Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

ABSTRACT Deblur provides a rapid and sensitive means to assess ecological patterns driven by differentiation of closely related taxa. This algorithm provides a solution to the problem of identifying real ecological differences between taxa whose amplicons differ by a single base pair, is applicable in an automated fashion to large-scale sequencing data sets, and can integrate sequencing runs collected over time. High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the inherent noise in PCR and DNA sequencing limits differentiation of closely related bacteria. Although many scientific questions can be addressed with broad taxonomic profiles, clinical, food safety, and some ecological applications require higher specificity. Here we introduce a novel sub-operational-taxonomic-unit (sOTU) approach, Deblur, that uses error profiles to obtain putative error-free sequences from Illumina MiSeq and HiSeq sequencing platforms. Deblur substantially reduces computational demands relative to similar sOTU methods and does so with similar or better sensitivity and specificity. Using simulations, mock mixtures, and real data sets, we detected closely related bacterial sequences with single nucleotide differences while removing false positives and maintaining stability in detection, suggesting that Deblur is limited only by read length and diversity within the amplicon sequences. Because Deblur operates on a per-sample level, it scales to modern data sets and meta-analyses. To highlight Deblur’s ability to integrate data sets, we include an interactive exploration of its application to multiple distinct sequencing rounds of the American Gut Project. Deblur is open source under the Berkeley Software Distribution (BSD) license, easily installable, and downloadable from https://github.com/biocore/deblur . IMPORTANCE Deblur provides a rapid and sensitive means to assess ecological patterns driven by differentiation of closely related taxa. This algorithm provides a solution to the problem of identifying real ecological differences between taxa whose amplicons differ by a single base pair, is applicable in an automated fashion to large-scale sequencing data sets, and can integrate sequencing runs collected over time.

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Mutation

Evolutionary Algorithms in Theory and Practice ◽

10.1093/oso/9780195099713.003.0012 ◽

1996 ◽

Author(s):

Thomas Bäck

Keyword(s):

Genetic Algorithms ◽

Base Pair ◽

Full Range ◽

Data Sets ◽

Phenotypic Effect ◽

Local Optima ◽

Single Base ◽

Biological Reality ◽

Single Base Pair ◽

Few Data

In section 1.1.3 it was clarified that a variety of different, more or less drastic changes of the genome are summarized under the term mutation by geneticists and evolutionary biologists. Several mutation events are within the bounds of possibility, ranging from single base pair changes to genomic mutations. The phenotypic effect of genotypic mutations, however, can hardly be predicted from knowledge about the genotypic change. In general, advantageous mutations have a relatively small effect on the phenotype, i.e., their expression does not deviate very much (in phenotype space) from the expression of the unmutated genotype ([Fut90], p. 85). More drastic phenotypic changes are usually lethal or become extinct due to a reduced capability of reproduction. The discussion, to which extent evolution based on phenotypic macro-mutations in the sense of “hopeful monsters” is important to facilitate the process of speciation, is still ongoing (such macromutations have been observed and classified for the fruitfly Drosophila melangonaster, see [Got89], p. 286). Actually, only a few data sets are available to assess the phylogenetic significance of macro-mutations completely, but small phenotypical effects of mutation are clearly observed to be predominant. This is the main argument justifying the use of normally distributed mutations with expectation zero in Evolutionary Programming and Evolution Strategies. It reflects the emphasis of both algorithms on modeling phenotypic rather than genotypic change. The model of mutation is quite different in Genetic Algorithms, where bit reversal events (see section 2.3.2) corresponding with single base pair mutations in biological reality implement a model of evolution on the basis of genotypic changes. As observed in nature, the mutation rate used in Genetic Algorithms is very small (cf. section 2.3.2). In contrast to the biological model, it is neither variable by external influences nor controlled (at least partially) by the genotype itself (cf. section 1.1.3). Holland defined the role of mutation in Genetic Algorithms to be a secondary one, of little importance in comparison to crossover (see [Hol75], p. 111): . . . Summing up: Mutation is a “background” operator, assuring that the crossover operator has a full range of alleles so that the adaptive plan is not trapped on local optima. . . .

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Neighboring-Nucleotide Effects on the Rates of Germ-Line Single-Base-Pair Substitution in Human Genes

The American Journal of Human Genetics ◽

10.1086/301965 ◽

1998 ◽

Vol 63 (2) ◽

pp. 474-488 ◽

Cited By ~ 189

Author(s):

Michael Krawczak ◽

Edward V. Ball ◽

David N. Cooper

Keyword(s):

Base Pair ◽

Germ Line ◽

Single Base ◽

Human Genes ◽

Single Base Pair Substitution ◽

Single Base Pair ◽

Base Pair Substitution

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The Arabic allele: A single base pair substitution activates a 10-base downstream cryptic splice acceptor site in exon 12 of LDLR and severely decreases LDLR expression in two unrelated Arab families with familial hypercholesterolemia

Atherosclerosis ◽

10.1016/j.atherosclerosis.2011.10.045 ◽

2012 ◽

Vol 220 (2) ◽

pp. 429-436 ◽

Cited By ~ 6

Author(s):

Said M. Shawar ◽

Mohammad A. Al-Drees ◽

Ahmad R. Ramadan ◽

Najat H. Ali ◽

Suad M. AlFadhli

Keyword(s):

