analysis by next-generation sequencing. Journal of Visualized Experiments: JoVE 96.
• 54. MAXIM A. M., GILBERT W., 1977 - A new method for sequencing DNA. Proceedings of the National Academy of Sciences 74, 560 - 564.
• 55. MCGIVNEY B. A., MCGETTIGAN P. A., BROWNE J. A., EVANS A. C., FONSECA R. G., LOFTUS B. J., LOHAN A., MACHUGH D. E., MURPHY B. A., KATZ L. M., HILL E. W., 2010 - Characterization of the equine skeletal muscle transcriptome identifies novel functional response to exercise training. BMC Genomics 11, 398.
• 56. MCKAY S. D., SCHNABEL R. D., MURDOCH B. M., MATUKUMALLI L. K., AERTS J., COPPIETERS W., CREWS D., NETO E. D., GILL C. A., GAO C., MANNEN H., WANG Z., VAN TASSELL C. P., WILLIAMS J. L., TAYLOR J. F., MOORE S. S., 2008 - An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. BMC Genetics 9, 37.
• 57. MEISEL R. P., HILLDORFER B. B., KOCH J. L., LOCKTON S., SCHAEFFER S. W„ 2010 - Adaptive evolution of genes duplicated from the Drosophila pseudoobscura neo-X chromosome. Molecular Biology and Evolution 27, 1963 - 1978.
• 58. MERTES F., ELSHARAWYA., SAUER S., VANHELVOORT J. M., VAN DERZAAG P. J., FRANK A., NILSSON M., LEHRACH H., BROOKES A. J., 2011 - Targeted enrichment of genomic DNA regions for next-generation sequencing. Briefings in Functional Genomics 10, 374 - 386.
• 59. METZGER J., TONDA R., BELTRAN S., AGUEDA L., GUT M., DISTL O., 2014 - Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication. BMC Genomics 15, 562.
• 60. MOROZOVA O., HIRST M., MARRA M. A., 2009 - Applications of new sequencing technologies for transcriptome analysis. Annual Review of Genomics and Human Genetics 10, 135 - 151.
• 61. NALPAS N. C., PARK S. D. E., MAGEE D. A., TARAKTSOGLOU M., BROWNE J. A., CONLON K. M., RUE-ALBRECHT K., KILLICK K. E., HOKAMP K., LOHAN A. J., LOFTUS B. J., GORMLEY E., GORDON S. V., MACHUGH D. E., 2013 - Whole-transcriptome, high-throughput RNA sequence analysis of the hovin macrophage response to Mycobacterium bovis infection in vitro. BMC Genomics 14, 230.
• 62. NIEDZICKA M., FIJARCZYK A., DUDEK K., STUGLIK M., BABIK W., 2016 - Molecular Inversion Probes for targeted resequencing in non-model organisms. Scientific Reports 6: 24051.
• 63. NIJMAN I. J., VAN MONTFRANS J. M., HOOGSTRAAT M., BOES M. L., VAN DER CORPUT L., RENNER E. D., VAN ZON P., VAN LIESHOUT S., ELFERINK M. G., VAN DER BURG M., VERMONT C. L., VAN DER ZWAAG B., JANSON E., CUPPEN E., PLOOS VAN AMSTEL J., VAN GUN M. E., 2014 - Targeted next-generation sequencing: a novel diagnostic tool for primary immunodeficiencies. Journal of Allergy and Clinical Immunology 133, 529 - 534.
• 53. ORLANDO L., GINOLHAC A., ZHANG G., FROESE D., ALBRECHTSEN A., STILLER M., SCHUBERT M., CAPPELLINIE., PETERSEN B., MOLTKE I., JOHNSON P. L. F., FUMAGALLI M., VILSTRUP J. T., RAGHAVAN M., KORNELIUSSEN T., MALASPINAS A. S., VOGT J., SZKLARCZYK D., KELSTRUP C. D.,VINTHERJ., DOLOCAN A., STENDERUP J., VELAZQUEZ A. M. V., CAHILL J., RASMUSSEN M., WANG X., MIN J., ZAZULA G. D., SEGUIN-ORLANDO A., MORTENSEN C., MAGNUSSEN K., THOMPSON J. F., WEINSTOCK J., GREGERSEN K., RŘED K. H., EISENMANN V., RUBIN C. J., MILLER D. C., ANTCZAK D. F., BERTELSEN M. F., BRUKAN S., AL-RASHIED K. A. S., RYDER O., ANDERSSON L., MUNDY J., KROGH A., GILBERT M. T. P., KJĆER K., SICHERITZ-PONTEN T., JENSEN L. J., OLSEN J. V., HOFREITER M., NIELSEN R., SHAPIRO B., WANG J., W1LLERSLEV E., 2013 - Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499, 74 - 78.
