Review and future prospects for DNA barcoding methods in forensic palynology

Forensic Science International: Genetics

Volumn 21, Issue , 2016, Pages 110-116

  Bell, Karen L ^a   Burgess, Kevin S ^b   Okamoto, Kazufusa C ^c   Aranda, Roman ^c   Brosi, Berry J ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b University System of Georgia   (United States)

^c Defense Forensic Science Center   (United States)

Author keywords

DNA barcoding; DNA metabarcoding; Forensic botany; Forensic palynology; High throughput sequencing; Metagenomics

Indexed keywords

ARTICLE; BIOINFORMATICS; CAMPANULACEAE; COPY NUMBER VARIATION; DNA BARCODING; ESCHSCHOLZIA; FORENSIC IDENTIFICATION; FORENSIC PALYNOLOGY; HIGH THROUGHPUT SEQUENCING; HUMAN; PALYNOLOGY; PAPAVER SOMNIFERUM; PLASTID GENOME; POLLEN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE DATABASE; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES COMPOSITION; FORENSIC SCIENCE; GENETICS; PALEONTOLOGY; PROCEDURES;

PLANT DNA;

DNA BARCODING, TAXONOMIC; DNA, PLANT; FORENSIC SCIENCES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PALEONTOLOGY; POLLEN;

EID: 84952780132     PISSN: 18724973     EISSN: 18780326     Source Type: Journal    
DOI: 10.1016/j.fsigen.2015.12.010     Document Type: Article

References (79)

