Streamlining DNA barcoding protocols: Automated DNA extraction and a new cox1 primer in arachnid systematics

PLoS ONE

Volumn 9, Issue 11, 2014, Pages

  Vidergar, Nina ^a,e   Toplak, Nataša ^d   Kuntner, Matjaž ^a,b,c  

^a Slovenian Academy of Sciences and Arts   (Slovenia)

^b HUBEI UNIVERSITY   (China)

^c DEPARTMENT OF PALEOBIOLOGY   (United States)

^d Iskra Feriti doo   (Slovenia)

^e INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C OXIDASE; CYTOCHROME C OXIDASE SUBUNIT 1; GENOMIC DNA; PRIMER DNA; UNCLASSIFIED DRUG; MITOCHONDRIAL DNA;

ANIMAL TISSUE; ARACHNID; ARTICLE; AUTOMATION; BASE PAIRING; CLADISTICS; CONTROLLED STUDY; COX1 GENE; DATA ANALYSIS; DNA BARCODING; DNA DETERMINATION; DNA EXTRACTION; DNA SEQUENCE; GENOMICS; HIGH THROUGHPUT SEQUENCING; MAGNETIC PARTICLE PROCESSOR; MOLECULAR SYSTEMATICS; NONHUMAN; PERFORMANCE MEASUREMENT SYSTEM; PHYLOGENY; PROCESS CONTROL; PROCESS DESIGN; PROCESS DEVELOPMENT; PROCESS MODEL; PROCESS OPTIMIZATION; QUALITY CONTROL; ROBOTICS; SIGNAL PROCESSOR; SPECIES RICHNESS; STANDARD; SYSTEM ANALYSIS; TISSUE DISTRIBUTION; ANIMAL; CHEMISTRY; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PROCEDURES; REPRODUCIBILITY; SEQUENCE HOMOLOGY; SPIDER;

ARACHNIDA;

ANIMALS; ARACHNIDA; BASE SEQUENCE; DNA BARCODING, TAXONOMIC; DNA PRIMERS; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX IV; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPIDERS;

EID: 84913554535     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0113030     Document Type: Article

References (43)

1. Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B-Biological Sciences 270: 313-321.
2. Hebert PDN, deWaard JR, Landry JF (2010) DNA barcodes for 1/1000 of the animal kingdom. Biology Letters 6: 359-362.
3. Hebert PDN, deWaard JR, Zakharov EV, Prosser SWJ, Sones JE, et al. (2013) A DNA 'Barcode Blitz': Rapid Digitization and Sequencing of a Natural History Collection. Plos One 8.
4. Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Systematic Biology 54: 852-859.
5. 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. Proceedings of the National Academy of Sciences of the United States of America 101: 14812-14817.
6. Hebert PDN, Ratnasingham S, deWaard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London Series B-Biological Sciences 270: S96-S99.
7. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. Plos Biology 2: 1657-1663.
8. Blagoev GA, Nikolova NI, Sobel CN, Hebert PDN, Adamowicz SJ (2013) Spiders (Araneae) of Churchill, Manitoba: DNA barcodes and morphology reveal high species diversity and new Canadian records. Bmc Ecology 13.
9. Agnarsson I, Gregoric M, Blackledge TA, Kuntner M (2013) The phylogenetic placement of Psechridae within Entelegynae and the convergent origin of orb-like spider webs. Journal of Zoological Systematics and Evolutionary Research 51: 100-106.
10. Arnedo MA, Coddington IA, Agnarsson I, Gillespie RG (2004) From a comb to a tree: phylogenetic relationships of the comb-footed spiders (Araneae, Theridiidae) inferred from nuclear and mitochondrial genes. Molecular Phylogenetics and Evolution 31: 225-245.
11. Bidegaray-Batista L, Arnedo MA (2011) Gone with the plate: the opening of the Western Mediterranean basin drove the diversification of ground-dweller spiders. Bmc Evolutionary Biology 11: 317.
12. Kuntner M, Arnedo MA, Trontelj P, Lokovsek T, Agnarsson I (2013) A molecular phylogeny of nephilid spiders: Evolutionary history of a model lineage. Molecular Phylogenetics and Evolution 69: 961-979.
13. Agnarsson I, Maddison WP, Aviles L (2007) The phylogeny of the social Anelosimus spiders (Araneae: Theridiidae) inferred from six molecular loci and morphology. Molecular Phylogenetics and Evolution 43: 833-851.
14. Agnarsson I, Coddington JA, Kuntner M (2013) Systematics: Progress in the Study of Spider Diversity and Evolution. In:, Penney D, editor. Spider Research in the 21st Century: Trends and Perspectives. Manchester: Siri Scientific Press. pp. 58-111.
15. Havird JC, Santos SR (2014) Performance of Single and Concatenated Sets of Mitochondrial Genes at Inferring Metazoan Relationships Relative to Full Mitogenome Data. Plos One 9.
16. Gomez-Zurita J, Cardoso A (2014) Systematics of the New Caledonian endemic genus Taophila Heller (Coleoptera: Chrysomelidae, Eumolpinae) combining morphological, molecular and ecological data, with description of two new species. Systematic Entomology 39: 111-126.
17. Brugler MR, Opresko DM, France SC (2013) The evolutionary history of the order Antipatharia (Cnidaria: Anthozoa: Hexacorallia) as inferred from mitochondrial and nuclear DNA: implications for black coral taxonomy and systematics. Zoological Journal of the Linnean Society 169: 312-361.
18. Ahrens D, Fabrizi S, Sipek P, Lago PK (2013) Integrative analysis of DNA phylogeography and morphology of the European rose chafer (Cetonia aurata) to infer species taxonomy and patterns of postglacial colonisation in Europe. Molecular Phylogenetics and Evolution 69: 83-94.
19. Lloyd RE, Foster PG, Guille M, Littlewood DTJ (2012) Next generation sequencing and comparative analyses of Xenopus mitogenomes. Bmc Genomics 13.
20. Horak M, Day MF, Barlow C, Edwards ED, Su YN, et al. (2012) Systematics and biology of the iconic Australian scribbly gum moths Ogmograptis Meyrick (Lepidoptera: Bucculatricidae) and their unique insect-plant interaction. Invertebrate Systematics 26: 357-398.
21. McDonagh LM, Stevens JR (2011) The molecular systematics of blowflies and screwworm flies (Diptera: Calliphoridae) using 28S rRNA, COX1 and EF-1 alpha: insights into the evolution of dipteran parasitism. Parasitology 138: 1760-1777.
22. Redmond NE, Raleigh J, van Soest RWM, Kelly M, Travers SAA, et al. (2011) Phylogenetic Relationships of the Marine Haplosclerida (Phylum Porifera) Employing Ribosomal (28S rRNA) and Mitochondrial (cox1, nad1) Gene Sequence Data. Plos One 6.
23. Cohen BL, Bitner MA, Harper EM, Lee DE, Mutschke E, et al. (2011) Vicariance and convergence in Magellanic and New Zealand long-looped brachiopod clades (Pan-Brachiopoda: Terebratelloidea). Zoological Journal of the Linnean Society 162: 631-645.
24. Gower DJ, San Mauro D, Giri V, Bhatta G, Govindappa V, et al. (2011) Molecular systematics of caeciliid caecilians (Amphibia: Gymnophiona) of the Western Ghats, India. Molecular Phylogenetics and Evolution 59: 698-707.
25. Borrero-Perez GH, Gomez-Zurita J, Gonzalez-Wanguemert M, Marcos C, Perez-Ruzafa A (2010) Molecular systematics of the genus Holothuria in the Mediterranean and Northeastern Atlantic and a molecular clock for the diversification of the Holothuriidae (Echinodermata: Holothuroidea). Molecular Phylogenetics and Evolution 57: 899-906.
26. Timmermans M, Dodsworth S, Culverwell CL, Bocak L, Ahrens D, et al. (2010) Why barcode? Highthroughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Research 38.
27. Mladineo I, Bott NJ, Nowak BF, Block BA (2010) Multilocus phylogenetic analyses reveal that habitat selection drives the speciation of Didymozoidae (Digenea) parasitizing Pacific and Atlantic bluefin tunas. Parasitology 137: 1013-1025.
28. Hedin MC, Maddison WP (2001) A combined molecular approach to phylogeny of the jumping spider subfamily Dendryphantinae (Araneae: Salticidae). Molecular Phylogenetics and Evolution 18: 386-403.
29. Arnedo MA, Coddington J, Agnarsson I, Gillespie RG (2004) From a comb to a tree: phylogenetic relationships of the comb-footed spiders (Araneae, Theridiidae) inferred from nuclear and mitochondrial genes. Molecular Phylogenetics and Evolution 31: 225-245.
30. Simon C, Frati F, Beckenbach A, Crespi B, Liu H, et al. (1994) Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Annals of the Entomological Society of America 87: 651-701.
31. Kuntner M, Agnarsson I (2011) Phylogeography of a successful aerial disperser: the golden orb spider Nephila on Indian Ocean islands. Bmc Evolutionary Biology 11.
32. Kuntner M, Agnarsson I (2011) Biogeography and diversification of hermit spiders on Indian Ocean islands (Nephilidae: Nephilengys). Molecular Phylogenetics and Evolution 59: 477-488.
33. 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. Molecular Marine Biology and Biotechnology 3: 294-299.
34. Francesconi A, Kasai M, Harrington SM, Beveridge MG, Petraitiene R, et al. (2008) Automated and manual methods of DNA extraction for Aspergillus fumigatus and Rhizopus oryzae analyzed by quantitative real-time PCR. Journal of Clinical Microbiology 46: 1978-1984.
35. Coddington JA (2005) Phylogeny and classification of spiders. In:, Ubick D, Paquin P, Cushing PE, Roth V, editors. Spiders of North America: An Identification Manual: American Arachnological Society. pp. 18-24.
36. Drummond A, Ashton B, Buxton S, Cheung M, Cooper A, et al. (2011) Geneious v 5.4.
37. Maddison WP, Maddison DR (2014) Mesquite: A modular system for evolutionary analysis, version 2.74. Available: http://mesquiteproject.org. Accessed 2014 May 31.
38. Hanner R (2009) Data standards for BARCODE records in INSDC (BRIs), version 2.3. Washington, DC.
39. Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinformatics 23: 1289-1291.
40. Meyer CP, Geller JB, Paulay G (2005) Fine scale endemism on coral reefs: Archipelagic differentiation in turbinid gastropods. Evolution 59: 113-125.
41. Lunt DH, Zhang DX, Szymura JM, Hewitt GM (1996) The insect cytochrome oxidase I gene: Evolutionary patterns and conserved primers for phylogenetic studies. Insect Molecular Biology 5: 153- 165.
42. Barrett RDH, Hebert PDN (2005) Identifying spiders through DNA barcodes. Canadian Journal of Zoology-Revue Canadienne De Zoologie 83: 481-491.
43. Cheng RC, Yang EC, Lin CP, Herberstein ME, Tso IM (2010) Insect form vision as one potential shaping force of spider web decoration design. Journal of Experimental Biology 213: 759-768.