Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale
暂无分享,去创建一个
Aaron Pomerantz | Stefan Prost | Jun Ying Lim | N. Patel | R. Gillespie | S. Prost | J. Y. Lim | H. Krehenwinkel | A. Pomerantz | J. B. Henderson | Susan R. Kennedy | Varun Swamy | Juan Diego Shoobridge | Natalie R Graham | Rosemary G Gillespie | Henrik Krehenwinkel | James B Henderson | Susan R Kennedy | Varun Swamy | Natalie Graham | Nipam H Patel
[1] C. Mazzoni,et al. Long-read DNA metabarcoding of ribosomal rRNA in the analysis of fungi from aquatic environments , 2018, bioRxiv.
[2] Beth Shapiro,et al. Minimizing polymerase biases in metabarcoding. , 2018, Molecular ecology resources.
[3] Niranjan Nagarajan,et al. A MinION-based pipeline for fast and cost-effective DNA barcoding , 2018, bioRxiv.
[4] R. Gillespie,et al. Scaling up DNA barcoding – Primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing , 2018, Methods in Ecology and Evolution.
[5] Gonzalo Giribet,et al. Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life , 2018, Current Biology.
[6] E. Kristiansson,et al. Introducing ribosomal tandem repeat barcoding for fungi , 2018, bioRxiv.
[7] Aaron Pomerantz,et al. Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building , 2018, GigaScience.
[8] C. Mazzoni,et al. Long-read DNA metabarcoding of ribosomal rRNA in the analysis of fungi from aquatic environments , 2018, bioRxiv.
[9] L. Tedersoo,et al. PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives. , 2018, The New phytologist.
[10] R. Gillespie,et al. The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota , 2018, PloS one.
[11] Wouter De Coster,et al. NanoPack: visualizing and processing long-read sequencing data , 2018, bioRxiv.
[12] Yingrui Li,et al. Construction of the third-generation Zea mays haplotype map , 2015, bioRxiv.
[13] Brent S. Pedersen,et al. Nanopore sequencing and assembly of a human genome with ultra-long reads , 2017, Nature Biotechnology.
[14] Jun Ying Lim,et al. Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding , 2017, Scientific Reports.
[15] D. Lodge,et al. Long‐range PCR allows sequencing of mitochondrial genomes from environmental DNA , 2017 .
[16] Hannah M. Wood,et al. The spider tree of life: phylogeny of Araneae based on target‐gene analyses from an extensive taxon sampling , 2017, Cladistics : the international journal of the Willi Hennig Society.
[17] Jing Li,et al. De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms , 2017, Scientific Reports.
[18] Niranjan Nagarajan,et al. Fast and accurate de novo genome assembly from long uncorrected reads. , 2017, Genome research.
[19] R. Gillespie,et al. A cost‐efficient and simple protocol to enrich prey DNA from extractions of predatory arthropods for large‐scale gut content analysis by Illumina sequencing , 2017 .
[20] A. Hochkirch. The insect crisis we can’t ignore , 2016, Nature.
[21] Arwyn Edwards,et al. Extreme metagenomics using nanopore DNA sequencing : a field report from Svalbard , 78 ° N , 2016 .
[22] Martin Sosic,et al. Edlib: a C/C++ library for fast, exact sequence alignment using edit distance , 2016, bioRxiv.
[23] C. Muster,et al. A phylogeographical survey of a highly dispersive spider reveals eastern Asia as a major glacial refugium for Palaearctic fauna , 2016 .
[24] Neo D. Martinez,et al. Community assembly on isolated islands: macroecology meets evolution , 2016 .
[25] David A. Matthews,et al. Real-time, portable genome sequencing for Ebola surveillance , 2016, Nature.
[26] Y. Sanz,et al. Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer , 2015, bioRxiv.
[27] R. Gillespie. Island time and the interplay between ecology and evolution in species diversification , 2015, Evolutionary applications.
[28] Y. Sanz,et al. Species-level resolution of 16S rRNA gene amplicons sequenced through the MinIONTM portable nanopore sequencer , 2015, bioRxiv.
[29] S. Pekár,et al. An Analysis of Factors Affecting Genotyping Success from Museum Specimens Reveals an Increase of Genetic and Morphological Variation during a Historical Range Expansion of a European Spider , 2015, PloS one.
[30] Mehrdad Hajibabaei,et al. Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform , 2015, Scientific Reports.
[31] N. Loman,et al. A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.
[32] Thomas K. F. Wong,et al. Phylogenomics resolves the timing and pattern of insect evolution , 2014, Science.
[33] J. L. Gittleman,et al. The biodiversity of species and their rates of extinction, distribution, and protection , 2014, Science.
[34] K. Kjer,et al. Moving toward species-level phylogeny using ribosomal DNA and COI barcodes : an example from the diverse caddisfly genus Chimarra ( Trichoptera : Philopotamidae ) , 2014 .
[35] Koichiro Tamura,et al. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.
