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Herbarium Genomics: Plant Archival DNA Explored

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Paleogenomics

Part of the book series: Population Genomics ((POGE))

Abstract

Herbarium genomics, allowing testing of historic biological hypotheses in plant science, is a promising field mainly driven by recent advances in next-generation sequencing (NGS) technology. Herbarium collections represent an enormous botanical repository of both specimens and of phenotypic observations and locality data, of sometimes long-extinct taxa. Herbarium specimens, a large part of which stem from the nineteenth and eighteenth century, are mostly pressed and mounted and were usually heat-treated and poisoned for preservation. Whereas the presence of post-mortem damage in herbarium DNA has been found to consist of mainly genome fragmentation (single- and double-stranded breaks), damage-derived miscoding lesions appear to be highly limited or even negligible. For organelle genomes and other repetitive genomic compartments, genome skimming appears effective in retrieving sequence data from plant herbarium specimens, whereas studies addressing herbarium nuclear-encoded genes and particularly whole genomes are still in minority. High levels of herbarium genomic fragmentation possibly lead to insert sizes being smaller than Illumina read lengths applied. Using a series of 93 herbarium DNA samples, representing 10 angiosperm families, near-complete plastomes were assembled for 80% of the specimens, some of which are 146 years old. Overlapping read pairs were found to occur in roughly 80% of all read pairs obtained. After merging such overlapping pairs, the resulting fragments and their distribution can be considered to reflect the ongoing process of genome fragmentation up to the moment of DNA extraction. Fragment length distributions appear to fit gamma distributions with either many small fragments present or an increasing number of longer fragments having accumulated. These distributions appear to differ from usually observed first-order genomic degradation kinetics, possibly due to the nonrepresentative nature of genome skimming samples.

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References

  • Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, Campos PF, Samaniego JA, Gilbert MTP, Willerslev E, Zhang G, Scofield RP, Holdaway RN, Michael B. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc R Soc B. 2012;279(1748):4724–33. https://doi.org/10.1098/rspb.2012.1745. Epub 2012 Oct 10.

    Article  CAS  PubMed  Google Scholar 

  • Ardui S, Ameur A, Vermeesch JR, Hestand MS. Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res. 2018;46:2159–68. https://doi.org/10.1093/nar/gky066.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bakker FT. DNA sequences from plant herbarium tissue. In: Hörandl E, Appelhans M, editors. Next-generation sequencing in plant systematics. Bratislava: International Association for Plant Taxonomy (IAPT); 2015. p. 271–84.

    Google Scholar 

  • Bakker FT. Herbarium genomics: skimming and plastomics from archival specimens. Webbia. 2017;72:35. https://doi.org/10.1080/00837792.2017.1313383.

    Article  Google Scholar 

  • Bakker FT, Lei D, Yu J, Mohammadin S, Wei Z, Van de Kerke S, Gravendeel B, Nieuwenhuis M, Staats M, Alquezar-Planas DE, Holmer R. Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an iterative organelle genome assembly (IOGA) pipeline. Biol J Linn Soc. 2016;117:33–43. https://doi.org/10.1111/bij.12642.

    Article  Google Scholar 

  • Bebber DP, Carine MA, Wood JRI, Wortley AH, Harris DJ, Prance GT, Davidse G, Paige J, Pennington TD, Robson NKB, Scotland RW. Herbaria are a major frontier for species discovery. PNAS. 2010;107:22169–71.

    Article  CAS  Google Scholar 

  • Beck JB, Semple JC. Next-generation sampling: pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae). Appl Plant Sci. 2015;3(6):1500014. https://doi.org/10.3732/apps.1500014.

    Article  Google Scholar 

  • Besnard G, Christin P-A, Malé P-JG, L’huillier E, Lauzeral C, Coissac E, Vorontsova MS. From museums to genomics: old herbarium specimens shed light on a C3 to C4 transition. J Exp Bot. 2014;65:6711. https://doi.org/10.1093/jxb/eru395.

