Abstract
The global market for animal health products and treatments is a multibillion-dollar business. Cost of animal disease outbreak is likely to increase with urbanization and a growing demand for animal products. Combating emerging diseases caused by drug-resistant pathogenic microorganisms is challenging. The “omics” and genetic engineering and their applications in biotechnology industry have revolutionized animal healthcare management by improving rapidity, specificity, and sensitivity of diagnostic assays and decreased rates of false positive assays.
Highlights
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Genome sequencing is now an integral component of livestock management
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The technologies have provided valuable information for managing infectious diseases.
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Anis E, Hawkins IK, Ilha MRS, Woldemeskel MW, Saliki JT, Wilkes RP (2018) Evaluation of targeted next-generation sequencing for detection of bovine pathogens in clinical samples. J Clin Microbiol 56(7). pii: e00399-18. https://doi.org/10.1128/jcm.00399-18 (Print 2018 Jul)
Aslam ML, Bastiaansen JW, Elferink MG, Megens HJ, Crooijmans RP, le Blomberg A, Fleischer RC, Van Tassell CP, Sonstegard TS, Schroeder SG, Groenen MA, Long JA (2012) Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo). BMC Genom 14(13):391. https://doi.org/10.1186/1471-2164-13-391
Azhikina TL, Skvortsov TA, Radaeva TV, Mardanov AV, Ravin NV, Apt AS, Sverdlov ED (2010) A new technique for obtaining whole pathogen transcriptomes from infected host tissues. Biotechniques 48:139–144
Bai Y, Sarto M, Cavalcoli J (2012) Current status and future perspectives for sequencing livestock genomes. J Anim Sci Biotechnol 3(1):8
Bayliss SC, Verner-Jeffreys DW, Bartie KL, Aanensen DM, Sheppard SK, Adams A, Feil EJ (2017) The promise of whole genome pathogen sequencing for the molecular epidemiology of emerging aquaculture pathogens. Front Microbiol 8:121. https://doi.org/10.3389/fmicb.2017.00121 (eCollection 2017)
Brooks-Pollock E, de Jong MC, Keeling MJ, Klinkenberg D, Wood JL (2015) Eight challenges in modelling infectious livestock diseases. Epidemics 10:1–5. https://doi.org/10.1016/j.epidem.2014.08.005
Bryant J, Chewapreecha C, Bentley SD (2012) Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genomesequences. Future Microbiol 7(11):1283–1296. https://doi.org/10.2217/fmb.12.108 (Review)
Buermans HP, Den Dunnen JT (2014) Next generation sequencing technology: advances and applications. Biochim Biophys Acta 1842(10):1932–1941. https://doi.org/10.1016/j.bbadis.2014.06.015 (Epub 2014 Jul 1. Review)
Camarena L, Bruno V, Euskirchen G, Poggio S, Snyder M (2010) Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing. PLoS Pathog 6:e1000834. https://doi.org/10.1371/journal.ppat.1000834
Challis GL (2014) Exploitation of the Streptomyces coelicolor A3(2) genome sequence for discovery of new natural products and biosynthetic pathways. J Ind Microbiol Biotechnol 41:219–232. https://doi.org/10.1007/s10295-013-1383-2
Deurenberg RH, Bathoorn E, Chlebowicz MA, Couto N, Ferdous M, García-Cobos S, Kooistra-Smid AM, Raangs EC, Rosema S, Veloo AC, Zhou K, Friedrich AW, Rossen JW (2017) Application of next generation sequencing in clinical microbiology and infection prevention. J Biotechnol 10(243):16–24. https://doi.org/10.1016/j.jbiotec.2016.12.022
Diaz-Sanchez S, Hanning I, Pendleton S, D’Souza D (2013) Next-generation sequencing: the future of molecular genetics in poultry production and food safety. Poult Sci 92(2):562–572. https://doi.org/10.3382/ps.2012-02741 (Review)
Djari A, Esquerré D, Weiss B, Martins F, Meersseman C, Boussaha M, Klopp C, Rocha D (2013) Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing. BMC Genom 14:307. https://doi.org/10.1186/1471-2164-14-307
