Advertisement

Methods for Target Enrichment Sequencing via Probe Capture in Legumes

  • Ze Peng
  • Dev Paudel
  • Liping Wang
  • Ziliang Luo
  • Qian You
  • Jianping WangEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2107)

Abstract

Target enrichment sequencing (TES) is a powerful approach to deep-sequencing the exome or genomic regions of interest with great depth. Although successfully and widely adopted in many plant species, TES is currently applied for genotyping of only a couple legume species. Here we describe an in-solution probe capture based method for application of TES in legumes. The topics cover probe design, library preparation, probe hybridization, as well as bioinformatic analysis for evaluation of target capture efficiency and identifying single nucleotide polymorphisms using generated sequencing data.

Key words

Legume Next generation sequencing Probe design Probe hybridization Single nucleotide polymorphism Target enrichment sequencing 

Notes

Acknowledgments

This work was supported by the Florida Peanut Producers Association and National Peanut Board.

References

  1. 1.
    Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178PubMedCrossRefPubMedCentralGoogle Scholar
  2. 2.
    Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA (2001) The sequence of the human genome. Science 291:1304–1351CrossRefPubMedGoogle Scholar
  3. 3.
    Fowler S, Thomashow MF (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14:1675–1690PubMedPubMedCentralCrossRefGoogle Scholar
  4. 4.
    Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM (2009) Transcriptome sequencing to detect gene fusions in cancer. Nature 458:97PubMedPubMedCentralCrossRefGoogle Scholar
  5. 5.
    Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511PubMedPubMedCentralCrossRefGoogle Scholar
  6. 6.
    Alkan C, Coe BP, Eichler EE (2011) Genome structural variation discovery and genotyping. Nat Rev Genet 12:363PubMedPubMedCentralCrossRefGoogle Scholar
  7. 7.
    Bhatia D, Wing R, Singh K (2013) Genotyping by sequencing, its implications and benefits. Crop Improv 40:101–111Google Scholar
  8. 8.
    Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499PubMedCrossRefPubMedCentralGoogle Scholar
  9. 9.
    Van Orsouw NJ, Hogers RC, Janssen A, Yalcin F, Snoeijers S, Verstege E, Schneiders H, van der Poel H, Van Oeveren J, Verstegen H (2007) Complexity reduction of polymorphic sequences (CRoPS™): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS One 2:e1172PubMedPubMedCentralCrossRefGoogle Scholar
  10. 10.
    Van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5:247PubMedCrossRefPubMedCentralGoogle Scholar
  11. 11.
    Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376PubMedPubMedCentralCrossRefGoogle Scholar
  12. 12.
    Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379PubMedPubMedCentralCrossRefGoogle Scholar
  13. 13.
    Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7:e37135PubMedPubMedCentralCrossRefGoogle Scholar
  14. 14.
    Sonah H, Bastien M, Iquira E, Tardivel A, Légaré G, Boyle B, Normandeau É, Laroche J, Larose S, Jean M (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS One 8:e54603PubMedPubMedCentralCrossRefGoogle Scholar
  15. 15.
    Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ (2010) Target-enrichment strategies for next-generation sequencing. Nat Methods 7:111PubMedPubMedCentralCrossRefGoogle Scholar
  16. 16.
    Mertes F, ElSharawy A, Sauer S, van Helvoort JM, Van Der Zaag P, Franke A, Nilsson M, Lehrach H, Brookes AJ (2011) Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief Funct Genomics 10:374–386PubMedPubMedCentralCrossRefGoogle Scholar
  17. 17.
    Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491PubMedCrossRefPubMedCentralGoogle Scholar
  18. 18.
    Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E, Dewdney J, Reuber TL, Stammers M, Federspiel N (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet 23:203PubMedCrossRefPubMedCentralGoogle Scholar
