[1] Klappenbach JA, Saxman PR, Cole JR, et al. rrndb:the ribosomal RNA operon copy number database[J] . Nucleic Acids Research, 2001, 29(1):181-184. [2] Sogin ML, Morrison HG, Huber JA, et al. Microbial diversity in the deep sea and the underexplored “rare biosphere”[J] . Proceedings of the National Academy of Sciences, 2006, 103(32):12115-12120. [3] Roh SW, Abell GC, Kim K-H, et al. Comparing microarrays and next-generation sequencing technologies for microbial ecology research[J] . Trends in Biotechnology, 2010, 28(6):291-299. [4] Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated high-density picolitre reactors[J] . Nature, 2005, 437(7057):376-380. [5] Bentley DR. Whole-genome re-sequencing[J] . Current Opinion in Genetics & Development, 2006, 16(6):545-552. [6] Clarke J, Wu H-C, Jayasinghe L, et al. Continuous base identification for single-molecule nanopore DNA sequencing[J] . Nature Nanotechnology, 2009, 4(4):265-270. [7] McCarthy A. Third generation DNA sequencing:pacific biosciences’ single molecule real time technology[J] . Chemistry & Biology, 2010, 17(7):675-676. [8] Mikheyev AS, Tin MM. A first look at the Oxford Nanopore MinION sequencer[J] . Molecular Ecology Resources, 2014, 14(6):1097-1102. [9] Chakravorty S, Helb D, Burday M, et al. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria[J] . Journal of Microbiological Methods, 2007, 69(2):330-339. [10] Kim M, Morrison M, Yu Z. Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes[J] . J Microbiol Methods, 2011, 84(1):81-87. [11] Rhoads A, Au KF. PacBio sequencing and its applications[J] . Genomics, Proteomics & Bioinformatics, 2015, 13(5):278-289. [12] Roberts RJ, Carneiro MO, Schatz MC. The advantages of SMRT sequencing[J] . Genome Biology, 2013, 14(7):405. [13] Mosher JJ, Bowman B, Bernberg EL, et al. Improved performance of the PacBio SMRT technology for 16S rDNA sequencing[J] . Journal of Microbiological Methods, 2014, 104:59-60. [14] Benitez-Paez A, Portune KJ, Sanz Y. Species-level resolution of 16S rRNA gene amplicons sequenced through the MinIONTM portable nanopore sequencer[J] . Gigascience, 2016, 5(1):1-9. [15] Schloss PD, Jenior ML, Koumpouras CC, et al. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system[J] . PeerJ, 2016, 4:e1869. [16] Lee CH, Bowman B, Hall R, et al. Developments in PacBio? metagenome sequencing:Shotgun whole genomes and full-length 16S[C] . International Plant and Animal Genome Conference Asia, 2014. [17] Laver T, Harrison J, O’Neill P, et al. Assessing the performance of the Oxford Nanopore Technologies MinION[J] . Biomolecular Detection and Quantification, 2015, 3:1-8. [18] Koren S, Schatz MC, Walenz BP, et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads[J] . Nature Biotechnology, 2012, 30(7):693-700. [19] Ross MG, Russ C, Costello M, et al. Characterizing and measuring bias in sequence data[J] . Genome Biology, 2013, 14(5):1. [20] Eid J, Fehr A, Gray J, et al. Real-time DNA sequencing from single polymerase molecules[J] . Science, 2009, 323(5910):133-138. [21] Quail MA, Smith M, Coupland P, et al. A tale of three next generation sequencing platforms:comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers[J] . BMC Genomics, 2012, 13(1):341. [22] Patel RK, Jain M. NGS QC Toolkit:a toolkit for quality control of next generation sequencing data[J] . PLoS One, 2012, 7(2):e30619. [23] Andrews, S. FastQC:a quality control tool for high throughput sequence data[EB] . http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. [24] Bowman B, Shin MY, Lee JE, et al. Analysis of full-length metagenomic 16S genes by SMRT? sequencing[J] . Chemistry, 2013, 4:C2. [25] Edgar RC, Haas BJ, Clemente JC, et al. UCHIME improves sensitivity and speed of chimera detection[J] . Bioinformatics, 2011, 27(16):2194-2200. [26] Haas BJ, Gevers D, Earl AM, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons[J] . Genome Research, 2011, 21(3):494-504. [27] Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project:improved data processing and web-based tools[J] . Nucleic Acids Research, 2013, 41(D1):D590-D596. [28] Maidak BL, Cole JR, Lilburn TG, et al. The RDP-II(ribosomal database project)[J] . Nucleic Acids Research, 2001, 29(1):173-174. [29] DeSantis TZ, Hugenholtz P, Larsen N, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB[J] . Applied and Environmental Microbiology, 2006, 72(7):5069-5072. [30] Bowman JS, Rasmussen S, Blom N, et al. Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene[J] . The ISME Journal, 2012, 6(1):11-20. [31] Tedersoo L, Nilsson RH, Abarenkov K, et al. 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases[J] . New Phytologist, 2010, 188(1):291-301. [32] Lücking R, Lawrey JD, Gillevet PM, et al. Multiple ITS haplotypes in the genome of the lichenized basidiomycete Cora inversa(Hygrophoraceae):fact or artifact?[J] . Journal of Molecular Evolution, 2014, 78(2):148-162. [33] Unterseher M, Jumpponen A, ?pik M, et al. Species abundance distributions and richness estimations in fungal metagenomics-lessons learned from community ecology[J] . Molecular Ecology, 2011, 20(2):275-285. [34] Kunin V, Engelbrektson A, Ochman H, et al. Wrinkles in the rare biosphere:pyrosequencing errors can lead to artificial inflation of diversity estimates[J] . Environmental Microbiology, 2010, 12(1):118-123. [35] Edgar RC. UPARSE:highly accurate OTU sequences from microbial amplicon reads[J] . Nature Methods, 2013, 10(10):996-998. [36] Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur:open-source, platform-independent, community-supported software for describing and comparing microbial communities[J] . Applied and Environmental Microbiology, 2009, 75(23):7537-7541. [37] Wang Q, Garrity GM, Tiedje JM, et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy[J] . Applied and Environmental Microbiology, 2007, 73(16):5261-5267. [38] Liu Z, DeSantis TZ, Andersen GL, et al. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers[J] . Nucleic Acids Research, 2008, 36(18):e120. [39] Burke CM, Darling AE. A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq[J] . Peer J, 2016, 4:e2492. [40] Langille MG, Zaneveld J, Caporaso JG, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences[J] . Nature Biotechnology, 2013, 31(9):814-821. |