    Article  CAS  Google Scholar 

  • Bieker VC, Martin MD. Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections. Bot Lett. 2018; https://doi.org/10.1080/23818107.2018.1458651.

    Article  CAS  Google Scholar 

  • Bressan EA, Rossi ML, Gerald LT, Figueira A. Extraction of high-quality DNA from ethanol-preserved tropical plant tissues. BMC Res Notes. 2014;7:268. https://doi.org/10.1186/1756-0500-7-268.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Briggs AW, Stenzel U, Johnson PLF, Green RE, Kelso J, Prufer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S. Patterns of damage in genomic DNA sequences from a Neandertal. PNAS. 2007;104:14616–21. https://doi.org/10.1073/pnas.0704665104.

    Article  CAS  Google Scholar 

  • Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, Austin J, Cooper A. Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Res. 2007;35(17):5717–28. https://doi.org/10.1093/nar/gkm588.

    Article  CAS  Google Scholar 

  • Buerki S, Baker WJ. Collections-based research in the genomic era. Biol J Linn Soc. 2015;117:5. https://doi.org/10.1111/bij.12721.

    Article  Google Scholar 

  • Chomicki G, Renner SS. Watermelon origin solved with molecular phylogenetics including Linnaean material: another example of museomics. New Phytol. 2015;205:526–32.

    Article  Google Scholar 

  • Clark SC, Egan R, Frazier PI, Wang Z. ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. Bioinformatics. 2013;29:435–43.

    Article  CAS  Google Scholar 

  • Costion CM, Lowe AJ, Rossetto M, Kooyman RM, Breed MF, Ford A, Crayn DM. Building a plant DNA barcode reference library for a diverse tropical flora: an example from Queensland, Australia. Divers Distrib. 2016;8:1–9. https://doi.org/10.3390/d8010005.

    Article  Google Scholar 

  • Délye C, Deulvot C, Chauvel B. DNA analysis of herbarium specimens of the grass weed Alopecurus myosuroides reveals herbicide resistance pre-dated herbicides. PLoS One. 2013;8(10):e75117.

    Article  Google Scholar 

  • Dodsworth S, Chase MW, Kelly LJ, Leitch IJ, Macas J, Novák P, et al. Genomic repeat abundances contain phylogenetic signal. Syst Biol. 2015;64(1):112–26. https://doi.org/10.1093/sysbio/syu080.

    Article  CAS  PubMed  Google Scholar 

  • Downie SR, Palmer JD. Use of chloroplast DNA rearrangements in reconstruction plant phylogeny. In: Soltis PS, et al., editors. Molecular systematics of plants. New York: Chapman and Hall; 1992. p. 1–13.

    Google Scholar 

  • Doyle JJ, Dickson EE. Preservation of plant species for DNA restriction endonuclease analysis. Taxon. 1987;36:715–22.

    Article  Google Scholar 

  • Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phyt Bull. 1987;19:11–5.

    Google Scholar 

  • Drábková L, Kirschner J, Vlcek C. Comparison of seven DNA extraction and amplification protocols in historic herbarium specimens of Juncaceae. Plant Mol Biol Rep. 2002;20:161–75.

    Article  Google Scholar 

  • Enan MR, Palakkott AR, Ksiksi TS. DNA barcoding of selected UAE medicinal plant species: a comparative assessment of herbarium and fresh samples. Phys Mol Biol Plants. 2017;23:221–7. https://doi.org/10.1007/s12298-016-0412-9.

    Article  CAS  Google Scholar 

  • Erkens RHJ, Cross H, Maas JW, Hoenselaar K, Chatrou LW. Age and greenness of herbarium specimens as predictors for successful extraction and amplification of DNA. Blumea. 2008;53:407–28.

    Article  Google Scholar 

  • Gansauge MT, Gerber T, Glocke I, Korlevic P, Lippik L, Nagel S, Riehl LM, Schmidt A, Meyer M. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Res. 2017;45(10):e79. https://doi.org/10.1093/nar/gkx033.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gilbert MTP, Hansen AJ, Willerslev E, Rudbeck L, Barnes I, Lynnerup N, Cooper A. Distribution patterns of postmortem damage in human mitochondrial DNA. Am J Hum Genet. 2003;72:48–61.

