Reinforcing plant evolutionary genomics using ancient DNA

Current Opinion in Plant Biology

Volumn 36, Issue , 2017, Pages 38-45

  Gutaker, Rafal M ^a   Burbano, Hernán A ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANCIENT DNA;

DNA SEQUENCE; GENOMICS; MOLECULAR EVOLUTION; PLANT GENOME;

DNA, ANCIENT; EVOLUTION, MOLECULAR; GENOME, PLANT; GENOMICS; SEQUENCE ANALYSIS, DNA;

EID: 85011397656     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2017.01.002     Document Type: Review

References (56)

1. 1 Higuchi, R., Bowman, B., Freiberger, M., Ryder, O.A., Wilson, A.C., DNA sequences from the quagga, an extinct member of the horse family. Nature 312 (1984), 282–284.
2. 2 Paabo, S., Molecular cloning of Ancient Egyptian mummy DNA. Nature 314 (1985), 644–645.
3. 3 Orlando, L., Gilbert, M.T., Willerslev, E., Reconstructing ancient genomes and epigenomes. Nat Rev Genet 16 (2015), 395–408.
4. 4 Shapiro, B., Hofreiter, M., A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Science, 343, 2014, 1236573.
5. 5 Krause, J., Paabo, S., Genetic time travel. Genetics 203 (2016), 9–12.
6. 6 Lindahl, T., Instability and decay of the primary structure of DNA. Nature 362 (1993), 709–715.
7. 7 Sawyer, S., Krause, J., Guschanski, K., Savolainen, V., Paabo, S., Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS One, 7, 2012, e34131.
8. 8•• Yoshida, K., Schuenemann, V.J., Cano, L.M., Pais, M., Mishra, B., Sharma, R., Lanz, C., Martin, F.N., Kamoun, S., Krause, J., et al. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. Elife, 2, 2013, e00731 This paper demostrated the power of using herbarium samples to understand the evolution of a plant pathogen and its host over long period of times. This study identified the unique strain of Phytopththora infestans that triggered the Great Irish Famine and caused the 19th century epidemic. This study also showed the change in ploidy level from diploid to triploid and tetraploid between 19th and 20th century P. infestans clonal lineages.
9. 9 Staats, M., Erkens, R.H., van de Vossenberg, B., Wieringa, J.J., Kraaijeveld, K., Stielow, B., Geml, J., Richardson, J.E., Bakker, F.T., Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens. PLoS One, 8, 2013, e69189.
10. 10• Weiss, C.L., Schuenemann, V.J., Devos, J., Shirsekar, G., Reiter, E., Gould, B.A., Stinchcombe, J.R., Krause, J., Burbano, H.A., Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens. R Soc Open Sci, 3, 2016, 160239 This study describes the biochemical properties of ancient DNA retrieved from herbarium specimens and how they change throughout time.
11. 11 Allentoft, M.E., Collins, M., Harker, D., Haile, J., Oskam, C.L., Hale, M.L., Campos, P.F., Samaniego, J.A., Gilbert, M.T.P., Willerslev, E., et al. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc R Soc B Biol Sci 279 (2012), 4724–4733.
12. 12 Sarkinen, T., Staats, M., Richardson, J.E., Cowan, R.S., Bakker, F.T., How to open the treasure chest? Optimising DNA extraction from herbarium specimens. PLoS One, 7, 2012, e43808.
13. 13 Dabney, J., Knapp, M., Glocke, I., Gansauge, M.T., Weihmann, A., Nickel, B., Valdiosera, C., Garcia, N., Paabo, S., Arsuaga, J.L., et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci U S A 110 (2013), 15758–15763.
14. 14 Gutaker, R.M., Reiter, E., Furtwangler, A., Schuenemann, V.J., Burbano, H.A., Extraction of ultrashort molecules from herbarium specimens. BioTechniques, 62, 2016, 10.2144/000114517.
15. 15 Barlow, A., Gonzalez-Fortes, G.M., Dalen, L., Pinhasi, R., Gasparyan, G., Rabeder, G., Frischchauf, J., Paijmans, J.L.A., Hofreiter, M., Massive influence of DNA isolation and library preparation approaches on palaeogenomic sequencing data. BioRxiv, 2016, 10.1101/075911.
16. 16 Wales, N., Caroe, C., Sandoval-Velasco, M., Gamba, C., Barnett, R., Samaniego, J.A., Madrigal, J.R., Orlando, L., Gilbert, M.T., New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA. Biotechniques 59 (2015), 368–371.
17. 17 Poinar, H.N., Schwarz, C., Qi, J., Shapiro, B., Macphee, R.D., Buigues, B., Tikhonov, A., Huson, D.H., Tomsho, L.P., Auch, A., et al. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311 (2006), 392–394.