• 54. PAREEK C. S., SMOCZYNSKI R., TRETYN A., 2011 - Sequencing technologies and genome sequencing. Journal of Applied Genetics 52, 413 - 435.
• 66. PĚREZ-MONTARELO D., MADSEN O., ALVES E., RODRIGUEZ M. C., FOLCH J. M., NOGUERA J. L., GROENEN M. A. M., FERNANDEZ A. I., 2014 - Identification of genes regulating growth and fatness traits in pig through hypothalamic transcriptome analysis. Physiological Genomics 46, 195 - 206.
• 67. PONTIUS J. W., MULLIKIN J. C., SMITH D. R., AGENCOURT SEQUENCING TEAM, LINDBLAD-TOH K., GNERRE S., CLAMP M., CHANG J., STEPHENS R., NEELAM B., VOLFOVSKY N., SCHAFFER A. A., RICHA A., NARFSTRÖM K., MURPHY W. J., GIGER U., ROCA A.L., ANTUNES A., MENOTTI-RAYMOND M., YUHKI N., PECON-SLATTERY J., JOHNSON W. E., BOURQUE G., TESLER F., NISC COMPARATIVE SEQUENCING PROGRAM, O’BRIEN S. J., 2007 - Initial sequence and comparative analysis of the cat genome. Genome Research 17, 1675 - 1689.
• 68. QIAN X., BAY., ZHUANG Q., ZHONG G., 2014 - RNA-Seq technology and its application in fish transcriptomics. Omics: a Journal of Integrative Biology 18, 98 - 110.
• 69. RABBANI B., TEKIN M., MAHDIEH N., 2014 - The promise of whole-exome sequencing in medical genetics. Journal of Human Genetics 59, 5 - 15.
• 70. RADWAN J., BABIK W., 2012 - The genomics of adaptation. Proceedings of the Royal Society 279, 5024 - 5028.
• 71. REIS-FILHO J. S., 2009 - Next-generation sequencing. Breast Cancer Research 11, s. 12.
• 72. ROHLAND N., REICH D., MALLICK S., MEYER M., GREEN R. E., GEORGIADIS N. J., ROCA A. L., HOFREITER M., 2010 - Genomic DNA sequences from mastodon and wolly mammoth reveal deep speciation of forest and savanna elephants. PLoS Biology 8, el000564.
• 73. RONAGHI M., 2001 - Pyrosequencing sheds light on DNA sequencing. Genome Research 11, 3 - 11.
• 74. RONAGHI M., KARAMOHAMED S., PETTERSSON B., UHLÉN M., NYRÉN R, 1996 - Realtime DNA sequencing using detection of pyrophosphate release. Analytical Biochemistry 242, 84 - 89.
• 75. RONAGHI M., UHLÉN M., NYRÉN P., 1998 - A sequencing method based on real-time pyrophosphate. Science 281, 363 - 365.
• 76. SANGER F., BROWNLEE G. G., BARRELL B. G., 1965 - A two-dimensional fractionation procedure for radioactive nucleotides. Journal of Molecular Biology 13, 373IN1-398IN4.
• 77. SANGER F., NICKLEN S., COULSON A., 1977 - DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences 74: 5463 - 5467.
• 78. SCHADT E. E., TURNER S., KASARSKIS A., 2010 - A window into third-generation sequencing. Human Molecular Genetics 19, R227 - R240.
• 79. SCHENA M., SHALON D., DAVIS R. W., BROWN P. P., 1995 - Quantitative monitoring of gene expression patterns with a complementary DNA microarrays. Science 270, 457 - 470.
• 80. SCHOLEY R. A., EVANS N. J., BLOWEY R. W., MASSEY J. P., MURRAY R. D., SMITH R. F., OLLIER W. R., CARTER S. ., 2013 - Identifying host pathogenic pathways in bovine digital dermatitis by RNA-Seq analysis. The Veterinary Journal 197, 699 - 706.