    Article  CAS  Google Scholar 

  • Gill SS, Tuteja N. Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem. 2010;48:909–30.

    Article  CAS  Google Scholar 

  • Gregory TR, Nicoll JA, Tamm H, Kullman B, Kullman K, Leitch IJ, Murray BG, Kapraun DF, Greilhuber J, Bennett MD. Eukaryotic genome size databases. Nucleic Acids Res. 2007;35(Database issue):D332–D338. https://doi.org/10.1093/nar/gkl828.

    Article  CAS  Google Scholar 

  • Gutaker RM, Reiter E, Furtwängler A, Schuenemann VJ, Burbano HA. Extraction of ultrashort DNA molecules from herbarium specimens. BioTechniques. 2017;62:76–9. https://doi.org/10.2144/000114517.

    Article  CAS  PubMed  Google Scholar 

  • Hahn C, Bachmann L, Chevreux B. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – a baiting and iterative mapping approach. Nucleic Acids Res. 2013;41(13):e129.

    Article  CAS  Google Scholar 

  • Harris SA. DNA analysis of tropical plant species: an assessment of different drying methods. Plant Syst Evol. 1993;188:57–64.

    CAS  Google Scholar 

  • Hart ML, Forrest LL, Nicholls JA, Kidner CA. Retrieval of hundreds of nuclear loci from herbarium specimens. Taxon. 2016;65(5):1081–92.

    Article  Google Scholar 

  • Heyn P, Stenzel U, Briggs AW, Kircher M, Hofreiter M, Meyer M. Road blocks on paleogenomes – polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA. Nucleic Acids Res. 2010;38(16):e161. https://doi.org/10.1093/nar/gkq572.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hofreiter M, Jaenicke V, Serre D, von Haeseler A, Pääbo S. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 2001;29:4793–9.

    Article  CAS  Google Scholar 

  • Hofreiter M, Paijmans JLA, Goodchild H, Speller CF, Barlow A, Fortes GG, Thomas JA, Ludwig A, Collins MJ. The future of ancient DNA: technical advances and conceptual shifts. BioEssays. 2015;37:284–93. https://doi.org/10.1002/bies.201400160.

    Article  Google Scholar 

  • James SA, Soltis PS, Belbin L, Chapman AD, Nelson G, Paul DL, Collins M. Herbarium data: global biodiversity and societal botanical needs for novel research. Appl Plant Sci. 2018;6:e1024. https://doi.org/10.1002/aps3.1024.

    Article  Google Scholar 

  • Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol. 2004;5:R12.

    Article  Google Scholar 

  • Lindahl T. Instability and decay of the primary structure of DNA. Nature. 1993;362:709–15.

    Article  CAS  Google Scholar 

  • Lindahl T, Andersson A. Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid. Biochemistry. 1972;11:3618–23.

    Article  CAS  Google Scholar 

  • Litt A. Comparative evolutionary genomics of land plants. Ann Plant Rev. 2013;45:227–76. https://doi.org/10.1002/9781118305881.ch8.

    Article  Google Scholar 

  • Lonardi S, Mirebrahim H, Wanamaker S, Alpert M, Ciardo G, Duma D, Close TJ. When less is more: ‘slicing’ sequencing data improves read decoding accuracy and de novo assembly quality. Bioinformatics. 2015;31:2972–80.

    Google Scholar 

  • Mateiu LM, Rannala BH. Bayesian inference of errors in ancient DNA caused by postmortem degradation. Mol Biol Evol. 2008;25(7):1503–11. https://doi.org/10.1093/molbev/msn095.

    Article  CAS  PubMed  Google Scholar 

  • McCabe PF, Levine A, Meijer PJ, Tapon NA, Pennell RI. A programmed cell death pathway activated in carrot cells cultured at low cell density. Plant J. 1997;12:267–80.