1. K.A. Holt, and K.D. Bennett Principles and methods for automated palynology New Phytol. 203 2014 735 742
2. CBOL Plant Working Group A DNA barcode for land plants Proc. Natl. Acad. Sci. U. S. A. 106 2009 12794 12797
3. Illumina MiSeq System User Guide 2014 Illumina San Diego, California
4. K. Kraaijeveld, L.A. de Weger, M. Ventayol García, H. Buermans, J. Frank, P.S. Hiemstra, and et al. Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing Mol. Ecol. Resour. 15 2015 8 16 10.1111/1755-0998.12288
5. A. Keller, N. Danner, G. Grimmer, M. Ankenbrand, K. von der Ohe, W. von der Ohe, and et al. Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples Plant Biol. 17 2015 558 566 10.1111/plb.12251
6. A. Valentini, C. Miquel, and P. Taberlet DNA barcoding for honey biodiversity Diversity 2 2010 610 617 10.3390/d2040610
7. R.T. Richardson, C.-H. Lin, D.B. Sponsler, J.O. Quijia, K. Goodell, and R.M. Johnson Application of ITS2 metabarcoding to determine the provenance of pollen collected by honey bees in an agroecosystem Appl. Plant Sci. 3 2015 1400066 10.3732/apps.1400066
8. M. Horrocks, and K.A.J. Walsh Forensic palynology: assessing the value of the evidence Rev. Palaeobot. Palynol. 103 1998 69 74
9. B. Taylor, and K.R. Skene Forensic palynology: spatial and temporal considerations of spora deposition in forensic investigations Aust. J. Forensic Sci. 35 2003 193 204 10.1080/00450610309410582
10. V.M. Bryant, and G.D. Jones Forensic palynology: current status of a rarely used technique in the United States of America Forensic Sci. Int. 163 2006 183 197
11. R.W. Mathewes Forensic palynology in Canada: an overview with emphasis on archaeology and anthropology Forensic Sci. Int. 163 2006 198 203 10.1016/j.forsciint.2006.06.069
12. E. Montali, A.M. Mercuri, G. Trevisan Grandi, and C.A. Accorsi Towards a crime pollen calendar - pollen analysis on corpses throughout one year Forensic Sci. Int. 163 2006 211 223 10.1016/j.forsciint.2005.11.020
13. P.E.J. Wiltshire Consideration of some taphonomic variables of relevance to forensic palynological investigation in the United Kingdom Forensic Sci. Int. 163 2006 173 182 10.1016/j.forsciint.2006.07.011
14. K.A.J. Walsh, and M. Horrocks Palynology: its position in the field of forensic science J. Forensic Sci. 53 2008 1053 1060 10.1111/j.1556-4029.2008.00802.x
15. D.C. Mildenhall, P.E.J. Wiltshire, and V.M. Bryant Forensic palynology: why do it and how it works Forensic Sci. Int. 163 2006 163 172 Editorial
16. P. Arguelles, K. Reinhard, and D.H. Shin Forensic palynological analysis of intestinal contents of a Korean mummy Anat. Rec. (Hoboken) 298 2015 1182 1190 10.1002/ar.23141
17. A.G. Brown The use of forensic botany and geology in war crimes investigations in NE Bosnia Forensic Sci. Int. 163 2006 204 210
18. D.C. Mildenhall Hypericum pollen determines the presence of burglars at the scene of a crime: an example of forensic palynology Forensic Sci. Int. 163 2006 231 235 10.1016/j.forsciint.2005.11.028
19. W. Meier-Augenstein Stable Isotope Forensics: An Introduction to the Forensic Application of Stable Isotope Analysis 2010 J. Wiley Chichester, West Sussex Hoboken, NJ
20. M. Rahl Microscopic identification and purity determination of pollen grains Methods Mol. Med. 138 2008 263 269 10.1007/978-1-59745-366-0-22
21. E. Khansari, S. Zarre, K. Alizadeh, F. Attar, F. Aghabeigi, and Y. Salmaki Pollen morphology of Campanula (Campanulaceae) and allied genera in Iran with special focus on its systematic implication Flora - Morphol. Distrib. Funct. Ecol. Plants 207 2012 203 211 10.1016/j.flora.2012.01.006
22. Y. Salmaki, Z. Jamzad, S. Zarre, and C. Bräuchler Pollen morphology of Stachys (Lamiaceae) in Iran and its systematic implication Flora - Morphol. Distrib. Funct. Ecol. Plants 203 2008 627 639 10.1016/j.flora.2007.10.005
