51. Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA
- Author
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Richard Cronn, David L. Erickson, Brook G. Milligan, Meaghan Parker-Forney, John L. Spouge, Jie Ren, Fengzhu Sun, and Kujin Tang
- Subjects
0301 basic medicine ,DNA, Plant ,lcsh:QH426-470 ,Java ,lcsh:Biotechnology ,Genomics ,Computational biology ,Biology ,Genome ,DNA sequencing ,Quercus ,03 medical and health sciences ,lcsh:TP248.13-248.65 ,Genetics ,Relevance (information retrieval) ,computer.programming_language ,Principal Component Analysis ,Geography ,High-Throughput Nucleotide Sequencing ,White (mutation) ,lcsh:Genetics ,030104 developmental biology ,Identification (biology) ,DNA microarray ,Sequence Alignment ,computer ,Algorithms ,Genome, Plant ,Research Article ,Biotechnology - Abstract
Background The 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. Results In this paper, we report the success of an alignment-free genome comparison method, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^{\ast }, $$\end{document}d2∗, 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. Conclusions This 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. Electronic supplementary material The online version of this article (10.1186/s12864-018-5253-1) contains supplementary material, which is available to authorized users. more...
- Published
- 2018
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