Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

Margaret Staton, Teodora Best, Sudhir Khodwekar, Sandra Owusu, Tao Xu, Yi Xu, Tara Jennings, Richard Cronn, A. Kathiravetpilla Arumuganathan, Mark Coggeshall, Oliver Gailing, Haiying Liang, Jeanne Romero-Severson, Scott Schlarbaum, John E. Carlson

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence.

Original languageEnglish (US)
Article numbere0145031
JournalPloS one
Volume10
Issue number12
DOIs
StatePublished - Dec 1 2015

Fingerprint

Hardwoods
hardwood
Genes
Genome
genomics
forest health
genome
Acer
Dinucleotide Repeats
Genome Size
loci
Acer saccharum subsp. saccharum
repetitive sequences
Nucleic Acid Repetitive Sequences
Climate Change
Health
Computer Simulation
nuclear genome
abiotic stress
flow cytometry

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Staton, Margaret ; Best, Teodora ; Khodwekar, Sudhir ; Owusu, Sandra ; Xu, Tao ; Xu, Yi ; Jennings, Tara ; Cronn, Richard ; Arumuganathan, A. Kathiravetpilla ; Coggeshall, Mark ; Gailing, Oliver ; Liang, Haiying ; Romero-Severson, Jeanne ; Schlarbaum, Scott ; Carlson, John E. / Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing. In: PloS one. 2015 ; Vol. 10, No. 12.
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Staton, M, Best, T, Khodwekar, S, Owusu, S, Xu, T, Xu, Y, Jennings, T, Cronn, R, Arumuganathan, AK, Coggeshall, M, Gailing, O, Liang, H, Romero-Severson, J, Schlarbaum, S & Carlson, JE 2015, 'Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing', PloS one, vol. 10, no. 12, e0145031. https://doi.org/10.1371/journal.pone.0145031

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing. / Staton, Margaret; Best, Teodora; Khodwekar, Sudhir; Owusu, Sandra; Xu, Tao; Xu, Yi; Jennings, Tara; Cronn, Richard; Arumuganathan, A. Kathiravetpilla; Coggeshall, Mark; Gailing, Oliver; Liang, Haiying; Romero-Severson, Jeanne; Schlarbaum, Scott; Carlson, John E.

In: PloS one, Vol. 10, No. 12, e0145031, 01.12.2015.

Research output: Contribution to journalArticle

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AU - Staton, Margaret

AU - Best, Teodora

AU - Khodwekar, Sudhir

AU - Owusu, Sandra

AU - Xu, Tao

AU - Xu, Yi

AU - Jennings, Tara

AU - Cronn, Richard

AU - Arumuganathan, A. Kathiravetpilla

AU - Coggeshall, Mark

AU - Gailing, Oliver

AU - Liang, Haiying

AU - Romero-Severson, Jeanne

AU - Schlarbaum, Scott

AU - Carlson, John E.

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N2 - Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence.

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