  19. 19.
    Wang DG, Fan J-B, Siao C-J, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280:1077–1082PubMedCrossRefPubMedCentralGoogle Scholar
  20. 20.
    Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, Kotsopoulos SK, Samuels ML, Hutchison JB, Larson JW (2009) Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol 27:1025PubMedPubMedCentralCrossRefGoogle Scholar
  21. 21.
    Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary BP, Landegren U (1994) Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265:2085–2088PubMedCrossRefPubMedCentralGoogle Scholar
  22. 22.
    Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F (2007) Multiplex amplification of large sets of human exons. Nat Methods 4:931PubMedCrossRefPubMedCentralGoogle Scholar
  23. 23.
    Turner EH, Lee C, Ng SB, Nickerson DA, Shendure J (2009) Massively parallel exon capture and library-free resequencing across 16 genomes. Nat Methods 6:315PubMedPubMedCentralCrossRefGoogle Scholar
  24. 24.
    Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME (2007) Microarray-based genomic selection for high-throughput resequencing. Nat Methods 4:907PubMedCrossRefPubMedCentralGoogle Scholar
  25. 25.
    Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27:182PubMedPubMedCentralCrossRefGoogle Scholar
  26. 26.
    Ballester LY, Luthra R, Kanagal-Shamanna R, Singh RR (2016) Advances in clinical next-generation sequencing: target enrichment and sequencing technologies. Expert Rev Mol Diagn 16:357–372PubMedCrossRefPubMedCentralGoogle Scholar
  27. 27.
    Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461:272PubMedPubMedCentralCrossRefGoogle Scholar
  28. 28.
    Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M (2011) Performance comparison of exome DNA sequencing technologies. Nat Biotechnol 29:908PubMedPubMedCentralCrossRefGoogle Scholar
  29. 29.
    Russell J, Mascher M, Dawson IK, Kyriakidis S, Calixto C, Freund F, Bayer M, Milne I, Marshall-Griffiths T, Heinen S (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nat Genet 48:1024PubMedCrossRefPubMedCentralGoogle Scholar
  30. 30.
    Mascher M, Schuenemann VJ, Davidovich U, Marom N, Himmelbach A, Hübner S, Korol A, David M, Reiter E, Riehl S (2016) Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nat Genet 48:1089PubMedCrossRefPubMedCentralGoogle Scholar
  31. 31.
    Grabowski PP, Evans J, Daum C, Deshpande S, Barry KW, Kennedy M, Ramstein G, Kaeppler SM, Buell CR, Jiang Y (2017) Genome—wide associations with flowering time in switchgrass using exome—capture sequencing data. New Phytol 213:154–169PubMedCrossRefPubMedCentralGoogle Scholar
  32. 32.
    Peng Z, Fan W, Wang L, Paudel D, Leventini D, Tillman BL, Wang J (2017) Target enrichment sequencing in cultivated peanut (Arachis hypogaea L.) using probes designed from transcript sequences. Mol Genet Genomics 292:955–965PubMedCrossRefPubMedCentralGoogle Scholar
  33. 33.
    Gasc C, Peyret P (2018) Hybridization capture reveals microbial diversity missed using current profiling methods. Microbiome 6:61PubMedPubMedCentralCrossRefGoogle Scholar
  34. 34.
    McCormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT (2013) A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS One 8:e54848PubMedPubMedCentralCrossRefGoogle Scholar
  35. 35.
    Kaur P, Gaikwad K (2017) From genomes to GENE-omes: exome sequencing concept and applications in crop improvement. Front Plant Sci 8:2164PubMedPubMedCentralCrossRefGoogle Scholar
  36. 36.
    Warr A, Robert C, Hume D, Archibald A, Deeb N, Watson M (2015) Exome sequencing: current and future perspectives. G3 Genomes Genet 5:1543–1550Google Scholar
  37. 37.
    Paux E, Roger D, Badaeva E, Gay G, Bernard M, Sourdille P, Feuillet C (2006) Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J 48:463–474PubMedCrossRefPubMedCentralGoogle Scholar
  38. 38.
