Sequencing degraded DNA from non-destructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics

PLoS ONE

Volumn 9, Issue 5, 2014, Pages

  Tin, Mandy Man Ying ^a   Economo, Evan Philip ^a   Mikheyev, Alexander Sergeyevich ^a  

^a OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY GRADUATE UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C OXIDASE; DNA;

ANIMAL TISSUE; ARTICLE; COI GENE; CONTROLLED STUDY; DNA DEGRADATION; DNA DETERMINATION; DNA EXTRACTION; DNA FRAGMENTATION; DNA SEQUENCE; DROSOPHILA; GENE DUPLICATION; GENE MAPPING; GENE TARGETING; GENETIC PROCEDURES; GENETIC VARIABILITY; INFORMATION CENTER; KARYOTYPE; KARYOTYPING; MITOCHONDRIAL GENE; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; RESTRICTION ASSOCIATED DNA TAGGING; SHOTGUN GENOME RESEQUENCING; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; ANT; CHEMISTRY; CHROMOSOME MAP; CLASSIFICATION; FOSSIL; GENETICS; HIGH THROUGHPUT SEQUENCING; INSECT CHROMOSOME; INSECT GENOME; LABORATORY AUTOMATION; LABORATORY DIAGNOSIS; PROCEDURES; SEQUENCE TAGGED SITE;

ANIMALS; ANTS; AUTOMATION, LABORATORY; CHROMOSOME MAPPING; CHROMOSOMES, INSECT; DNA FRAGMENTATION; DROSOPHILA; FOSSILS; GENOME, INSECT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MUSEUMS; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE TAGGED SITES; SPECIMEN HANDLING;

EID: 84901300928     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0096793     Document Type: Article

References (45)

