PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Ramirez Gonzalez, Ricardo ^a   Yu, Douglas W ^b,c   Bruce, Catharine ^c   Heavens, Darren ^a   Caccamo, Mario ^a   Emerson, Brent C ^c,d  

^a EARLHAM INSTITUTE   (United Kingdom)

^b KUNMING INSTITUTE OF ZOOLOGY   (China)

^c UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^d INSTITUTO DE PRODUCTOS NATURALES Y AGROBIOLOGÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

AMPLICON; ANALYTICAL ERROR; ARTICLE; COLLEMBOLA; CONTROLLED STUDY; DNA SEQUENCE; FOREST; GENE AMPLIFICATION; GENETIC ALGORITHM; GENETIC VARIABILITY; MITOCHONDRION; NONHUMAN; POLYMERASE CHAIN REACTION; PYROCLEAN; PYROSEQUENCING;

ALGORITHMS; ANIMALS; ARTHROPODS; BASE SEQUENCE; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX IV; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; POLYMERASE CHAIN REACTION; RIBOSOMES; SEQUENCE ANALYSIS, DNA; SIGNAL-TO-NOISE RATIO; SOFTWARE;

EID: 84874575602     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0057615     Document Type: Article

References (32)

1. Chu HY, Fierer N, Lauber CL, Caporaso JG, Knight R, et al. (2010) Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environmental Microbiology 12: 2998-3006.
2. Fulthorpe RR, Roesch LFW, Riva A, Triplett EW, (2008) Distantly sampled soils carry few species in common. Isme Journal 2: 901-910.
3. Lauber CL, Hamady M, Knight R, Fierer N, (2009) Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale. Applied and Environmental Microbiology 75: 5111-5120.
4. Rousk J, Baath E, Brookes PC, Lauber CL, Lozupone C, et al. (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. Isme Journal 4: 1340-1351.
5. Huber JA, Mark Welch D, Morrison HG, Huse SM, Neal PR, et al. (2007) Microbial population structures in the deep marine biosphere. Science 318: 97-100.
6. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, et al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. Isme Journal 1: 283-290.
7. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences of the United States of America 103: 12115-12120.
8. Medinger R, Nolte V, Pandey RV, Jost S, Ottenwalder B, et al. (2010) Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Molecular Ecology 19: 32-40.
9. Nolte V, Pandey RV, Jost S, Medinger R, Ottenwalder B, et al. (2010) Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Molecular Ecology 19: 2908-2915.
10. Creer S, Fonseca VG, Porazinka DL, Giblin-Davis RM, Sung W, et al. (2010) Ultra-deep sequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology 19: 4-20.
11. Fonseca VG, Carvalho GR, Sung W, Johnson HF, Power DM, et al. (2010) Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature Communications 1: 98.
12. Porazinska DL, Giblin-Davis RM, Esquivel A, Powers TO, Sung W, et al. (2010) Ecometagenetics confirms high tropical rainforest nematode diversity. Molecular Ecology 19: 5521-5530.
13. Emerson BC, Cicconardi F, Fanciulli PP, Shaw PJA, (2011) Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities. Philosophical Transactions of the Royal Society B 336: 2391-2404.
14. Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, et al. (2012) Sequencing out way towards understanding global eukaryote biodiversity. Trends in Ecology and Evolution 27: 233-243.
15. Yu DW, Ji YQ, Emerson BC, Wang XY, Ye CX, et al. (2012) Biodiversity soup: Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution 3: 613-623.
16. 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.
17. Hajibabaei M, Shokralla S, Zhou X, Singer GAC, Baird DJ, (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE 6: e17497.
18. Shokralla S, Zhou X, Janzen DH, Hallwachs W, Landry J-F, et al. (2011) Pyrosequencing for mini-barcoding of fresh and old museum specimens. PLoS ONE 6: e21252.
19. Boyce R, Chilana P, Rose TP, (2009) iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences. Nucleic Acids Research 37: w222-w228.
20. Rose TM, Henikoff JG, Henikoff S, (2003) CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. Nucleic Acids Research 31: 3763-3766.
21. Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods 6: 639-641.
22. Reeder J, Knight R, (2009) The 'rare biosphere': a reality check. Nature Methods 6: 636-637.
23. Ratnasingham S, Hebert PDN, (2007) BOLD: The Barcode of Life Data System. Molecular Ecology Notes 7: 355-364.
24. Ranwez V, Harispe S, Delsuc F, Douzery EJP, (2011) MACSE: Multiple alignment of coding sequences accounting for frameshifts and stop codons. PLoS ONE 6: e22594.
25. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7: 335-336.
26. Quince C, Lanzen A, Davenport RJ, J TP (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12.
27. Wu T, Ayres E, Bardgett RD, Wall DH, Garey JR, (2011) Molecular study of worldwide distribution and diversity of soil animals. Proceedings of the National Academy of Sciences of the United States of America 108: 17720-17725.
28. Rice P, Longden I, Bleasby A, (2000) EMBOSS: The European Molecular Biology Open Source Software Suite. Trends in Genetics 16: 276-277.
29. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739.
30. Amend AS, Seifert KA, Bruns TD, (2010) Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Molecular Ecology 19: 5555-5565.
31. Porazinska DL, Sung W, Giblin-Davis RM, Kelly Thomas W, (2009) Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composotion. Molecular Ecology Resources 10: 666-676.
32. Arechavaleta M, Rodríquez S, Zurita N, García A (2010) Lista de especies silvestres de Canarias. Hongos, plantas y animales terrestres. 2009. Santa Cruz de Tenerife: Gobierno de Canarias. 579 p.