23. H.C. Lee, C. Ladd, M.T. Bourke, and et al. DNA typing in forensic science. I. Theory and background Am. J. Forensic Med. Pathol. 15 1994 269 282
24. A. Linacre, and D. Graham Role of molecular diagnostics in forensic science Expert Rev. Mol. Diagn. 2 2002 346 353 10.1586/14737159.2.4.346
25. C. Børsting, and N. Morling Next generation sequencing and its applications in forensic genetics Forensic Sci. Int. Genet. 2015 10.1016/j.fsigen.2015.02.002
26. R. Ogden, and A. Linacre Wildlife forensic science: a review of genetic geographic origin assignment Forensic Sci. Int. Genet. 2015 10.1016/j.fsigen.2015.02.008
27. I.C.T. Mello, A.S.D. Ribeiro, V.H.G. Dias, R. Silva, B.D. Sabino, R.G. Garrido, and et al. A segment of rbcL gene as a potential tool for forensic discrimination of Cannabis sativa seized at Rio de Janeiro, Brazil Int. J. Legal Med. 2015 10.1007/s00414-015-1170-x
28. A. Galimberti, F. De Mattia, A. Losa, I. Bruni, S. Federici, M. Casiraghi, and et al. DNA barcoding as a new tool for food traceability Food Res. Int. 50 2013 55 63 10.1016/j.foodres.2012.09.036
29. I. Bosmali, I. Ganopoulos, P. Madesis, and A. Tsaftaris Microsatellite and DNA-barcode regions typing combined with High Resolution Melting (HRM) analysis for food forensic uses: a case study on lentils (Lens culinaris) Food Res. Int. 46 2012 141 147 10.1016/j.foodres.2011.12.013
30. P.D.N. Hebert, S. Ratnasingham, and J.R. DeWaard Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species Proc. Biol. Sci. 270 Suppl 2003 S96 S99 10.1098/rsbl.2003.0025
31. M.L. Coghlan, J. Haile, J. Houston, D.C. Murray, N.E. White, P. Moolhuijzen, and et al. Deep sequencing of plant and animal DNA contained within traditional Chinese medicines reveals legality issues and health safety concerns PLoS Genet. 8 2012 10.1371/journal.pgen.1002657
32. J.M. Young, L.S. Weyrich, and A. Cooper Forensic soil DNA analysis using high-throughput sequencing: a comparison of four molecular markers Forensic Sci. Int. Genet. 13 2014 176 184 10.1016/j.fsigen.2014.07.014
33. S. Giampaoli, A. Berti, R.M. Di Maggio, E. Pilli, A. Valentini, F. Valeriani, and et al. The environmental biological signature: NGS profiling for forensic comparison of soils Forensic Sci. Int. 240 2014 41 47 10.1016/j.forsciint.2014.02.028
34. G. Ferri, B. Corradini, F. Ferrari, A.L. Santunione, F. Palazzoli, and M. Alu' Forensic botany II, DNA barcode for land plants: which markers after the international agreement? Forensic Sci. Int. Genet. 2014 10.1016/j.fsigen.2014.10.005
35. M.L. Hollingsworth, A.A. Clark, L.L. Forrest, J. Richardson, R.T. Pennington, D.G. Long, and et al. Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants Mol. Ecol. Resour. 9 2009 439 457 10.1111/j.1755-0998.2008.02439.x
36. K.L. Bell, K.S. Burgess, and B.J. Brosi DNA barcoding of pollen N. de Vere, Plant DNA Barcoding Methods and Protocols 2016 Springer New York, NY in press
37. J. Shendure, and H. Ji Next-generation DNA sequencing Nat. Biotechnol. 26 2008 1135 1145
38. P. Taberlet, E. Coissac, F. Pompanon, C. Brochmann, and E. Willerslev Towards next-generation biodiversity assessment using DNA metabarcoding Mol. Ecol. 21 2012 2045 2050 10.1111/j.1365-294x.2012.05470.x
39. D.P. Little A DNA mini-barcode for land plants Mol. Ecol. Resour. 2013 10.1111/1755-0998.12194
40. A. Valentini, C. Miquel, M.A. Nawaz, E. Bellemain, E. Coissac, F. Pompanon, and et al. New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach Mol. Ecol. Resour. 9 2009 51 60 10.1111/j.1755-0998.2008.02352.x