Familial Hypercholesterolemia ◽

Base Pair ◽

Splice Acceptor Site ◽

Acceptor Site ◽

Splice Acceptor ◽

Single Base ◽

Single Base Pair Substitution ◽

Single Base Pair ◽

Base Pair Substitution

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Development of the PCR method for sequencing single base pair changes in the hprt gene of man, mouse and hamster: different mutation spectra in normal and repair-deficient UV-sensitive V79 Chinese hamster cells

Mutation Research/Environmental Mutagenesis and Related Subjects ◽

10.1016/0165-1161(89)90034-4 ◽

1989 ◽

Vol 216 (1) ◽

pp. 82-83 ◽

Cited By ~ 1

Author(s):

H. Vrieling ◽

M.L. van Rooijen ◽

M.Z. Zdzienicka ◽

J.W.I.M. Simons ◽

P.H.M. Lohman ◽

...

Keyword(s):

Base Pair ◽

Chinese Hamster ◽

Hprt Gene ◽

Single Base ◽

Chinese Hamster Cells ◽

Single Base Pair ◽

Pcr Method ◽

Mutation Spectra

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Overexpression of the MtrC-MtrD-MtrE Efflux Pump Due to an mtrR Mutation Is Required for Chromosomally Mediated Penicillin Resistance in Neisseria gonorrhoeae

Journal of Bacteriology ◽

10.1128/jb.184.20.5619-5624.2002 ◽

2002 ◽

Vol 184 (20) ◽

pp. 5619-5624 ◽

Cited By ~ 113

Author(s):

Wendy L. Veal ◽

Robert A. Nicholas ◽

William M. Shafer

Keyword(s):

Neisseria Gonorrhoeae ◽

Base Pair ◽

Efflux Pump ◽

Penicillin Resistance ◽

Single Base ◽

Base Pair Deletion ◽

Resistance To Penicillin ◽

Single Base Pair ◽

High Level ◽

Level Resistance

ABSTRACT The importance of the mtrCDE-encoded efflux pump in conferring chromosomally mediated penicillin resistance on certain strains of Neisseria gonorrhoeae was determined by using genetic derivatives of penicillin-sensitive strain FA19 bearing defined mutations (mtrR, penA, and penB) donated by a clinical isolate (FA6140) expressing high-level resistance to penicillin and antimicrobial hydrophobic agents (HAs). When introduced into strain FA19 by transformation, a single base pair deletion in the mtrR promoter sequence from strain FA6140 was sufficient to provide high-level resistance to HAs (e.g., erythromycin and Triton X-100) but only a twofold increase in resistance to penicillin. When subsequent mutations in penA and porIB were introduced from strain FA6140 into strain WV30 (FA19 mtrR) by transformation, resistance to penicillin increased incrementally up to a MIC of 1.0 μg/ml. Insertional inactivation of the gene (mtrD) encoding the membrane transporter component of the Mtr efflux pump in these transformant strains and in strain FA6140 decreased the MIC of penicillin by 16-fold. Genetic analyses revealed that mtrR mutations, such as the single base pair deletion in its promoter, are needed for phenotypic expression of penicillin and tetracycline resistance afforded by the penB mutation. As penB represents amino acid substitutions within the third loop of the outer membrane PorIB protein that modulate entry of penicillin and tetracycline, the results presented herein suggest that PorIB and the MtrC-MtrD-MtrE efflux pump act synergistically to confer resistance to these antibiotics.

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Dinucleotide microsatellites from Eucalyptus sieberi: inheritance, diversity, and improved scoring of single-base differences

Genome ◽

10.1139/g01-106 ◽

2001 ◽

Vol 44 (6) ◽

pp. 1041-1045 ◽

Cited By ~ 25

Author(s):

J C Glaubitz ◽

L C Emebiri ◽

G F Moran

Keyword(s):

Base Pair ◽

Mendelian Inheritance ◽

Null Alleles ◽

Fixation Index ◽

Eucalyptus Nitens ◽

Internal Reference ◽

Single Base ◽

Hardy Weinberg Equilibrium ◽

Single Base Pair ◽

Flanking Regions

Eight dinucleotide microsatellites were developed in Eucalyptus sieberi L. Johnson (silvertop ash), a member of the subgenus Eucalyptus. Transfer of six of these to the subgenus Symphyomyrtus and their Mendelian inheritance are demonstrated using a full-sib cross in Eucalyptus nitens. Genetic diversity parameters are presented for the eight loci based on a sample of 100 old-growth E. sieberi trees from a single natural stand. One locus, Es266, had an atypically high fixation index, and significantly deviated from Hardy-Weinberg equilibrium genotypic proportions, indicating the likely presence of null alleles. Two of the loci, Es076 and Es140, had many alleles that differed in size by only a single base pair, possibly because of short poly(A) or poly(T) stretches in their flanking regions. These two loci were by far the most polymorphic, but were difficult to score reliably on a capillary DNA sequencer. Reliability of scoring of these two one-base microsatellite loci was markedly improved by the incorporation of internal reference alleles into each sample analysed.Key words: SSRs, single base pair alleles, null alleles, internal reference alleles.

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