    Article  CAS  Google Scholar 

  • Mikić AM. The first attested extraction of ancient DNA in legumes (Fabaceae). Front Plant Sci. 2015;6:1006. https://doi.org/10.3389/fpls.2015.01006.

    Article  PubMed  PubMed Central  Google Scholar 

  • Mohammadin S, Peterse K, van de Kerke SJ, Chatrou LW, Dönmez AA, Mummenhoff K, Pires JC, Edger PP, Al-Shehbaz IA, Schranz ME. Anatolian origins and diversification of Aethionema, the sister lineage of the core Brassicaceae. Am J Bot. 2017;104:1042–54.

    Google Scholar 

  • Murray BG, Leitch IJ, Bennett MD. Gymnosperm DNA C-values database. Release 4.0, Dec 2010. http://data.kew.org/cvalues.

  • Olofsson JK, Bianconi M, Besnard G, Dunning LT, Lundgren MR, Holota H, Vorontsova MS, et al. Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait. Mol Ecol. 2016;25(24):6107–123.

    Article  CAS  Google Scholar 

  • Osmundson TW, Robert VA, Schoch CL, Baker LJ, Smith A, Robich G, Mizzan L, Garbelotto M. Filling gaps in biodiversity knowledge for macrofungi: contributions and assessment of an herbarium collection DNA barcode sequencing project. PLoS One. 2013;8:1–8.

    Article  CAS  Google Scholar 

  • Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M. Genetic analyses from ancient DNA. Annu Rev Genet. 2004;38:645–79.

    Article  Google Scholar 

  • Pyle MM, Adams RP. In situ preservation of DNA in plant specimens. Taxon. 1989;38:576–81.

    Article  Google Scholar 

  • Queenborough S. Collections-based studies of plant functional traits. In: Friis I, Balslev H, editors. Tropical plant collections: legacies from the past? Essential tools for the future? Scientia Danica B (Biologica). Vol 6. 2017. p. 15–38, 223–36.

    Google Scholar 

  • Reape TJ, Molony EM, McCabe PF. Programmed cell death in plants: distinguishing between different modes. J Exp Bot. 2008;59:435–44.

    Article  CAS  Google Scholar 

  • Roldán-Arjona T, Ariza RR. Repair and tolerance of oxidative DNA damage in plants. Mutat Res. 2009;681:169–79.

    Article  Google Scholar 

  • Särkinen T, Staats M, Richardson JE, Cowan RS, Bakker FT. How to open the treasure chest? Optimising DNA extraction from herbarium specimens. PLoS One. 2012;7:e43808. https://doi.org/10.1371/journal.pone.0043808.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Savolainen V, Cuénoud P, Spichiger R, Martinez MDP, Crèvecoeur M, Manen J-F. The use of hebarium specimens in DNA phylogenetics: evaluation and improvement. Plant Syst Evol. 1995;197:87–98.

    Article  CAS  Google Scholar 

  • Schrenk J. Schweinfurth’s method of preserving plants for herbaria. Bull Torrey Bot Club. 1888;15:292–3.

    Article  Google Scholar 

  • Sebastian P, Schaefer H, Telford IRH, Renner SS. Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia. PNAS. 2010;107:14269–73.

    Article  CAS  Google Scholar 

  • Shapiro B, Hofreiter M. A Paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Science. 2014;343:1236573. https://doi.org/10.1126/science.1236573.

    Article  CAS  PubMed  Google Scholar 

  • Soltis PS. Digitization of herbaria enables novel research. Am J Bot. 2017;104:1–4.

    Article  Google Scholar 

  • Staats M, Cuence A, Richardson JE, Vrielink-van Ginkel R, Petersen G, Seberg O, Bakker FT. DNA damage in plant herbarium tissue. PLoS One. 2011;6:e28448.

