title: De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms.
abstract: Horseweed (Conyza canadensis), a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate. Horseweed, one of the most problematic weeds in the world, is a true diploid (2n = 2x = 18), with the smallest genome of any known agricultural weed (335 Mb). Thus, it is an appropriate candidate to help us understand the genetic and genomic bases of weediness. We undertook a draft de novo genome assembly of horseweed by combining data from multiple sequencing platforms (454 GS-FLX, Illumina HiSeq 2000, and PacBio RS) using various libraries with different insertion sizes (approximately 350 bp, 600 bp, 3 kb, and 10 kb) of a Tennessee-accessed, glyphosate-resistant horseweed biotype. From 116.3 Gb (approximately 350× coverage) of data, the genome was assembled into 13,966 scaffolds with 50% of the assembly = 33,561 bp. The assembly covered 92.3% of the genome, including the complete chloroplast genome (approximately 153 kb) and a nearly complete mitochondrial genome (approximately 450 kb in 120 scaffolds). The nuclear genome is composed of 44,592 protein-coding genes. Genome resequencing of seven additional horseweed biotypes was performed. These sequence data were assembled and used to analyze genome variation. Simple sequence repeat and single-nucleotide polymorphisms were surveyed. Genomic patterns were detected that associated with glyphosate-resistant or -susceptible biotypes. The draft genome will be useful to better understand weediness and the evolution of herbicide resistance and to devise new management strategies. The genome will also be useful as another reference genome in the Compositae. To our knowledge, this article represents the first published draft genome of an agricultural weed.
authors.affiliation: Department of Plant Science, University of Tennessee, Knoxville, Tennessee 37996 (Y.P., T.L., M.N.-R., C.N.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Z.L., L.H.R.);Department of Plant Sciences (M.O., M.J.) and Genome Center (H.O., R.W.K.), University of California, Davis, California 95616;Monsanto, Inc., St. Louis, Missouri 63130 (R.D.S.); andDepartment of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (L.H.R.).
authors.forename: Yanhui
authors.initials: Y
authors.lastname: Peng
authors.affiliation: Department of Plant Science, University of Tennessee, Knoxville, Tennessee 37996 (Y.P., T.L., M.N.-R., C.N.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Z.L., L.H.R.);Department of Plant Sciences (M.O., M.J.) and Genome Center (H.O., R.W.K.), University of California, Davis, California 95616;Monsanto, Inc., St. Louis, Missouri 63130 (R.D.S.); andDepartment of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (L.H.R.).
authors.forename: Zhao
authors.initials: Z
authors.lastname: Lai
authors.affiliation: Department of Plant Science, University of Tennessee, Knoxville, Tennessee 37996 (Y.P., T.L., M.N.-R., C.N.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Z.L., L.H.R.);Department of Plant Sciences (M.O., M.J.) and Genome Center (H.O., R.W.K.), University of California, Davis, California 95616;Monsanto, Inc., St. Louis, Missouri 63130 (R.D.S.); andDepartment of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (L.H.R.).
authors.forename: Thomas
authors.initials: T
authors.lastname: Lane
authors.affiliation: Department of Plant Science, University of Tennessee, Knoxville, Tennessee 37996 (Y.P., T.L., M.N.-R., C.N.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Z.L., L.H.R.);Department of Plant Sciences (M.O., M.J.) and Genome Center (H.O., R.W.K.), University of California, Davis, California 95616;Monsanto, Inc., St. Louis, Missouri 63130 (R.D.S.); andDepartment of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (L.H.R.).
authors.forename: Madhugiri
authors.initials: M
authors.lastname: Nageswara-Rao
authors.affiliation: Department of Plant Science, University of Tennessee, Knoxville, Tennessee 37996 (Y.P., T.L., M.N.-R., C.N.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Z.L., L.H.R.);Department of Plant Sciences (M.O., M.J.) and Genome Center (H.O., R.W.K.), University of California, Davis, California 95616;Monsanto, Inc., St. Louis, Missouri 63130 (R.D.S.); andDepartment of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (L.H.R.).