41. F. Pompanon, B.E. Deagle, W.O.C. Symondson, D.S. Brown, S.N. Jarman, and P. Taberlet Who is eating what: diet assessment using next generation sequencing Mol. Ecol. 21 2012 1931 1950 10.1111/j.1365-294x.2011.05403.x
42. S. Shokralla, J.F. Gibson, H. Nikbakht, D.H. Janzen, W. Hallwachs, and M. Hajibabaei Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens Mol. Ecol. Resour. 2014 892 901 10.1111/1755-0998.12236
43. M.G. Ross, C. Russ, M. Costello, A. Hollinger, N.J. Lennon, R. Hegarty, and et al. Characterizing and measuring bias in sequence data Genome Biol. 14 2013 R51 10.1186/gb-2013-14-5-r51
44. Illumina Targeted Next-Generation Sequencing for Forensic Genomics Table of Contents 2015 Illumina
45. S.L. Pimm, and L.N. Joppa How many plant species are there, where are they, and at what rate are they going extinct? Ann. Missouri Bot. Gard. 100 2015 170 176 10.3417/2012018
46. R.S. Sangwan, and B.S. Sangwan-Norreel Ultrastructural cytology of plastids in pollen grains of certain androgenic and nonandrogenic plants Protoplasma 138 1987 11 22 10.1007/bf01281180
47. J.L. Corriveau, and A.W. Coleman Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species Am. J. Bot. 1988 1443 1458
48. N. Nagata, C. Saito, A. Sakai, H. Kuroiwa, and T. Kuroiwa The selective increase or decrease of organellar DNA in generative cells just after pollen mitosis one controls cytoplasmic inheritance Planta 209 1999 53 65
49. Q. Zhang, and Y. Liu Sodmergen, examination of the cytoplasmic DNA in male reproductive cells to determine the potential for cytoplasmic inheritance in 295 angiosperm species Plant Cell Physiol. 44 2003 941 951
50. Q. Zhang, and Sodmergen Why does biparental plastid inheritance revive in angiosperms? J. Plant Res. 123 2010 201 206 10.1007/s10265-009-0291-z
51. P.M. Hollingsworth, S.W. Graham, and D.P. Little Choosing and using a plant DNA barcode PLoS One 6 2011 e19254 10.1371/journal.pone.0019254
52. O. Seberg, and G. Petersen How many loci does it take to DNA barcode a Crocus? PLoS One 4 2009 e4598
53. D.M. Spooner DNA barcoding will frequently fail in complicated groups: An example in wild potatoes Am. J. Bot. 96 2009 1177 1189
54. S. Chen, H. Yao, J. Han, C. Liu, J. Song, L. Shi, and et al. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species PLoS One 5 2010 e8613 10.1371/journal.pone.0008613
55. W.J. Kress, D.L. Erickson, F.A. Jones, N.G. Swenson, R. Perez, O. Sanjur, and et al. Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama Proc. Natl. Acad. Sci. U. S. A. 106 2009 18621 18626 10.1073/pnas.0909820106
56. K.S. Burgess, A.J. Fazekas, P.R. Kesanakurti, S.W. Graham, B.C. Husband, S.G. Newmaster, and et al. Discriminating plant species in a local temperate flora using the rbcL + matK DNA barcode Methods Ecol. Evol. 2 2011 333 340 10.1111/j.2041-210x.2011.00092.x
57. A. Galimberti, F. De Mattia, I. Bruni, D. Scaccabarozzi, A. Sandionigi, M. Barbuto, and et al. A DNA barcoding approach to characterize pollen collected by honeybees PLoS One 9 2014 e109363 10.1371/journal.pone.0109363
58. F. Meyer, D. Paarmann, M. D'souza, R. Olson, E.M. Glass, M. Kubal, and et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes BMC Bioinf. 9 2008 386 10.1186/1471-2105-9-386
59. W. Sickel, M.J. Ankenbrand, G. Grimmer, A. Holzschuh, S. Härtel, J. Lanzen, and et al. Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach BMC Ecol. 15 2015 10.1186/s12898-015-0051-y
60. M.T. Fujiwara, H. Hashimoto, Y. Kazama, T. Hirano, Y. Yoshioka, S. Aoki, and et al. Dynamic morphologies of pollen plastids visualised by vegetative-specific FtsZ1-GFP in Arabidopsis thaliana Protoplasma 242 2010 19 33 10.1007/s00709-010-0119-7
61. W. Sakamoto, S. Miyagishima, and P. Jarvis Chloroplast biogenesis: control of plastid development, protein import, division and inheritance Arabidopsis B. 6 2008 e0110 10.1199/tab.0110
