Skip to main content
Log in

From one linear genome to a graph-based pan-genome: a new era for genomics

  • Insight
  • Published:
Science China Life Sciences Aims and scope Submit manuscript

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

References

  • Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., et al. (2020). Major impacts of widespread structural variation on gene expression and crop improvement in tomato. Cell 182, 145–161.e23.

    Article  CAS  Google Scholar 

  • Ameur, A. (2019). Goodbye reference, hello genome graphs. Nat Biotechnol 37, 866–868.

    Article  CAS  Google Scholar 

  • Ballouz, S., Dobin, A., and Gillis, J.A. (2019). Is it time to change the reference genome? Genome Biol 20, 159.

    Article  Google Scholar 

  • Cheng, S., Melkonian, M., Smith, S.A., Brockington, S., Archibald, J.M., Delaux, P.M., Li, F.W., Melkonian, B., Mavrodiev, E.V., Sun, W., et al. (2018). 10KP: A phylodiverse genome sequencing plan. GigaScience 7, 1–9.

    Article  CAS  Google Scholar 

  • Danilevicz, M.F., Tay Fernandez, C.G., Marsh, J.I., Bayer, P.E., and Edwards, D. (2020). Plant pangenomics: approaches, applications and advancements. Curr Opin Plant Biol 54, 18–25.

    Article  CAS  Google Scholar 

  • Eggertsson, H.P., Kristmundsdottir, S., Beyter, D., Jonsson, H., Skuladottir, A., Hardarson, M.T., Gudbjartsson, D.F., Stefansson, K., Halldorsson, B.V., and Melsted, P. (2019). GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs. Nat Commun 10, 5402.

    Article  Google Scholar 

  • Gan, X., Stegle, O., Behr, J., Steffen, J.G., Drewe, P., Hildebrand, K.L., Lyngsoe, R., Schultheiss, S.J., Osborne, E.J., Sreedharan, V.T., et al. (2011). Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477, 419–423.

    Article  CAS  Google Scholar 

  • Garrison, E., Sirén, J., Novak, A.M., Hickey, G., Eizenga, J.M., Dawson, E. T., Jones, W., Garg, S., Markello, C., Lin, M.F., et al. (2018). Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat Biotechnol 36, 875–879.

    Article  CAS  Google Scholar 

  • Golicz, A.A., Batley, J., and Edwards, D. (2016a). Towards plant pangenomics. Plant Biotechnol J 14, 1099–1105.

    Article  Google Scholar 

  • Golicz, A.A., Bayer, P.E., Barker, G.C., Edger, P.P., Kim, H.R., Martinez, P. A., Chan, C.K.K., Severn-Ellis, A., McCombie, W.R., Parkin, I.A.P., et al. (2016b). The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun 7, 13390.

    Article  CAS  Google Scholar 

  • Iqbal, Z., Caccamo, M., Turner, I., Flicek, P., and McVean, G. (2012). De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat Genet 44, 226–232.

    Article  CAS  Google Scholar 

  • Kim, D., Paggi, J.M., Park, C., Bennett, C., and Salzberg, S.L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915.

    Article  CAS  Google Scholar 

  • Lewin, H.A., Robinson, G.E., Kress, W.J., Baker, W.J., Coddington, J., Crandall, K.A., Durbin, R., Edwards, S.V., Forest, F., Gilbert, M.T.P., et al. (2018). Earth BioGenome Project: sequencing life for the future of life. Proc Natl Acad Sci USA 115, 4325–4333.

    Article  CAS  Google Scholar 

  • Liu, Y., Du, H., Li, P., Shen, Y., Peng, H., Liu, S., Zhou, G.A., Zhang, H., Liu, Z., Shi, M., et al. (2020). Pan-genome of wild and cultivated soybeans. Cell 182, 162–176.e13.

    Article  CAS  Google Scholar 

  • Sanger, F., Nicklen, S., and Coulson, A.R. (1977). DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74, 5463–5467.

    Article  CAS  Google Scholar 

  • Shendure, J., Balasubramanian, S., Church, G.M., Gilbert, W., Rogers, J., Schloss, J.A., and Waterston, R.H. (2017). DNA sequencing at 40: past, present and future. Nature 550, 345–353.

    Article  CAS  Google Scholar 

  • Sherman, R.M., and Salzberg, S.L. (2020). Pan-genomics in the human genome era. Nat Rev Genet 21, 243–254.

    Article  CAS  Google Scholar 

  • Tettelin, H., Masignani, V., Cieslewicz, M.J., Donati, C., Medini, D., Ward, N.L., Angiuoli, S.V., Crabtree, J., Jones, A.L., Durkin, A.S., et al. (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pangenome”. Proc Natl Acad Sci USA 102, 13950–13955.

    Article  CAS  Google Scholar 

  • Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G. G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., et al. (2001). The sequence of the human genome. Science 291, 1304–1351.

    Article  CAS  Google Scholar 

  • Yang, X., Lee, W.P., Ye, K., and Lee, C. (2019). One reference genome is not enough. Genome Biol 20, 104.

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by the Ministry of Agriculture of China (2016ZX08009-003), the Chinese Academy of Sciences (ZDRWZS-2019-2) and the National Natural Science Foundation of China (31788103). We thank Ms. Anita K. Snyder for revising the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Zhixi Tian.

Additional information

Compliance and ethics

The author(s) declare that they have no conflict of interest.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Liu, Y., Tian, Z. From one linear genome to a graph-based pan-genome: a new era for genomics. Sci. China Life Sci. 63, 1938–1941 (2020). https://doi.org/10.1007/s11427-020-1808-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11427-020-1808-0

Navigation