authors.forename: Miki
authors.initials: M
authors.lastname: Okada
authors.affiliation: Department of Plant Science, University of Tennessee, Knoxville, Tennessee 37996 (Y.P., T.L., M.N.-R., C.N.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Z.L., L.H.R.);Department of Plant Sciences (M.O., M.J.) and Genome Center (H.O., R.W.K.), University of California, Davis, California 95616;Monsanto, Inc., St. Louis, Missouri 63130 (R.D.S.); andDepartment of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (L.H.R.).
authors.forename: Marie
authors.initials: M
authors.lastname: Jasieniuk
authors.affiliation: Department of Plant Science, University of Tennessee, Knoxville, Tennessee 37996 (Y.P., T.L., M.N.-R., C.N.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Z.L., L.H.R.);Department of Plant Sciences (M.O., M.J.) and Genome Center (H.O., R.W.K.), University of California, Davis, California 95616;Monsanto, Inc., St. Louis, Missouri 63130 (R.D.S.); andDepartment of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (L.H.R.).
authors.forename: Henriette
authors.initials: H
authors.lastname: O'Geen
authors.affiliation: Department of Plant Science, University of Tennessee, Knoxville, Tennessee 37996 (Y.P., T.L., M.N.-R., C.N.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Z.L., L.H.R.);Department of Plant Sciences (M.O., M.J.) and Genome Center (H.O., R.W.K.), University of California, Davis, California 95616;Monsanto, Inc., St. Louis, Missouri 63130 (R.D.S.); andDepartment of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (L.H.R.).
authors.forename: Ryan W
authors.initials: RW
authors.lastname: Kim
authors.affiliation: Department of Plant Science, University of Tennessee, Knoxville, Tennessee 37996 (Y.P., T.L., M.N.-R., C.N.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Z.L., L.H.R.);Department of Plant Sciences (M.O., M.J.) and Genome Center (H.O., R.W.K.), University of California, Davis, California 95616;Monsanto, Inc., St. Louis, Missouri 63130 (R.D.S.); andDepartment of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (L.H.R.).
authors.forename: R Douglas
authors.initials: RD
authors.lastname: Sammons
authors.affiliation: Department of Plant Science, University of Tennessee, Knoxville, Tennessee 37996 (Y.P., T.L., M.N.-R., C.N.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Z.L., L.H.R.);Department of Plant Sciences (M.O., M.J.) and Genome Center (H.O., R.W.K.), University of California, Davis, California 95616;Monsanto, Inc., St. Louis, Missouri 63130 (R.D.S.); andDepartment of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (L.H.R.).
authors.forename: Loren H
authors.initials: LH
authors.lastname: Rieseberg
authors.affiliation: Department of Plant Science, University of Tennessee, Knoxville, Tennessee 37996 (Y.P., T.L., M.N.-R., C.N.S.);Department of Biology, Indiana University, Bloomington, Indiana 47405 (Z.L., L.H.R.);Department of Plant Sciences (M.O., M.J.) and Genome Center (H.O., R.W.K.), University of California, Davis, California 95616;Monsanto, Inc., St. Louis, Missouri 63130 (R.D.S.); andDepartment of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (L.H.R.) nealstewart@utk.edu.
authors.forename: C Neal
authors.initials: CN
authors.lastname: Stewart
mesh_terms: D005075:Biological Evolution; D035401:Conyza / Q000187:drug effects / Q000235:genetics*; D054628:Genome, Chloroplast / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics*; D023281:Genomics; D005998:Glycine / Q000031:analogs & derivatives* / Q000494:pharmacology; D053209:Herbicide Resistance; D006540:Herbicides / Q000494:pharmacology*; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D000097797:Glyphosate
chemical_list: D005998:Glycine; D006540:Herbicides; D000097797:Glyphosate