Feng J, Lupien A, Gingras H, Wasserscheid J, Dewar K, Légaré D, Ouellette M (2009) Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance. Genome Res 19(7):1214–1223. https://doi.org/10.1101/gr.089342.108
Ghosh M, Sharma N, Singh AK, Gera M, Pulicherla KK, Jeong DK (2018) Transformation of animal genomics by next-generation sequencing technologies: a decade of challenges and their impact on genetic architecture. Crit Rev Biotechnol 38(8):1157–1175. https://doi.org/10.1080/07388551.2018.1451819
Gibbs EP (2005) Emerging zoonotic epidemics in the interconnected global community. Vet Rec. 157(22):673–9
Gomez-Escribano JP, Castro JF, Razmilic V, Chandra G, Andrews B, Asenjo JA, Bibb MJ (2015) The Streptomyces leeuwenhoekii genome: de novo sequencing and assembly in single contigs of the chromosome, circular plasmid pSLE1 and linear plasmid pSLE2. BMC Genom 30(16):485. https://doi.org/10.1186/s12864-015-1652-8
Greenwood JM, Ezquerra AL, Behrens S, Branca A, Mallet L (2016) Current analysis of host-parasite interactions with a focus on next generation sequencing data. Zoology (Jena) 119(4):298–306. https://doi.org/10.1016/j.zool.2016.06.010
Greub G, Kebbi-Beghdadi C, Bertelli C, Collyn F, Riederer BM, Yersin C, Croxatto A, Raoult D (2009) High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach. PLoS ONE 4(12):e8423. https://doi.org/10.1371/journal.pone.0008423
Iheshiulor OO, Woolliams JA, Yu X, Wellmann R, Meuwissen TH (2016) Within- and across-breed genomic prediction using whole-genome sequence and single nucleotide polymorphism panels. Genet Sel Evol 19(48):15. https://doi.org/10.1186/s12711-016-0193-1
Kim M, Park T, Yu Z (2017) Metagenomic investigation of gastrointestinal microbiome in cattle. Asian Aust J Anim Sci 30:1515
Langridge GC, Phan MD, Turner DJ, Perkins TT, Parts L, Haase J, Charles I, Maskell DJ, Peters SE, Dougan G, Wain J, Parkhill J, Turner AK (2009) Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res 19(12):2308–2316. https://doi.org/10.1101/gr.097097.109
Lefrançois T, Pineau T (2014) Public health and livestock: emerging diseases in food animals. Anim Front 4(1):4–6
Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ 3rd, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SM, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G, Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L, Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger JP, Lennon N, Leuper L, LeVine S, Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K, Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T, Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt P, O’Neill B, O’Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J, Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I, Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander ES (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803–819
Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30(5):434–439. https://doi.org/10.1038/nbt.2198 (Erratum. In: Nat Biotechnol. 2012 Jun; 30(6):562)
Martin J, Zhu W, Passalacqua KD, Bergman N, Borodovsky M (2010) Bacillus anthracis genome organization in light of whole transcriptome sequencing. BMC Bioinform 11(Suppl 3):S10. https://doi.org/10.1186/1471-2105-11-S3-S10
McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT (2013) Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol 66(2):526–538. https://doi.org/10.1016/j.ympev.2011.12.007
Mertes F, Elsharawy A, Sauer S, van Helvoort JM, van der Zaag PJ, Franke A, Nilsson M, Lehrach H, Brookes AJ (2011) Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief Funct Genom 10(6):374–386. https://doi.org/10.1093/bfgp/elr033
Miller RR, Montoya V, Gardy JL, Patrick DM, Tang P (2013) Metagenomics for pathogen detection in public health. Genome Med 5(9):81. https://doi.org/10.1186/gm485 (eCollection 2013)
Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92(5):255–264. https://doi.org/10.1016/j.ygeno.2008.07.001
Nakano K, Shiroma A, Shimoji M, Tamotsu H, Ashimine N, Ohki S, Shinzato M, Minami M, Nakanishi T, Teruya K, Satou K, Hirano T (2017) Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Hum Cell 30(3):149–161. https://doi.org/10.1007/s13577-017-0168-8