• 81. SEEHAUSEN O., BUTLIN R. K., KELLER I., WAGNER C. E., BOUGHMAN J. W., HOGENLOHE P. A., PEICHEL C. L., SAETRE G. P., BANKC., BRÄNNSTRÖM A., BRELSFORD A., CLARKSON C. S., EROUKHMANOFF F., FEDER J. L., FISCHER M. C., FOOTE A. D., FRANCHINI P., JIGGINS C.D., JONES F.C., LINDHOLM A.K., LUCEK K., MAAN M.E., MARQUES D.A., MARTIN S. H., MATTHEWS B., MEITER J. I., MÖST M., MACHMAN M. W., NONAKA E., RENNISON D. J., SCHWARZER J., WATSON E. T., WESTRAM A. M., WIDMER A., 2014 - Genomics and the origin of species. Nature Reviews Genetics 15, 176 - 192.
• 82. SHAFFER H. B., MINX P., WARREN D. E., SHEDLOCK A. M., THOMSON R. C., VALENZUELA N., ABRAMYAN J., AMEMIYA C. T., BADENHORST D., BIGGAR K. K., BORCHERT G. M., BOTKA C. W., BOWDEN R. M., BRAUN E. L., BRONIKOWSKI A. M., BRUNEAU B. G., BUCK L. T., CAPEL B., CASTOE T. A., CZERWINSKI M., DELEHAUNTY K. D., EDWARDS S. V., FRONICK C. C., FUJITA M. K., FULTON L., GRAVES T. A., GREEN R. E., HEARTY W., HARIHARAN R., HERNANDEZ O., HILLER L. W., HOLLOWAY A. K., JANES D., JANZEN F. J., KANDOTH C., KONG L., DE KONING A. P. J., LI Y., LITERMAN R., MCGAUGH S. E., MORK L., O’LAUGHIN M., PAITZ R. T., POLLOCK D. D., PONTING C. P., RADHAKRISHNAN S., RANEY B. J., RICHMAN J. M., ST JOHN J., SCHWARTZ T., SETHURAMAN A., SPINKS P. Q., STOREY K. B., THANE N., VINAR T., ZIMMERMAN L. M., WATTEN W. C., MARDIS E. R., WILSON R. K., 2013 - The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology 14: R28.
• 83. SHENDURE J., JI H., 2008 - Next-generation DNA sequencing. Nature Biotechnology 26, 1135 - 1145.
• 84. SHIN D. H., LEE H. J., CHO S., KIM H. J., HWANG J. Y., LEE C. K., JEONG J. Y., YOON D., KIM H., 2014 - Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level. BMC Genomics 15: 240.
• 85. SIKKEMA-RADDATZ B., JOHANSSON L. F., DE BOER E. N., ALMOMANI R., BOVEN L. G., VAN DER BERG M. P., VAN DER SPAENDONCK-ZWARTS K. Y., VAN TINTELEN J. P., SIJMONS R. ., JONGBLOED J. D., SINKE R. J., 2013 - Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics. Human Mutation 34, 1035 - 1042.
• 86. SIWEK M., SŁAWINSKA A., RYDZANICZ M., WESOLY J., FRASZCZAK M., SUCHOCKI T., SKIBA J., SKIBA K., SZYDA J., 2015 - Identification of candidate genes and mutations in QTL regions for immune response in chicken. Animal Genetics 46, 247 - 254.
• 87. STAHLHUT ESPINOSA C. E., SLACK F. J., 2006 - The role of microRNA in cancer. Yale Journal of Biology and Medicine 79, 131 - 140.
• 88. ST LAURENT G., VYATKIN Y., KAPRANOV P., 2014 - Dark matter RNA illuminates the puzzle of genome-wide association studies. BMC Medicine 12, 97.
• 89. STEFAN C. P., KOEHLER J. W., MINOGUE T. D., 2016 - Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes. Scientific Reports 6, 25904.
• 90. TAN B. F., NG C. M., NSHIMYIMANA J. P., LOH L. L., GIN K. Y., THOMPSON J. R., 2015 -Next- generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities. Frontiers in Microbiology 6, 1027.
• 91. THOMAS S., UNDERWOOD J. G., TSENG E., HOLLOWAY A. K., 2014 - Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PLoS One 9, e94650.
• 92. TYDÉN E., DAHLBERG J., KARLSBERG O., HÖGLUND J., 2014 - Deep amplicon sequencing of preselected isolates of Parascaris equorum in ß-tubulin codons associated with benzimidazole resistance in other nematodes. Parasit Vectors 7, 410.
• 93. VENTER J. C., ADAMS M. D., MYERS E. W., LI P. W., MURAL R. J., et al. 2001 - The sequence of the human genome. Science 291, 1304 - 1351.
• 94. VIERHEILIG J., SAVIO D., LEY R. E., MACH R. L., FARNLEITNER A. H., REISCHER G. H., 2015 - Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring. Water Science and Technology 72, 1962 - 1972.
