title: Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing.
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.
authors.affiliation: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States of America.
authors.forename: Margaret
authors.initials: M
authors.lastname: Staton
authors.affiliation: The Schatz Center for Tree Molecular Genetics, Pennsylvania State University, University Park, PA, United States of America.
authors.forename: Teodora
authors.initials: T
authors.lastname: Best
authors.affiliation: School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, United States of America.
authors.forename: Sudhir
authors.initials: S
authors.lastname: Khodwekar
authors.affiliation: School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, United States of America.
authors.forename: Sandra
authors.initials: S
authors.lastname: Owusu
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States of America.
authors.forename: Tao
authors.initials: T
authors.lastname: Xu
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States of America.
authors.forename: Yi
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America.
authors.forename: Tara
authors.initials: T
authors.lastname: Jennings
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America.
authors.forename: Richard
authors.initials: R
authors.lastname: Cronn
authors.affiliation: Flow Cytometry and Imaging Core Lab, Benaroya Research Institute at Virginia Mason, Seattle, WA, United States of America.
authors.forename: A Kathiravetpilla
authors.initials: AK
authors.lastname: Arumuganathan
authors.affiliation: Department of Forestry, University of Missouri, Columbia, MO, United States of America.
authors.forename: Mark
authors.initials: M
authors.lastname: Coggeshall
authors.affiliation: School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, United States of America.
authors.forename: Oliver
authors.initials: O
authors.lastname: Gailing
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States of America.
authors.forename: Haiying
authors.initials: H
authors.lastname: Liang
authors.affiliation: Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America.
authors.forename: Jeanne
authors.initials: J
authors.lastname: Romero-Severson
authors.affiliation: Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States of America.
authors.forename: Scott
authors.initials: S
authors.lastname: Schlarbaum
authors.affiliation: The Schatz Center for Tree Molecular Genetics, Pennsylvania State University, University Park, PA, United States of America.
authors.forename: John E
authors.initials: JE
authors.lastname: Carlson
mesh_terms: D057231:Climate Change; D018744:DNA, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D014197:Trees / Q000235:genetics* / Q000254:growth & development
chemical_list: D018744:DNA, Plant