An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes Article Swipe
Thomas K. F. Wong
,
Teng Li
,
Louis Ranjard
,
Steven Wu
,
Jeet Sukumaran
,
Allen G. Rodrigo
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pcbi.1008949
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pcbi.1008949
A current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogenetic tree according to the SNP patterns. AFPhyloMix adopts a Bayesian inference model to estimate the phylogeny of the haplotypes and their relative abundances, given that the number of haplotypes is known. In our simulations, AFPhyloMix achieved at least 80% accuracy at recovering the phylogenies and relative abundances of the constituent haplotypes, for mixtures with up to 15 haplotypes. AFPhyloMix also worked well on a real data set of kangaroo mitochondrial DNA sequences.
Related Topics
Concepts
Haplotype
Amplicon
Phylogenetics
Biology
Phylogenetic tree
Barcode
Evolutionary biology
SNP
DNA barcoding
Mitochondrial DNA
Single-nucleotide polymorphism
Computational biology
Genetics
Sequence (biology)
Computer science
Polymerase chain reaction
Gene
Genotype
Operating system
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1371/journal.pcbi.1008949
- https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008949&type=printable
- OA Status
- gold
- References
- 27
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3200833116
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3200833116Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1371/journal.pcbi.1008949Digital Object Identifier
- Title
-
An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodesWork title
- Type
-
articleOpenAlex work type
- Language
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enPrimary language
- Publication year
-
2021Year of publication
- Publication date
-
2021-09-13Full publication date if available
- Authors
-
Thomas K. F. Wong, Teng Li, Louis Ranjard, Steven Wu, Jeet Sukumaran, Allen G. RodrigoList of authors in order
- Landing page
-
https://doi.org/10.1371/journal.pcbi.1008949Publisher landing page
- PDF URL
-
https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008949&type=printableDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008949&type=printableDirect OA link when available
- Concepts
-
Haplotype, Amplicon, Phylogenetics, Biology, Phylogenetic tree, Barcode, Evolutionary biology, SNP, DNA barcoding, Mitochondrial DNA, Single-nucleotide polymorphism, Computational biology, Genetics, Sequence (biology), Computer science, Polymerase chain reaction, Gene, Genotype, Operating systemTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
0Total citation count in OpenAlex
- References (count)
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27Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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