• 95. WALSH S. W., MEHTA J. P., MCGETTIGAN P. A., BROWNE J. A., FÖRDEN., ALIBRAH1M R. M., MULLIGAN F. J., LOFTUS B., CROWE M. A., MATTHEWS D., DISKIN M., MIHM M., EVANS A. C. O., 2012 - Effect of the metabolic environment at key stages of follicle development in cattle: focus on steroid biosynthesis. Physiological Genomics 44, 504 - 517.
• 96. WANG K., DEL CASTILLO C., CORRE E., ESPINOSA E. P., ALLAM B., 2016 - Clam focal and systemic immune responses to QPX infection revealed by RNA-seq technology. BMC Genomics 17, 146.
• 97. WANG Z., GERSTEIN M., SNYDER M., 2009 - RNA-seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10, 57 - 63.
• 98. WILKIE G. S., DAVISON A. J., KERR K., STIDWORTHLY M. F., REDROBE S., STEINVACH F., DASTIJERDI A., DENK D., 2014 - First fatality associated with elephant endotheliotropic herpesvirus 5 in an Asian Elephant: pathological findings and complete viral genome sequence. Scientific Reports 4, 6299.
• 99. Yan X. J., XU J., GU Z. H., PAN C. M., LU G., SHEN Y., SHI J. Y., ZHU Y. M., TANG L., ZHANG X. W., LIANG W. X, MI J. Q, SONG H. D., LI K. Q., CHEN Z., CHEN S. J., 2011 - Exorne sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nature Genetics 43, 309 - 315.
• 100. YIM H. S., CHO Y. S., GUANG X., KANG S. G., JEONG J. Y., CHA S. S., OH H. M., LEE J. H., YANG E. C., KWON K. K., KIM Y. J., KIM T. W., KIM W., JEON J. H., KIM S. J., CHOI D. H., JHO S., KIM H. M., KO J., KIM H., SHIN Y. A., JUNG H. J., ZHENG Y., WANG Z., CHEN Y., CHEN M., JIANG A., LI E., ZHANG S., HOU H., KIM T. H., YU L., LIU S., AHN K., COOPER J., PARK S. G., HONG C. P., JIN W., KIM H. S., PARK C., LEE K., CHUN S., MORIN P.A., O’BRIEN S. J., LEE H., KIMURA J., MOON D. Y., MANICA A., EDWARDS J., KIM B. C., KIM S., WANG J., BHAK J., LEE H. S., LEE J. H., 2014 - Minke whale genome and aquatic adapration in cetaceans. Nature genetics 46, 88 - 92.
• 101. ZHANG Q., ZHU F., LIU L., ZHENG C. W., HOU Z. C.,NINGZ.H., 2015 - Integrating transcriptome and genome re-sequencing data to identify key genes and mutations affecting chicken eggshell qualities. PLoS one 10, e0125890.
• 102. ZHANG S. J., LIU C. J., SHI M., KONG L., CHEN J. Y., ZHOU W. Z., ZHU X., YU P., WANG J., YANG X., HOU N., YE Z., ZHANG R., XIAO R., ZHANG X., LI C. Y., 2013 – RhesusBase: a knowledgebase for the monkey research community. Nucleic Acids Research 41, D892 - 905.
• 103. ZHAO P., LI J., KANG H., WANG H., FAN Z., YIN Z., WANG J., ZHANG Q., WANG Z., LIU J. F., 2016 - Structural Variant Detection by Large-scale Sequencing Reveals New Evolutionary Evidence on Breed Divergence between Chinese and European Pigs. Scientific Reports 6: 18501.
• 104. ZHENG Z., LIEBERS M., ZHELYAZKOVA B., CAO Y., PANDITI D., LYNCH K. D., CHEN J., ROBINSON H. E., SHIM H. S., CHMIELECKI J., PAO W., ENGELMAN J. A., IAFRATE A. J., LE L. P., 2014 - Anchored multiplex PCR for targeted next-generation sequencing. Nature Medicine 20, 1479 - 1484.
• 105. ZIMIN A. V., DELCHER A. L., FLOREA L., KELLEY D. R., SCHATZ M. C., PUIU D., HANRAHAN F., PERTEA G., VAN TASSELL C. P., SONSTEGARD T. S., MARÇAIS G., ROBERTS M., SUBRAMANIAN P., YORKE J. A., SALZBERG S. L., 2009 - A whole-genome assembly of the domestic cow Bos taurus. Genome Biology 10, R42.