Evidence map›Paper›PMID 30526482›Full record

ArticleBMC genomics2018

Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA.

Kujin Tang, Jie Ren, Richard Cronn, David L Erickson, Brook G Milligan, Meaghan Parker-Forney, John L Spouge, Fengzhu Sun

Abstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Kujin TangQuantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA.
Jie RenQuantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA.
Richard CronnPacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA. rcronn@fs.fed.us.
David L EricksonDNA4 Technologies LLC, bwtech@UMBC Research & Technology Park, Baltimore, MD, 21227, USA.
Brook G MilliganConservation Genomics Laboratory, Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA.
Meaghan Parker-ForneyWorld Resources Institute, Washington, DC, 20002, USA.
John L SpougeNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
Fengzhu SunQuantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA. fsun@usc.edu.

Funding

National Science Foundation DMS-1518001
6 · The paper itself

Abstract

backgroundThe application of genomic data and bioinformatics for the identification of restricted or illegally-sourced natural products is urgently needed. The taxonomic identity and geographic provenance of raw and processed materials have implications in sustainable-use commercial practices, and relevance to the enforcement of laws that regulate or restrict illegally harvested materials, such as timber. Improvements in genomics make it possible to capture and sequence partial-to-complete genomes from challenging tissues, such as wood and wood products.

resultsIn this paper, we report the success of an alignment-free genome comparison method, [Formula: see text] that differentiates different geographic sources of white oak (Quercus) species with a high level of accuracy with very small amount of genomic data. The method is robust to sequencing errors, different sequencing laboratories and sequencing platforms.

conclusionsThis method offers an approach based on genome-scale data, rather than panels of pre-selected markers for specific taxa. The method provides a generalizable platform for the identification and sourcing of materials using a unified next generation sequencing and analysis framework.

Indexed as

Genome, PlantGeographyAlgorithmsDNA, PlantHigh-Throughput Nucleotide SequencingPrincipal Component AnalysisQuercusSequence AlignmentDNA, Plant

Identifiers

PMID30526482
PMCPMC6288960

What OpenQuestion holds

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LicenceCC BY
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.