Ramos AM, Crooijmans RP, Affara NA, Amaral AJ, Archibald AL, Beever JE, Bendixen C, Churcher C, Clark R, Dehais P, Hansen MS, Hedegaard J, Hu ZL, Kerstens HH, Law AS, Megens HJ, Milan D, Nonneman DJ, Rohrer GA, Rothschild MF, Smith TP, Schnabel RD, Van Tassell CP, Taylor JF, Wiedmann RT, Schook LB, Groenen MA (2009) Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS ONE 4(8):e6524. https://doi.org/10.1371/journal.pone.0006524
Senol Cali D, Kim JS, Ghose S, Alkan C, Mutlu O (2018) Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. Brief Bioinform. https://doi.org/10.1093/bib/bby017
Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464(7286):250–255. https://doi.org/10.1038/nature08756
Sharma D, Mal G, Kannan A, Bhar R, Sharma R, Singh B (2017) Degradation of euptox A by tannase-producing rumen bacteria from migratory goats. J Appl Microbiol 123(5):1194–1202. https://doi.org/10.1111/jam.13563 (Epub 2017 Sep 19)
Sharma D, Sharma A, Verma SK, Singh B (2018) Targeting metabolic pathways proteins of Orientia tsutsugamushi using combined hierarchical approach to combat scrub typhus J Mol Recognit. 32(4):e2766. https://doi.org/10.1002/jmr.2766
Singh B, Gautam SK, Verma V, Kumar M, Singh B (2008) Metagenomics in animal gastrointestinal ecosystem: potential biotechnological prospects. Anaerobe 14(3):138–144. https://doi.org/10.1016/j.anaerobe.2008.03.002 (Epub 2008 Mar 26. Review)
Singh B, Bhat TK, Sharma OP, Kanwar SS, Rahi P, Gulati A (2012) Isolation of tannase-producing Enterobacter ludwigii GRT-1 from the rumen of migratory goats. Small Rumin Res 102(2–3):172–176
Sorek R, Cossart P (2010) Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 11(1):9–16. https://doi.org/10.1038/nrg2695
Srivatsan A, Han Y, Peng J, Tehranchi AK, Gibbs R, Wang JD, Chen R (2008) High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet 4(8):e1000139. https://doi.org/10.1371/journal.pgen.1000139
Tellam RL, Lemay DG, Van Tassell CP, Lewin HA, Worley KC, Elsik CG (2009) Unlocking the bovine genome. BMC Genom 24(10):193. https://doi.org/10.1186/1471-2164-10-193
Tomley FM, Shirley MW (2009) Livestock infectious diseases and zoonoses. Philos Trans R Soc Lond B Biol Sci 364(1530):2637–2642. https://doi.org/10.1098/rstb.2009.0133
Urbaniak C, Sielaff AC, Frey KG, Allen JE, Singh N, Jaing C, Wheeler K, Venkateswaran K (2018) Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces. Sci Rep 8:814. https://doi.org/10.1038/s41598-017-18506-4
van Opijnen T, Bodi KL, Camilli A (2009) Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat Methods 6(10):767–772. https://doi.org/10.1038/nmeth.1377
Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res 17(8):1195–1201
Williams JL (2005) The use of marker-assisted selection in animal breeding and biotechnology. Rev Sci Tech 24(1):379–391
Williams JL, Iamartino D, Pruitt KD, Sonstegard T, Smith TPL, Low WY, Biagini T, Bomba L, Capomaccio S, Castiglioni B, Coletta A, Corrado F, Ferré F, Iannuzzi L, Lawley C, Macciotta N, McClure M, Mancini G, Matassino D, Mazza R, Milanesi M, Moioli B, Morandi N, Ramunno L, Peretti V, Pilla F, Ramelli P, Schroeder S, Strozzi F, Thibaud-Nissen F, Zicarelli L, Ajmone-Marsan P, Valentini A, Chillemi G, Zimin A (2017) Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50). Gigascience 6(10):1–6. https://doi.org/10.1093/gigascience/gix088
Zhang J, Chiodini R, Badr A, Zhang G (2011) The impact of next-generation sequencing on genomics. J Genet Genomics. 38(3):95–109. https://doi.org/10.1016/j.jgg.2011.02.003
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Singh, B., Mal, G., Gautam, S.K., Mukesh, M. (2019). Next-Generation Sequencing Vis-à-Vis Veterinary Health Management. In: Advances in Animal Biotechnology. Springer, Cham. https://doi.org/10.1007/978-3-030-21309-1_43
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