    Weitemier K, Straub SC, Cronn RC, Fishbein M, Schmickl R, McDonnell A, Liston A (2014) Hyb-Seq: combining target enrichment and genome skimming for plant phylogenomics. Appl Plant Sci 2:1400042CrossRefGoogle Scholar
  39. 39.
    Comer JR, Zomlefer WB, Barrett CF, Davis JI, Stevenson DW, Heyduk K, JH L‐M (2015) Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using plastid sequences derived from next-generation sequencing. Am J Bot 102:888–899PubMedCrossRefPubMedCentralGoogle Scholar
  40. 40.
    Muraya MM, Schmutzer T, Ulpinnis C, Scholz U, Altmann T (2015) Targeted sequencing reveals large-scale sequence polymorphism in maize candidate genes for biomass production and composition. PLoS One 10:e0132120PubMedPubMedCentralCrossRefGoogle Scholar
  41. 41.
    Saintenac C, Jiang D, Akhunov ED (2011) Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol 12(9):R88PubMedPubMedCentralCrossRefGoogle Scholar
  42. 42.
    Winfield MO, Allen AM, Burridge AJ, Barker GL, Benbow HR, Wilkinson PA, Coghill J, Waterfall C, Davassi A, Scopes G (2016) High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool. Plant Biotechnol J 14:1195–1206PubMedPubMedCentralCrossRefGoogle Scholar
  43. 43.
    Wendler N, Mascher M, Nöh C, Himmelbach A, Scholz U, Ruge‐Wehling B, Stein N (2014) Unlocking the secondary gene-pool of barley with next-generation sequencing. Plant Biotechnol J 12:1122–1131PubMedCrossRefPubMedCentralGoogle Scholar
  44. 44.
    Neves LG, Davis JM, Barbazuk WB, Kirst M (2013) Whole-exome targeted sequencing of the uncharacterized pine genome. Plant J 75:146–156PubMedCrossRefPubMedCentralGoogle Scholar
  45. 45.
    Galvão VC, Nordström KJ, Lanz C, Sulz P, Mathieu J, Posé D, Schmid M, Weigel D, Schneeberger K (2012) Synteny-based mapping-by-sequencing enabled by targeted enrichment. Plant J 71:517–526PubMedPubMedCentralGoogle Scholar
  46. 46.
    Song J, Yang X, Resende MF Jr, Neves LG, Todd J, Zhang J, Comstock JC, Wang J (2016) Natural allelic variations in highly polyploidy Saccharum complex. Front Plant Sci 7:804PubMedPubMedCentralGoogle Scholar
  47. 47.
    Yang X, Song J, Todd J, Peng Z, Paudel D, Luo Z, Ma X, You Q, Hanson E, Zhao Z (2019) Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a ‘sweet’crop with ‘bitter’genomes. Plant Biotechnol J 17:488–498PubMedCrossRefPubMedCentralGoogle Scholar
  48. 48.
    Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ, Richmond T, Jeddeloh JA, Jia G, Springer NM, Vance CP (2011) The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiol 155:645–655PubMedCrossRefPubMedCentralGoogle Scholar
  49. 49.
    Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659PubMedCrossRefPubMedCentralGoogle Scholar
  50. 50.
    Kent WJ (2002) BLAT—the BLAST-like alignment tool. Genome Res 12:656–664PubMedPubMedCentralCrossRefGoogle Scholar
  51. 51.
    Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16:276–277PubMedPubMedCentralCrossRefGoogle Scholar
  52. 52.
    Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120PubMedPubMedCentralCrossRefGoogle Scholar
  53. 53.
    Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 2013:1303.3997Google Scholar
  54. 54.
    Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079PubMedPubMedCentralCrossRefGoogle Scholar
  55. 55.
    Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842PubMedPubMedCentralCrossRefGoogle Scholar
  56. 56.
    Pruitt KD, Tatusova T, Maglott DR (2006) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35:D61–D65PubMedPubMedCentralCrossRefGoogle Scholar
  57. 57.
    Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829PubMedPubMedCentralCrossRefGoogle Scholar
  58. 58.
    Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Ze Peng
    • 1
  • Dev Paudel
    • 1
  • Liping Wang
    • 1
  • Ziliang Luo
    • 1
  • Qian You
    • 1
  • Jianping Wang
    • 1
    • 2
    Email author
  1. 1.Agronomy DepartmentUniversity of FloridaGainesvilleUSA
  2. 2.Plant Molecular and Cellular Biology Program, Genetics InstituteUniversity of FloridaGainesvilleUSA

Personalised recommendations