    Article  CAS  Google Scholar 

  • Staats M, Erkens RHJ, van de Vossenberg B, Wieringa JJ, Kraaijeveld K, Stielow B, Geml J, Richardson JE, Bakker FT. Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens. PLoS One. 2013;8(7):e69189. https://doi.org/10.1371/journal.pone.0069189.

    Article  CAS  Google Scholar 

  • Straub SCK, Parks M, Weitemeir K, Fishbein M, Cronn R, et al. Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics. Am J Bot. 2012;99:349–64.

    Article  CAS  Google Scholar 

  • Telle S, Thines M. Amplification of cox2 (~620 bp) from 2 mg of up to 129 years old herbarium specimens, comparing 19 extraction methods and 15 polymerases. PLoS One. 2008;3:e3584.

    Article  Google Scholar 

  • The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012;485:635. https://doi.org/10.1038/nature11119.

    Article  CAS  Google Scholar 

  • Turner FS. Assessment of insert sizes and adapter content in fastq data from NexteraXT libraries. Front Genet. 2014;5:1–7. https://doi.org/10.3389/fgene.2014.00005.

    Article  CAS  Google Scholar 

  • Wei Z, Zhu SX, van den Berg RG, Bakker FT, Schranz ME. Phylogenetic relationships within Lactuca L. (Asteraceae), including African species, based on chloroplast DNA sequence comparisons. Genet Resour Crop Evol. 2017;64:55–71.

    Article  Google Scholar 

  • Weiss CL, Schuenemann VJ, Devos J, Shirsekar G, Reiter E, Gould BA, Stinchcombe JR, Krause J, Burbano HA. Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens. R Soc Open Sci. 2016;3:160239.

    Article  Google Scholar 

  • Welch AJ, Collins K, Ratan A, Drautz-Moses DI, Schuster SC, Lindqvist C. The quest to resolve recent radiations: plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae). Mol Phylogenet Evol. 2016;99:16–33.

    Article  Google Scholar 

  • Wicke S, Schneeweiss GM. Next-generation organellar genomics: potentials and pitfalls of high-throughput technologies for molecular evolutionary studies and plant systematics. In: Hörandl E, Appelhans MS, editors. Next generation sequencing in plant systematics. Bratislava: International Association for Plant Taxonomy (IAPT); 2015. p. 9–50.

    Google Scholar 

  • Xu C, Dong W, Shi S, Cheng T, Li C, Liu Y, Wu P, Wu H, Gao P, Zhou S. Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques. Mol Ecol Resour. 2015;15:1366–74. https://doi.org/10.1111/1755-0998.12413.

    Article  CAS  Google Scholar 

  • Yao W, Mei C, Nan X, Hui L. Evaluation and comparison of in vitro degradation kinetics of DNA in serum, urine and saliva: a qualitative study. Gene. 2016;590(1):142–8. https://doi.org/10.1016/j.gene.2016.06.033. Epub 2016 June 16.

    Article  CAS  PubMed  Google Scholar 

  • Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, et al. Mining herbaria for plant pathogen genomes: back to the future. PLoS Pathog. 2014;10(4):e1004028. https://doi.org/10.1371/journal.ppat.1004028.

    Article  PubMed  PubMed Central  Google Scholar 

  • Yoshida K, Sasaki E, Kamoun S. Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects. Front Plant Sci. 2015;6:771.

    Article  Google Scholar 

  • Zedane L, Hong-Wa C, Murienne J, Jeziorsky C, Baldwin BG, Besnard G. Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico. Biol J Linn Soc. 2015;117:44–57.

    Article  Google Scholar 

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Authors and Affiliations

  1. Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands

    Freek T. Bakker

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Correspondence to Freek T. Bakker .

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  1. Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY, USA

    Charlotte Lindqvist

  2. Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada

    Om P. Rajora

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Bakker, F.T. (2018). Herbarium Genomics: Plant Archival DNA Explored. In: Lindqvist, C., Rajora, O. (eds) Paleogenomics. Population Genomics. Springer, Cham. https://doi.org/10.1007/13836_2018_40

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