An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.

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...

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Autores principales:	Thomas K F Wong, Teng Li, Louis Ranjard, Steven H Wu, Jeet Sukumaran, Allen G Rodrigo
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/c08e727eb951407faed64eb0bb8fe146
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spelling	oai:doaj.org-article:c08e727eb951407faed64eb0bb8fe1462021-12-02T19:57:48ZAn assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.1553-734X1553-735810.1371/journal.pcbi.1008949https://doaj.org/article/c08e727eb951407faed64eb0bb8fe1462021-09-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1008949https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358A 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.Thomas K F WongTeng LiLouis RanjardSteven H WuJeet SukumaranAllen G RodrigoPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 9, p e1008949 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Thomas K F Wong Teng Li Louis Ranjard Steven H Wu Jeet Sukumaran Allen G Rodrigo An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.
description	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.
format	article
author	Thomas K F Wong Teng Li Louis Ranjard Steven H Wu Jeet Sukumaran Allen G Rodrigo
author_facet	Thomas K F Wong Teng Li Louis Ranjard Steven H Wu Jeet Sukumaran Allen G Rodrigo
author_sort	Thomas K F Wong
title	An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.
title_short	An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.
title_full	An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.
title_fullStr	An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.
title_full_unstemmed	An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.
title_sort	assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/c08e727eb951407faed64eb0bb8fe146
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An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.

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