Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification
暂无分享,去创建一个
Qing Yang | Yiyuan Li | Shanlin Liu | Xin Zhou | Min Tang | Quanfei Huang | Q. Yang | Yiyuan Li | Shanlin Liu | Xin Zhou | Jiguang Li | Xu Su | Min Tang | Lili Zhou | Xu Su | Lili Zhou | Ribei Fu | Jiguang Li | Quanfei Huang | Ribei Fu
[1] N. Saintilan,et al. Principles for the monitoring and evaluation of wetland extent, condition and function in Australia , 2011, Environmental Monitoring and Assessment.
[2] V. Resh,et al. Water quality monitoring and aquatic organisms: the importance of species identification. , 1975, Journal - Water Pollution Control Federation.
[3] V. Resh,et al. After site selection and before data analysis: sampling, sorting, and laboratory procedures used in stream benthic macroinvertebrate monitoring programs by USA state agencies , 2001, Journal of the North American Benthological Society.
[4] C. Hawkins,et al. Assessing Macroinvertebrate Biodiversity in Freshwater Ecosystems: Advances and Challenges in DNA-based Approaches , 2010, The Quarterly Review of Biology.
[5] Pierre Taberlet,et al. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases , 2010, BMC Microbiology.
[6] Sujeevan Ratnasingham,et al. Critical factors for assembling a high volume of DNA barcodes , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.
[7] R. Vrijenhoek,et al. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. , 1994, Molecular marine biology and biotechnology.
[8] Susan M. Huse,et al. Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing , 2008, PLoS genetics.
[9] J. Landry,et al. A universal DNA mini-barcode for biodiversity analysis , 2008, BMC Genomics.
[10] H. Khan,et al. Limited efficiency of universal mini-barcode primers for DNA amplification from desert reptiles, birds and mammals. , 2011, Genetics and molecular research : GMR.
[11] G. Olsen,et al. Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes , 2008, Applied and Environmental Microbiology.
[12] H. Swerdlow,et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers , 2012, BMC Genomics.
[13] L. Tedersoo,et al. 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. , 2010, The New phytologist.
[14] Pierre Taberlet,et al. Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures , 2009, Frontiers in Zoology.
[15] Douglas W. Yu,et al. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring , 2012 .
[16] P. Taberlet,et al. Towards next‐generation biodiversity assessment using DNA metabarcoding , 2012, Molecular ecology.
[17] B. Deagle,et al. Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces , 2009, Molecular ecology.
[18] D. Baird,et al. Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos , 2011, PloS one.
[19] Natalia Ivanova,et al. Universal primer cocktails for fish DNA barcoding , 2007 .
[20] R. Clarke,et al. Assessing the impact of errors in sorting and identifying macroinvertebrate samples , 2006, Hydrobiologia.
[21] M. McGeoch. The selection, testing and application of terrestrial insects as bioindicators , 2007 .
[22] P. Taberlet,et al. Environmental DNA , 2012, Molecular ecology.
[23] David S. Brown,et al. Pyrosequencing of prey DNA in reptile faeces: analysis of earthworm consumption by slow worms , 2012, Molecular ecology resources.
[24] D. M. Rosenberg,et al. Freshwater biomonitoring and benthic macroinvertebrates. , 1994 .
[25] Mark L. Blaxter,et al. Second-generation environmental sequencing unmasks marine metazoan biodiversity , 2010, Nature communications.
[26] T. Brereton,et al. The development of butterfly indicators in the United Kingdom and assessments in 2010 , 2011, Journal of Insect Conservation.
[27] Jeremy R. deWaard,et al. Biological identifications through DNA barcodes , 2003, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[28] J. Hódar. The use of regresion equations for the estimation of prey length and biomass in diet studies of insectivore vertebrates , 1997 .
[29] Jonathan A. Eisen,et al. PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data , 2011, PLoS Comput. Biol..
[30] L. Farinelli,et al. Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments , 2011, Proceedings of the National Academy of Sciences.
[31] D. Janzen,et al. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[32] Siu-Ming Yiu,et al. SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..
[33] William A. Walters,et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms , 2012, The ISME Journal.
[34] Robert K. Jansen,et al. Automatic annotation of organellar genomes with DOGMA , 2004, Bioinform..
[35] Rick Gunn,et al. Assessing the impact of errors in sorting and identifying macroinvertebrate samples , 2006 .
[36] B. Statzner,et al. Developments in aquatic insect biomonitoring: a comparative analysis of recent approaches. , 2006, Annual review of entomology.
[37] M. Nei,et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.
[38] R. Giblin-Davis,et al. Reproducibility of read numbers in high‐throughput sequencing analysis of nematode community composition and structure , 2009, Molecular ecology resources.
[39] Sergei L. Kosakovsky Pond,et al. Windshield splatter analysis with the Galaxy metagenomic pipeline. , 2009, Genome research.
[40] Tracy K. Teal,et al. Systematic artifacts in metagenomes from complex microbial communities , 2009, The ISME Journal.
[41] Huanming Yang,et al. De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.
[42] Jian Wang,et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.
[43] D. Gruner. Regressions of Length and Width to Predict Arthropod Biomass in the Hawaiian Islands , 2003 .
[44] W. Murphy,et al. Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens. , 2011, Genome research.
[45] Mehrdad Hajibabaei,et al. Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next‐generation DNA sequencing , 2012, Molecular ecology.
[46] S. R. Ganihar. Biomass estimates of terrestrial arthropods based on body length , 1997, Journal of Biosciences.
[47] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[48] Sujeevan Ratnasingham,et al. Molecular analysis of parasitoid linkages (MAPL): gut contents of adult parasitoid wasps reveal larval host , 2011, Molecular ecology.
[49] William A. Walters,et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample , 2010, Proceedings of the National Academy of Sciences.
[50] Pierre Taberlet,et al. Influence of management practices on large herbivore diet—Case of European bison in Białowieża Primeval Forest (Poland) , 2011 .
[51] R. Durbin,et al. GeneWise and Genomewise. , 2004, Genome research.
[52] Peer Bork,et al. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy , 2011, Nucleic Acids Res..
[53] Xun Xu,et al. Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx) , 2009, Science.
[54] P. Taberlet,et al. Universal primers for amplification of three non-coding regions of chloroplast DNA , 1991, Plant Molecular Biology.
[55] Eric Coissac,et al. Bioinformatic challenges for DNA metabarcoding of plants and animals , 2012, Molecular ecology.
[56] Marcus J. Claesson,et al. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions , 2010, Nucleic acids research.
[57] Mehrdad Hajibabaei,et al. Next‐generation sequencing technologies for environmental DNA research , 2012, Molecular ecology.
[58] Mehrdad Hajibabaei,et al. Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol , 2012, BMC Ecology.
[59] Da-Wei Huang,et al. COI and ITS2 sequences delimit species, reveal cryptic taxa and host specificity of fig‐associated Sycophila (Hymenoptera, Eurytomidae) , 2010, Molecular ecology resources.
[60] K. Tamura,et al. Rapid isolation method of animal mitochondrial DNA by the alkaline lysis procedure , 1988, Biochemical Genetics.
[61] T. Reynoldson,et al. Biomonitoring in North American Rivers: A Comparison of Methods Used for Benthic Macroinvertebrates in Canada and the United States , 2006 .