62. 2+-dependent exonuclease degrades organelle DNA during Arabidopsis pollen development Plant Cell 23 2011 1608 1624 10.1105/tpc.111.084012
63. E. Willerslev, A.J. Hansen, J. Binladen, T.B. Brand, M.T.P. Gilbert, B. Shapiro, and et al. Diverse plant and animal genetic records from Holocene and Pleistocene sediments Science 300 80 2003 791 795 10.1126/science.1084114
64. C.A. Kearns, and D.W. Inouye Techniques for Pollination Biologists 1993 University Press of Colorado Niwot, Colorado
65. H. Golczyk, S. Greiner, G. Wanner, A. Weihe, R. Bock, T. Börner, and et al. Chloroplast DNA in mature and senescing leaves: a reappraisal Plant Cell 26 2014 847 854 10.1105/tpc.113.117465
66. B.A. Rowan, D.J. Oldenburg, and A.J. Bendich A multiple-method approach reveals a declining amount of chloroplast DNA during development in Arabidopsis BMC Plant Biol. 9 2009 3 10.1186/1471-2229-9-3
67. D.B. Udy, S. Belcher, R. Williams-Carrier, J.M. Gualberto, and A. Barkan Effects of reduced chloroplast gene copy number on chloroplast gene expression in maize Plant Physiol. 160 2012 1420 1431 10.1104/pp.112.204198
68. R. Szibor, C. Schubert, R. Schöning, D. Krause, and U. Wendt Pollen analysis reveals murder season Nature 395 1998 449 450 10.1038/26646
69. F.J. Goodman, J.W. Doughty, C. Gary, C.T. Christou, B.B. Hu, E.A. Hultman, and et al. PIGLT: a Pollen Identification and Geolocation system for forensic applications 2015 IEEE Int. Symp. Technol. Homel. Secur., IEEE 2015 1 7 10.1109/THS.2015.7225271
70. N. de Vere, T.C.G. Rich, C.R. Ford, S.A. Trinder, C. Long, C.W. Moore, and et al. DNA barcoding the native flowering plants and conifers of Wales PLoS One 7 2012 e37945 10.1371/journal.pone.0037945
71. J. Elith, and J.R. Leathwick Species distribution models: ecological explanation and prediction across space and time Annu. Rev. Ecol. Evol. 40 2009 677 697
72. F. Sanger, S. Nicklen, and A.R. Coulson DNA sequencing with chain-terminating inhibitors Proc. Natl. Acad. Sci. U. S. A. 74 1977 5463 5467 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=431765&tool=pmcentrez&rendertype=abstract (accessed 10.07.14)
73. Y. Matsuki, Y. Isagi, and Y. Suyama The determination of multiple microsatellite genotypes and DNA sequences from a single pollen grain Mol. Ecol. Notes 7 2007 194 198
74. A.N. Aziz, and R.J. Sauve Genetic mapping of Echinacea purpurea via individual pollen DNA fingerprinting Mol. Breed. 21 2008 227 232
75. Y. Yang, B. Xie, and J. Yan Application of Next-generation Sequencing Technology in Forensic Science Genomics Proteomics Bioinformatics 12 2014 190 197 10.1016/j.gpb.2014.09.001
76. E.L. van Dijk, H. Auger, Y. Jaszczyszyn, and C. Thermes Ten years of next-generation sequencing technology Trends Genet. 30 2014 418 426 10.1016/j.tig.2014.07.001
77. K. Lagerstrom, L. Arzhaeva, S. Haberle, F. Hopf, and et al. Pollen image classification using the Classifynder system: algorithm comparison and a case study on New Zealand honey T. Sun, T.D. Bednarz, P. Pham, Signal and Image Analysis for Biomedical and Life Sciences 2015 Springer International Publishing Cham 207 226 10.1007/978-3-319-10984-8
78. J. Hawkins, N. de Vere, A. Griffith, C.R. Ford, J. Allainguillaume, M.J. Hegarty, and et al. Using DNA metabarcoding to identify the floral composition of honey: a new tool for investigating honey bee foraging preferences PLoS One 10 2015 e0134735 10.1371/journal.pone.0134735
79. I. Bruni, A. Galimberti, L. Caridi, D. Scaccabarozzi, F. De Mattia, M. Casiraghi, and et al. A DNA barcoding approach to identify plant species in multiflower honey Food Chem. 170 2015 308 315 10.1016/j.foodchem.2014.08.060