Skip to main content
SpringerLink
Log in
Book cover

The Potato Genome pp 81–93Cite as

Strategies and Tools for Sequencing and Assembly of Plant Genomes

  • Chapter
  • First Online:

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

This chapter highlights strategies and tools for sequencing and assembly of plant genomes. It discusses in brief the methods of sequencing technologies (the first, second and third generations), details the approaches of genome assembly (the de novo and reference assembly) and presents the challenges of plant genome assembly.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Ariyaratne PN, Sung WK (2011) PE-Assembler: de novo assembler using short paired-end reads. Bioinformatics 27(2):167–174

    Article  CAS  PubMed  Google Scholar 

  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bartels D, Kespohl S, Albaum S, Druke T, Goesmann A, Herold J, Kaiser O, Puhler A, Pfeiffer F, Raddatz G, Stoye J, Meyer F, Schuster SC (2005) BACCardI—a tool for the validation of genomic assemblies, assisting genome finishing and inter genome comparison. Bioinformatics 21(7):853–859

    Article  CAS  PubMed  Google Scholar 

  • Boisvert S, Laviolette F, Corbeil J (2010) Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol 17:1519–1533

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bonfield J, Smith K, Staden R (1995) A new DNA sequence assembly program. Nucleic Acids Res 23(24):4992–4999

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Butle J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB (2008) ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 18(5):810–820

    Article  Google Scholar 

  • Chaisson M, Pevzner P, Tang H (2004) Fragment assembly with short reads. Bioinformatics 20:2067–2074

    Article  CAS  PubMed  Google Scholar 

  • Chaisson MJ, Brinza D, Pevzner PA (2009) De novo fragment assembly with short mate-paired reads: does the read length matter? Genome Res 19:336–346

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chikhi R, Rizk G (2012) Space-efficient and exact de Bruijn graph representation based on a Bloom filter. Algorithms Mol Biol 8:22

    Article  Google Scholar 

  • Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2007) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res 17(11):1697–1706

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Glenn TC (2011) Field guide to next-generation DNA sequencers. Mol Ecol Resour 11:759–769

    Article  CAS  PubMed  Google Scholar 

  • Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8(3):195–202

    Article  CAS  PubMed  Google Scholar 

  • Gordon D, Desmarais C, Green P (2001) Automated finishing with auto finish. Genome Res 11(4):614–625

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jason R, Miller SK, Sutton G (2010) Assembly algorithms for next-generation sequencing data. Genomics 95:315–327

    Article  Google Scholar 

  • Jeck WR, Reinhardt JA, Baltrus DA (2007) Extending assembly of short DNA sequences to handle error. Bioinformatics 23:2942–2944

    Article  CAS  PubMed  Google Scholar 

  • Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M (2014) Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24:1384–1395

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotech 30:693–700

    Article  CAS  Google Scholar 

  • Laver T, Harrison J, O’Neill PA, Moore K, Farbos A, Paszkiewicz K (2015) Assessing the performance of the Oxford Nanopore Technologies MinION. Biomol Detect Quantif 3:1–8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee H, Gurtowski J, Yoo S, Marcus S, McCombie WR, Schatz M (2014) Error correction and assembly complexity of single molecule sequencing reads. bioRxiv doi:10.1101/006395

  • Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang JI, Wang JU (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20(2):265–272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li Z, Chen Y, Mu D, Yuan J, Shi Y, Zhang H, Gan J, Li N, Hu X, Liu B, Yang B, Fan W (2011) Comparison of the two major classes of assembly algorithms: overlap layout consensus and de-bruijn graph. Brief Funct Genomics 11(1):25–37

    Article  CAS  PubMed  Google Scholar 

  • Liu L, Li Y, Li S, Hu N, He Y, Pong R (2012) Comparison of next-generation sequencing systems. J Bio Med Res Int 2012:e251364

    Google Scholar 

  • Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G et al (2012) SOAPdenovo2: an empirically improved memory-efficient short read de novo assembly. GigaScience 1:18

    Article  PubMed  PubMed Central  Google Scholar 

  • Maxum A, Gilbert W (1977) A new method for sequencing DNA. Procd Natl Acad Sci 74:560–564

    Article  Google Scholar 

  • Miclotte G, Heydari M, Demeester P, Rombauts S, Van de Peer Y, Audenaert P, Fostier J (2016) Jabba: hybrid error correction for long sequencing reads. Algorithms Mol Biol 11:10

    Article  PubMed  PubMed Central  Google Scholar 

  • Mikheyev AS, Tin MMY (2014) A first look at the Oxford Nanopore MinION sequencer. Mol Ecol Resour 14:1097–1102

    Article  CAS  PubMed  Google Scholar 

  • Miller JR (2008) Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24(24):2818–2824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Niedringhaus TP, Milanova D, Kerby MB, Snyder MP (2011) Barron Landscape of next-generation sequencing technologies. Anal Chem 83:4327–4341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genom 13:341

    Article  CAS  Google Scholar 

  • Salmela L, Rivals E (2014) LoRDEC: accurate and efficient long read error correction. Bioinformatics 30:3506–3514

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Procd Natl Acad Sci 74:5463–5467

    Article  CAS  Google Scholar 

  • Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145

    Article  CAS  PubMed  Google Scholar 

  • Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I (2009) ABySS: A parallel assembler for short read sequence data. Genome Res 19:1117–1123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Utturkar SM, Klingeman DM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA, Brown SD (2014) Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. Bioinformatics 30:2709–2716

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Yu Y, Pan B, Hao P, Li Y, Shao Z, Xu X, Li X (2012) Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome. BMC Systems Biol 6(Suppl 3):S21

    Article  Google Scholar 

  • Warren RL, Sutton GG, Jones SJ, Holt RA (2007) Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23:500–501

    Article  CAS  PubMed  Google Scholar 

  • Ye C, Cannon CH, Ma ZS, Yu DW, Pop M (2012) Sparseassembler2: Sparse k-mer graph for memory efficient genome assembly. ArXiv:1108.3556

    Google Scholar 

  • Ye C, Hill CM, Wu S, Ruan J, Ma Z (2016) DBG2OLC: Efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies. Scientific Rep 6:31900–31906

    Article  CAS  Google Scholar 

  • Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zimin AV, Marcais G, Puiu D, Roberts M, Salzberg SL, Yorke JA (2013) The MaSuRCA genome assembler. Bioinformatics 29(21):2669–2677

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Center for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India

    D. C. Mishra, S. B. Lal, Anu Sharma, Sanjeev Kumar, Neeraj Budhlakoti & Anil Rai

Authors
  1. D. C. Mishra
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. S. B. Lal
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Anu Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sanjeev Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Neeraj Budhlakoti
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Anil Rai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Anil Rai .

Editor information

Editors and Affiliations

  1. ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India

    Swarup Kumar Chakrabarti

  2. Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China

    Conghua Xie

  3. ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India

    Jagesh Kumar Tiwari

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Mishra, D.C., Lal, S.B., Sharma, A., Kumar, S., Budhlakoti, N., Rai, A. (2017). Strategies and Tools for Sequencing and Assembly of Plant Genomes. In: Kumar Chakrabarti, S., Xie, C., Kumar Tiwari, J. (eds) The Potato Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-66135-3_5

Download citation

Publish with us

Policies and ethics

Search

Navigation