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Title: sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing

Abstract

The genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, a pipeline for the characterization of interspecies hybrids and pure species, that illuminates the complete composition of genomes. sppIDer maps short-read sequencing data to a combination genome built from reference genomes of several species of interest and assesses the genomic contribution and relative ploidy of each parental species, producing a series of colorful graphical outputs ready for publication. As a proof-of-concept, we use the genus Saccharomyces to detect and visualize both interspecies hybrids and pure strains, even with missing parental reference genomes. Through simulation, we show that sppIDer is robust to variable reference genome qualities and performs well with low-coverage data. We further demonstrate the power of this approach in plants, animals, and other fungi. sppIDer is robust to many different inputs and provides visually intuitive insight into genome composition that enables the rapid identification of species and their interspecies hybrids. sppIDer exists as a Docker image, which is a reusable, reproducible, transparent, and simple-to-run package that automates the pipeline and installation of the required dependenciesmore » (https://github.com/GLBRC/sppIDer; last accessed September 6, 2018).« less

Authors:
 [1];  [2];  [1];  [1];  [3]
  1. Univ. of Wisconsin, Madison, WI (United States)
  2. Univ. of Wisconsin, Madison, WI (United States); Spanish National Research Council (CSIC), Valencia (Spain). Inst. of Agrochemistry and Food Technology (IATA)
  3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1506670
Grant/Contract Number:  
SC0018409
Resource Type:
Accepted Manuscript
Journal Name:
Molecular Biology and Evolution
Additional Journal Information:
Journal Volume: 35; Journal Issue: 11; Journal ID: ISSN 0737-4038
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; hybrid; next-generation DNA sequencing; allopolyploidization; yeasts; species identification; bioinformatic software

Citation Formats

Langdon, Quinn K., Peris, David, Kyle, Brian, Hittinger, Chris Todd, and Rosenberg, Michael. sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing. United States: N. p., 2018. Web. doi:10.1093/molbev/msy166.
Langdon, Quinn K., Peris, David, Kyle, Brian, Hittinger, Chris Todd, & Rosenberg, Michael. sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing. United States. doi:https://doi.org/10.1093/molbev/msy166
Langdon, Quinn K., Peris, David, Kyle, Brian, Hittinger, Chris Todd, and Rosenberg, Michael. Sat . "sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing". United States. doi:https://doi.org/10.1093/molbev/msy166. https://www.osti.gov/servlets/purl/1506670.
@article{osti_1506670,
title = {sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing},
author = {Langdon, Quinn K. and Peris, David and Kyle, Brian and Hittinger, Chris Todd and Rosenberg, Michael},
abstractNote = {The genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, a pipeline for the characterization of interspecies hybrids and pure species, that illuminates the complete composition of genomes. sppIDer maps short-read sequencing data to a combination genome built from reference genomes of several species of interest and assesses the genomic contribution and relative ploidy of each parental species, producing a series of colorful graphical outputs ready for publication. As a proof-of-concept, we use the genus Saccharomyces to detect and visualize both interspecies hybrids and pure strains, even with missing parental reference genomes. Through simulation, we show that sppIDer is robust to variable reference genome qualities and performs well with low-coverage data. We further demonstrate the power of this approach in plants, animals, and other fungi. sppIDer is robust to many different inputs and provides visually intuitive insight into genome composition that enables the rapid identification of species and their interspecies hybrids. sppIDer exists as a Docker image, which is a reusable, reproducible, transparent, and simple-to-run package that automates the pipeline and installation of the required dependencies (https://github.com/GLBRC/sppIDer; last accessed September 6, 2018).},
doi = {10.1093/molbev/msy166},
journal = {Molecular Biology and Evolution},
number = 11,
volume = 35,
place = {United States},
year = {2018},
month = {9}
}

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