Data from: Phylogenomics from whole genome sequences using aTRAM ...
Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for org...
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Online Access: | https://dx.doi.org/10.5061/dryad.26j38 https://datadryad.org/stash/dataset/doi:10.5061/dryad.26j38 |
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ftdatacite:10.5061/dryad.26j38 2024-02-04T09:55:24+01:00 Data from: Phylogenomics from whole genome sequences using aTRAM ... Allen, Julie M. Boyd, Bret Nguyen, Nam-Phuong Vachaspati, Pranjal Warnow, Tandy Huang, Daisie I. Grady, Patrick G. S. Bell, Kayce C. Cronk, Quentin C.B. Mugisha, Lawrence Pittendrigh, Barry R. Soledad Leonardi, M. Reed, David L. Johnson, Kevin P. 2016 https://dx.doi.org/10.5061/dryad.26j38 https://datadryad.org/stash/dataset/doi:10.5061/dryad.26j38 en eng Dryad https://dx.doi.org/10.1093/sysbio/syw105 Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 Bureelia antiqua Osborniella crotophagae Pedicinus badii gene assembly Haematopinus eurysternus Degeeriella rufa Pthirus gorillae Neohaematopinus pacificus Genome sequencing Linognathus spicatus Pthirus pubis Pediculus humanus Pediculus schaeffi Proechinopthirus fluctus aTRAM Hoplopleura arboricola Stimulopalpus japonicus present day Antarctopthirus microchir Bothriometopus macrocnemus Holocene Dataset dataset 2016 ftdatacite https://doi.org/10.5061/dryad.26j3810.1093/sysbio/syw105 2024-01-05T01:14:15Z Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (<1000 Mbp) it is feasible to sequence the entire genome at modest coverage (10−30×). Computational challenges for handling these large data sets can be alleviated by assembling targeted reads, rather than assembling the entire genome, to produce a phylogenomic data matrix. Here we demonstrate the use of automated Target Restricted Assembly Method (aTRAM) to assemble 1107 single-copy ortholog genes from whole genome sequencing of sucking lice (Anoplura) and out-groups. We developed a pipeline to extract exon sequences from the aTRAM assemblies by ... : Concatenated alignment and treeAlignment and phylogenetic tree of the concatenated 1,101 exon DNA alignment from 15 louse taxa. Genes were assembled from raw genomic DNA with aTRAM and exons extracted and stitched together. Third codon position was removed due to base composition bias, and tree build in RAxML.Dataset_1.zipIndividual Gene Trees and AlignmentsAll 1,101 gene trees and alignments for the 15 taxon dataset. Each gene was aligned using PASTA and UPP for fragmentary sequences. Each gene tree was built using ASTRAL.Dataset_2.zipSupplementaryTableDNA extraction, and quality clean up for each dataset. Illumina reads. Alignments of each gene and the tree analysis.Supplementary FigureBox plot of the standard deviations away from mean for each codon position for each of the GTR rate parameters. The majorities of the extreme outliers fell above 10 standard deviations from the mean and were removed from the analysis.SupplementalFigure1.pdf ... Dataset Antarc* DataCite Metadata Store (German National Library of Science and Technology) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
Bureelia antiqua Osborniella crotophagae Pedicinus badii gene assembly Haematopinus eurysternus Degeeriella rufa Pthirus gorillae Neohaematopinus pacificus Genome sequencing Linognathus spicatus Pthirus pubis Pediculus humanus Pediculus schaeffi Proechinopthirus fluctus aTRAM Hoplopleura arboricola Stimulopalpus japonicus present day Antarctopthirus microchir Bothriometopus macrocnemus Holocene |
spellingShingle |