[36] John G Kenny,et al. Can Long-Range PCR Be Used to Amplify Genetically Divergent Mitochondrial Genomes for Comparative Phylogenetics? A Case Study within Spiders (Arthropoda: Araneae) , 2013, PloS one.
[37] N. Knowlton,et al. PCR Primers for Metazoan Nuclear 18S and 28S Ribosomal DNA Sequences , 2012, PloS one.
[38] Cuong Q. Tang,et al. The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna , 2012, Proceedings of the National Academy of Sciences.
[39] Douglas W. Yu,et al. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring , 2012 .
[40] R. Lanfear,et al. Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. , 2012, Molecular biology and evolution.
[41] John L. Spouge,et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi , 2012, Proceedings of the National Academy of Sciences.
[42] Mark Fishbein,et al. Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. , 2012, American journal of botany.
[43] G. Edgecombe,et al. Reevaluating the arthropod tree of life. , 2012, Annual review of entomology.
[44] De‐Zhu Li,et al. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants , 2011, Proceedings of the National Academy of Sciences.
[45] S. Kotchoni,et al. A simplified arthropod genomic-DNA extraction protocol for polymerase chain reaction (PCR)-based specimen identification through barcoding , 2010, Molecular Biology Reports.
[46] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[47] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[48] C. Graham,et al. Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. , 2008, Ecology letters.
[49] Anne-Béatrice Dufour,et al. The ade4 Package: Implementing the Duality Diagram for Ecologists , 2007 .
[50] Rita Sipos,et al. Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. , 2007, FEMS microbiology ecology.
[51] D. Tautz,et al. An evaluation of LSU rDNA D1-D2 sequences for their use in species identification , 2007, Frontiers in Zoology.
[52] F. Jiggins,et al. Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts , 2005, Proceedings of the Royal Society B: Biological Sciences.
[53] P. Boursot,et al. Invasion from the cold past: extensive introgression of mountain hare (Lepus timidus) mitochondrial DNA into three other hare species in northern Iberia , 2005, Molecular ecology.
[54] Todd A Blackledge,et al. Convergent evolution of behavior in an adaptive radiation of Hawaiian web-building spiders. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[55] R. Gillespie. Community Assembly Through Adaptive Radiation in Hawaiian Spiders , 2004, Science.
[56] P. Hebert,et al. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species , 2003, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[57] Resource use within a community of Hawaiian spiders (Araneae: Tetragnathidae) , 2003 .
[58] John P. Huelsenbeck,et al. MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..
[59] John M. Hancock,et al. Extreme length and length variation in the first ribosomal internal transcribed spacer of ladybird beetles (Coleoptera: Coccinellidae). , 2001, Molecular biology and evolution.
[60] R. B. Jackson,et al. Global biodiversity scenarios for the year 2100. , 2000, Science.
[61] C. Moritz,et al. GENETIC STRUCTURE AND MALE‐MEDIATED GENE FLOW IN THE GHOST BAT (MACRODERMA GIGAS) , 1999, Evolution; international journal of organic evolution.
[62] R. Gillespie. COMPARISON OF RATES OF SPECIATION IN WEB-BUILDING AND NON-WEB-BUILDING GROUPS WITHIN A HAWAIIAN SPIDER RADIATION , 1999 .
[63] M. Valero,et al. Short allele dominance as a source of heterozygote deficiency at microsatellite loci: experimental evidence at the dinucleotide locus Gv1CT in Gracilaria gracilis (Rhodophyta) , 1998 .
[64] D. Soltis,et al. Molecular Evolution of 18S rDNA in Angiosperms: Implications for Character Weighting in Phylogenetic Analysis , 1998 .
[65] C. Fleming,et al. The rDNA Internal Transcribed Spacer Region as a Taxonomic Marker for Nematodes. , 1997, Journal of nematology.
[66] R. Gillespie,et al. Phylogenetic Relationships and Adaptive Shifts among Major Clades of Tetragnatha Spiders (Araneae: Tetragnathidae) in Hawai'i , 1997 .
[67] W. Black,et al. Phylogenetic relationships among tick subfamilies (Ixodida: Ixodidae: Argasidae) based on the 18S nuclear rDNA gene. , 1997, Molecular phylogenetics and evolution.
[68] S. Giovannoni,et al. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR , 1996, Applied and environmental microbiology.
[69] Chris C. Wilson,et al. Introgression and fixation of Arctic char (Salvelinus alpinus) mitochondrial genome in an allopatric population of brook trout (Salvelinus fontinalis) , 1995 .
[70] D. Hillis,et al. Ribosomal DNA: Molecular Evolution and Phylogenetic Inference , 1991, The Quarterly Review of Biology.
[71] R. Gillespie. HAWAIIAN SPIDERS OF THE GENUS TETRAGNATHA: I. SPINY LEG CLAD E , 1991 .
[72] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[73] Vladimir I. Levenshtein,et al. Binary codes capable of correcting deletions, insertions, and reversals , 1965 .