18. 18 Hofreiter, M., Jaenicke, V., Serre, D., von Haeseler, A., Paabo, S., DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res 29 (2001), 4793–4799.
19. 19 Briggs, A.W., Stenzel, U., Johnson, P.L., Green, R.E., Kelso, J., Prufer, K., Meyer, M., Krause, J., Ronan, M.T., Lachmann, M., et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci U S A 104 (2007), 14616–14621.
20. 20 Orlando, L., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499 (2013), 74–78.
21. 21 Pedersen, M.W., Ruter, A., Schweger, C., Friebe, H., Staff, R.A., Kjeldsen, K.K., Mendoza, M.L., Beaudoin, A.B., Zutter, C., Larsen, N.K., et al. Postglacial viability and colonization in North America's ice-free corridor. Nature 537 (2016), 45–49.
22. 22 Prufer, K., Meyer, M., Comment on Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans. Science, 347, 2015, 835.
23. 23 Weiss, C.L., Dannemann, M., Prufer, K., Burbano, H.A., Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data. Elife, 4, 2015.
24. 24 Jonsson, H., Ginolhac, A., Schubert, M., Johnson, P.L., Orlando, L., mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29 (2013), 1682–1684.
25. 25 Briggs, A.W., Stenzel, U., Meyer, M., Krause, J., Kircher, M., Paabo, S., Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res, 38, 2010, e87.
26. 26 Ziesemer, K.A., Mann, A.E., Sankaranarayanan, K., Schroeder, H., Ozga, A.T., Brandt, B.W., Zaura, E., Waters-Rist, A., Hoogland, M., Salazar-Garcia, D.C., et al. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Sci Rep, 5, 2015, 16498.
27. 27 Kawecki, T.J., Lenski, R.E., Ebert, D., Hollis, B., Olivieri, I., Whitlock, M.C., Experimental evolution. Trends Ecol Evol 27 (2012), 547–560.
28. 28 Hu, G., Hawkins, J.S., Grover, C.E., Wendel, J.F., The history and disposition of transposable elements in polyploid Gossypium. Genome 53 (2010), 599–607.
29. 29• Palmer, S.A., Clapham, A.J., Rose, P., Freitas, F.O., Owen, B.D., Beresford-Jones, D., Moore, J.D., Kitchen, J.L., Allaby, R.G., Archaeogenomic evidence of punctuated genome evolution in Gossypium. Mol Biol Evol 29 (2012), 2031–2038 To the best of our knowledge, this is the first study that utilize next generation sequencing methods for archaeological remains.
30. 30 Comai, L., The advantages and disadvantages of being polyploid. Nat Rev Genet 6 (2005), 836–846.
31. 31 Therrien, C.D., Ritch, D.L., Davidse, L.C., Jespers, A.B., Spielman, L.J., Nuclear DNA content, mating type and metalaxyl sensitivity of eighty-three isolates of Phytophthora infestans from The Netherlands. Mycol Res 92 (1989), 140–146.
32. 32 Zhu, Y.O., Sherlock, G., Petrov, D.A., Whole genome analysis of 132 clinical saccharomyces cerevisiae strains reveals extensive ploidy variation. GenesGenomesGenetics 6 (2016), 2421–2434.
33. 33 Subramanian, S., Lambert, D.M., Selective constraints determine the time dependency of molecular rates for human nuclear genomes. Genome Biol Evol 4 (2012), 1127–1132.
34. 34 Green, R.E., Shapiro, B., Human evolution: turning back the clock. Curr Biol 23 (2013), R286–288.
35. 35 Fu, Q., Mittnik, A., Johnson, P.L., Bos, K., Lari, M., Bollongino, R., Sun, C., Giemsch, L., Schmitz, R., Burger, J., et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr Biol 23 (2013), 553–559.
36. 36 Martin, M.D., Ho, S.Y., Wales, N., Ristaino, J.B., Gilbert, M.T., Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant new world Phytophthora infestans. Mol Biol Evol 31 (2014), 1414–1420.
37. 37 Drummond, A.J., Nicholls, G.K., Rodrigo, A.G., Solomon, W., Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161 (2002), 1307–1320.
38. 38•• Exposito-Alonso, M., Becker, C., Schuenemann, V.J., Reitter, E., Setzer, C., Slovak, R., Brachi, B., Hagmann, J., Grimm, D., Jiahui, C., et al. The rate and effect of de novo mutations in Arabidopsis thaliana natural populations. BioRxiv, 2016, 10.1101/050203 Owing to the whole genome sequencing of tens of herbarium specimens, this study represents the most comprehensive plat aDNA investigation to date. Authors reported historical movements of the plant Arabidopsis thaliana after its coloniyation of North America, found candidate genes under selection, and reported substitution rates in the wild.