1. Suarez AV, Tsutsui ND (2004) The value of museum collections for research and society. BioScience 54: 66-74. (Pubitemid 38086444)
2. Graham CH, Ferrier S, Huettman F, Moritz C, Peterson AT (2004) New developments in museum-based informatics and applications in biodiversity analysis. Trends Ecol Evol 19: 497-503. doi:10.1016/j.tree.2004.07.006. (Pubitemid 39151670)
3. Shaffer HB, Fisher RN, Davidson C (1998) The role of natural history collections in documenting species declines. Trends Ecol Evol 13: 27-30. (Pubitemid 28069359)
4. Porco D, Rougerie R, Deharveng L, Hebert P (2010) Coupling non-destructive DNA extraction and voucher retrieval for small soft-bodied arthropods in a high-throughput context: the example of collembola. Mol Ecol Res 10: 942-945. doi:10.1111/j.1755-0998.2010.2839.x.
5. Gilbert MTP, Moore W, Melchior L, Worobey M (2007) DNA extraction from dry museum beetles without conferring external morphological damage. PLoS ONE 2: e272. doi:10.1371/journal.pone.0000272.t001.
6. Rohland N, Siedel H, Hofreiter M (2004) Nondestructive DNA extraction method for mitochondrial DNA analyses of museum specimens. BioTechniques 36: 814-6-818-21.
7. Hunter SJ, Goodall TI, Walsh KA, Owen R, Day JC (2008) Nondestructive DNA extraction from blackflies (Diptera: Simuliidae): retaining voucher specimens for DNA barcoding projects. Mol Ecol Res 8: 56-61. doi:10.1111/j.1471-8286.2007. 01879.x. (Pubitemid 350231171)
8. Favret C (2005) A new non-destructive DNA extraction and specimen clearing technique for aphids (Hemiptera). Proc Entomol Soc Wash 107: 469-470.
9. Mikheyev A, Bresson S, Conant P (2009) Single-queen introductions characterize regional and local invasions by the facultatively clonal little fire ant Wasmannia auropunctata . Mol Ecol 18: 2937-2944.
10. Thomsen PF, Elias S, Gilbert MTP, Haile J, Munch K, et al. (2009) Non-destructive sampling of ancient insect DNA. PLoS ONE 4: e5048. doi:10.1371/journal.pone.0005048.t001.
11. Andersen JC, Mills NJ (2012) DNA extraction from museum specimens of parasitic Hymenoptera. PLoS ONE 7: e45549.
12. Reiss RA (2006) Ancient DNA from ice age insects: proceed with caution. Quaternary Sci Rev 25: 1877-1893.
13. Rowe KC, Singhal S, Macmanes MD, Ayroles JF, Morelli TL, et al. (2011) Museum genomics: low-cost and high-accuracy genetic data from historical specimens. Mol Ecol Res 11: 1082-1092. doi:10.1111/j.1755-0998.2011.03052.x.
14. Meyer M, Kircher M, Gansauge M-T, Li H, Racimo F, et al. (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science 338: 222-226. doi:10.1126/science.1224344.
15. Gansauge M-T, Meyer M (2013) Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat Protoc 8: 737-748. doi:doi:10.1038/nprot.2013.038.
16. Li TW, Weeks KM (2006) Structure-independent and quantitative ligation of single-stranded DNA. Anal Biochem 349: 242-246. doi:10.1016/j.ab.2005.11.002. (Pubitemid 43184304)
17. Miller M, Dunham J, Amores A, Cresko W, Johnson E (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17: 240.
18. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, et al. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3: e3376. doi:10.1371/journal.pone.0003376.
19. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, et al. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12: 499-510. doi:10.1038/nrg3012.
20. McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT (2013) Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol 66: 526-538. doi:10.1016/j.ympev.2011.12.007.
21. Wagner CE, Keller I, Wittwer S, Selz OM, Mwaiko S, et al. (2013) Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Mol Ecol 22: 787-798. doi:10.1111/mec.12023.
22. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Marine Biol Biotechnol 3: 294-299.
23. Jansen G, Savolainen R, Vepsäläinen K (2009) DNA barcoding as a heuristic tool for classifying undescribed Nearctic Myrmica ants (Hymenoptera: Formicidae). Zoologica Scripta 38: 527-536.
24. Yue D, Tabor S, Nichols NM (2008) Template-independent DNA polymerases. Curr Protoc Mol Biol. Wiley Online Library. doi:10.1002/0471142727.mb0306s84.
25. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal 17: 10-12.
26. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods 9: 357-359. doi:10.1038/nmeth.1923.
27. Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, et al. (2011) Draft genome of the red harvester ant Pogonomyrmex barbatus. PNAS 108: 5667-5672. doi:10.1073/pnas.1007901108.
28. Smith CD, Zimin A, Holt C, Abouheif E, Benton R, et al. (2011) Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). PNAS. doi:10.1073/pnas.1008617108.
29. Bonasio R, Zhang G, Ye C, Mutti NS, Fang X, et al. (2010) Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator. Science 329: 1068-1071. doi:10.1126/science.1192428.
30. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, et al. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450: 219-232. (Pubitemid 350100553)
31. Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, et al. (2013) From FastQ data to high-confidence variant calls: the Genome Analysis Toolkit Best practices pipeline. Curr Protoc Bioinformatics: 11.10.1-11.10.33.
32. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079. doi:10.1093/bioinformatics/btp352.
33. Smit A, Hubley R, Green P. RepeatMasker Open-3.0. Available: http://www.repeatmasker.org.
34. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842. doi:10.1093/ bioinformatics/btq033.
35. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574. (Pubitemid 37038874)
36. Zimmermann J, Hajibabaei M, Blackburn DC, Hanken J, Cantin E, et al. (2008) DNA damage in preserved specimens and tissue samples: a molecular assessment. Frontiers in Zoology 5: 18. doi:10.1186/1742-9994-5-18.
37. Waugh J (2007) DNA barcoding in animal species: progress, potential and pitfalls. Bioessays 29: 188-197. doi:10.1002/bies.20529.
38. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. PNAS 101: 14812-14817. doi:10.1073/pnas. 0406166101. (Pubitemid 39410757)
39. Bonacum J, O'Grady PM, Kambysellis M, Desalle R (2005) Phylogeny and age of diversification of the planitibia species group of the Hawaiian Drosophila. Mol Phylogenet Evol 37: 73-82. doi:10.1016/j.ympev.2005.03.008. (Pubitemid 41338031)
40. Carson HL, Kaneshiro KY (1976) Drosophila of Hawaii: systematics and ecological genetics. Annu Rev Ecol Syst 7: 311-345.
41. O'Grady PM, Baker RH, Durando CM, Etges WJ, DeSalle R (2001) Polytene chromosomes as indicators of phylogeny in several species groups of Drosophila. BMC Evol Biol 1: 6.
42. O'Grady PM, Lapoint RT, Bonacum J, Lasola J, Owen E, et al. (2011) Phylogenetic and ecological relationships of the Hawaiian Drosophila inferred by mitochondrial DNA analysis. Mol Phylogenet Evol 58: 244-256. doi:10.1016/j.ympev.2010.11.022.
43. Alex Buerkle C, Gompert Z (2013) Population genomics based on low coverage sequencing: how low should we go? Mol Ecol 22: 3028-3035. doi:10.1111/mec.12105.
44. Schmidt WM, Mueller MW (1996) Controlled ribonucleotide tailing of cDNA ends (CRTC) by terminal deoxynucleotidyl transferase: a new approach in PCR-mediated analysis of mRNA sequences. Nucleic Acids Res 24: 1789-1791. (Pubitemid 26137942)
45. Edwards KA, Doescher LT, Kaneshiro KY, Yamamoto D (2007) A Database of Wing Diversity in the Hawaiian Drosophila. PLoS ONE 2: e487. doi:10.1371/journal.pone.0000487.t001.