Bureelia antiqua Osborniella crotophagae Pedicinus badii gene assembly Haematopinus eurysternus Degeeriella rufa Pthirus gorillae Neohaematopinus pacificus Genome sequencing Linognathus spicatus Pthirus pubis Pediculus humanus Pediculus schaeffi Proechinopthirus fluctus aTRAM Hoplopleura arboricola Stimulopalpus japonicus present day Antarctopthirus microchir Bothriometopus macrocnemus Holocene Allen, Julie M. Boyd, Bret Nguyen, Nam-Phuong Vachaspati, Pranjal Warnow, Tandy Huang, Daisie I. Grady, Patrick G. S. Bell, Kayce C. Cronk, Quentin C.B. Mugisha, Lawrence Pittendrigh, Barry R. Soledad Leonardi, M. Reed, David L. Johnson, Kevin P. Data from: Phylogenomics from whole genome sequences using aTRAM ... |
topic_facet |
Bureelia antiqua Osborniella crotophagae Pedicinus badii gene assembly Haematopinus eurysternus Degeeriella rufa Pthirus gorillae Neohaematopinus pacificus Genome sequencing Linognathus spicatus Pthirus pubis Pediculus humanus Pediculus schaeffi Proechinopthirus fluctus aTRAM Hoplopleura arboricola Stimulopalpus japonicus present day Antarctopthirus microchir Bothriometopus macrocnemus Holocene |
description |
Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (<1000 Mbp) it is feasible to sequence the entire genome at modest coverage (10−30×). Computational challenges for handling these large data sets can be alleviated by assembling targeted reads, rather than assembling the entire genome, to produce a phylogenomic data matrix. Here we demonstrate the use of automated Target Restricted Assembly Method (aTRAM) to assemble 1107 single-copy ortholog genes from whole genome sequencing of sucking lice (Anoplura) and out-groups. We developed a pipeline to extract exon sequences from the aTRAM assemblies by ... : Concatenated alignment and treeAlignment and phylogenetic tree of the concatenated 1,101 exon DNA alignment from 15 louse taxa. Genes were assembled from raw genomic DNA with aTRAM and exons extracted and stitched together. Third codon position was removed due to base composition bias, and tree build in RAxML.Dataset_1.zipIndividual Gene Trees and AlignmentsAll 1,101 gene trees and alignments for the 15 taxon dataset. Each gene was aligned using PASTA and UPP for fragmentary sequences. Each gene tree was built using ASTRAL.Dataset_2.zipSupplementaryTableDNA extraction, and quality clean up for each dataset. Illumina reads. Alignments of each gene and the tree analysis.Supplementary FigureBox plot of the standard deviations away from mean for each codon position for each of the GTR rate parameters. The majorities of the extreme outliers fell above 10 standard deviations from the mean and were removed from the analysis.SupplementalFigure1.pdf ... |
format |
Dataset |
author |
Allen, Julie M. Boyd, Bret Nguyen, Nam-Phuong Vachaspati, Pranjal Warnow, Tandy Huang, Daisie I. Grady, Patrick G. S. Bell, Kayce C. Cronk, Quentin C.B. Mugisha, Lawrence Pittendrigh, Barry R. Soledad Leonardi, M. Reed, David L. Johnson, Kevin P. |
author_facet |
Allen, Julie M. Boyd, Bret Nguyen, Nam-Phuong Vachaspati, Pranjal Warnow, Tandy Huang, Daisie I. Grady, Patrick G. S. Bell, Kayce C. Cronk, Quentin C.B. Mugisha, Lawrence Pittendrigh, Barry R. Soledad Leonardi, M. Reed, David L. Johnson, Kevin P. |
author_sort |
Allen, Julie M. |
title |
Data from: Phylogenomics from whole genome sequences using aTRAM ... |
title_short |
Data from: Phylogenomics from whole genome sequences using aTRAM ... |
title_full |
Data from: Phylogenomics from whole genome sequences using aTRAM ... |
title_fullStr |
Data from: Phylogenomics from whole genome sequences using aTRAM ... |
title_full_unstemmed |
Data from: Phylogenomics from whole genome sequences using aTRAM ... |
title_sort |
data from: phylogenomics from whole genome sequences using atram ... |
publisher |
Dryad |
publishDate |
2016 |
url |
https://dx.doi.org/10.5061/dryad.26j38 https://datadryad.org/stash/dataset/doi:10.5061/dryad.26j38 |
genre |
Antarc* |
genre_facet |
Antarc* |
op_relation |
https://dx.doi.org/10.1093/sysbio/syw105 |
op_rights |
Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 |
op_doi |
https://doi.org/10.5061/dryad.26j3810.1093/sysbio/syw105 |
_version_ |
1789959365938118656 |