39. 39 Platt, A., Horton, M., Huang, Y.S., Li, Y., Anastasio, A.E., Mulyati, N.W., Agren, J., Bossdorf, O., Byers, D., Donohue, K., et al. The scale of population structure in Arabidopsis thaliana. PLoS Genet, 6, 2010, e1000843.
40. 40 Zohary, D., Hopf, M., Weiss, E., Domestication of Plants in the Old World: The origin and Spread of Domesticated Plants in Southwest Asia, Europe, and the Mediterranean Basin. 2012, Oxford University Press on Demand.
41. 41 Brown, T.A., Jones, M.K., Powell, W., Allaby, R.G., The complex origins of domesticated crops in the Fertile Crescent. Trends Ecol Evol 24 (2009), 103–109.
42. 42 Allaby, R.G., Gutaker, R., Clarke, A.C., Pearson, N., Ware, R., Palmer, S.A., Kitchen, J.L., Smith, O., Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops. Philos Trans R Soc Lond B Biol Sci, 370, 2015, 20130377.
43. 43 Mascher, M., Schuenemann, V.J., Davidovich, U., Marom, N., Himmelbach, A., Hubner, S., Korol, A., David, M., Reiter, E., Riehl, S., et al. Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nat Genet 48 (2016), 1089–1093.
44. 44 Palmer, S.A., Moore, J.D., Clapham, A.J., Rose, P., Allaby, R.G., Archaeogenetic evidence of ancient nubian barley evolution from six to two-row indicates local adaptation. PLoS One, 4, 2009, e6301.
45. 45 Smith, O., Clapham, A.J., Rose, P., Liu, Y., Wang, J., Allaby, R.G., Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process. Sci Rep, 4, 2014, 5559.
46. 46 Jaenicke-Despres, V., Buckler, E.S., Smith, B.D., Gilbert, M.T., Cooper, A., Doebley, J., Paabo, S., Early allelic selection in maize as revealed by ancient DNA. Science 302 (2003), 1206–1208.
47. 47•• da Fonseca, R.R., Smith, B.D., Wales, N., Cappellini, E., Skoglund, P., Fumagalli, M., Samaniego, J.A., Caroe, C., Avila-Arcos, M.C., Hufnagel, D.E., et al. The origin and evolution of maize in the Southwestern United States. Nat Plants, 1, 2015, 14003 This study is unique owing to the high number of archaeobotanical samples used for genomic analyses. The broad temporal distribution of those samples coupled with gene capture strategy enable stratification of the selection signal during different phases of maize domestication.
48. 48 Yoshida, K., Burbano, H.A., Krause, J., Thines, M., Weigel, D., Kamoun, S., Mining herbaria for plant pathogen genomes: back to the future. PLoS Pathog, 10, 2014, e1004028.
49. 49 van Kleunen, M., Dawson, W., Essl, F., Pergl, J., Winter, M., Weber, E., Kreft, H., Weigelt, P., Kartesz, J., Nishino, M., et al. Global exchange and accumulation of non-native plants. Nature 525 (2015), 100–103.
50. 50 Lankau, R.A., Nuzzo, V., Spyreas, G., Davis, A.S., Evolutionary limits ameliorate the negative impact of an invasive plant. Proc Natl Acad Sci U S A 106 (2009), 15362–15367.
51. 51 Colautti, R., Franks, S.J., Hufbauer, R.A., Kotanen, P.M., Torchin, M., Byers, J.E., Pyšek, P., Bossdorf, O., The Global Garlic Mustard Field Survey (GGMFS): challenges and opportunities of a unique, large-scale collaboration for invasion biology. NeoBiota, 21, 2014, 29.
52. 52 Martin, M.D., Zimmer, E.A., Olsen, M.T., Foote, A.D., Gilbert, M.T., Brush, G.S., Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance. Mol Ecol 23 (2014), 1701–1716.
53. 53 Haak, W., Balanovsky, O., Sanchez, J.J., Koshel, S., Zaporozhchenko, V., Adler, C.J., Der Sarkissian, C.S., Brandt, G., Schwarz, C., Nicklisch, N., et al. Ancient DNA from European early neolithic farmers reveals their near eastern affinities. PLoS Biol, 8, 2010, e1000536.
54. 54 Roullier, C., Benoit, L., McKey, D.B., Lebot, V., Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination. Proc Natl Acad Sci U S A 110 (2013), 2205–2210.
55. 55 Erickson, D.L., Smith, B.D., Clarke, A.C., Sandweiss, D.H., Tuross, N., An Asian origin for a 10,000-year-old domesticated plant in the Americas. Proc Natl Acad Sci U S A 102 (2005), 18315–18320.
56. 56•• Kistler, L., Montenegro, A., Smith, B.D., Gifford, J.A., Green, R.E., Newsom, L.A., Shapiro, B., Transoceanic drift and the domestication of African bottle gourds in the Americas. Proc Natl Acad Sci U S A 111 (2014), 2937–2941 This paper describes successful sequencing of chloroplast genomes from ancient bottle gourds. This data allowed authors to infer the introductions of bottle gourds to North America from Africa through oceanic drift.