DOI: 10.5061/dryad.cm7td
title: Data from: Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

description: PREMISE OF THE STUDY: Weeds cause considerable environmental and economic
 damage. However, genomic characterization of weeds has lagged behind that
 of model plants and crop species. Here we report on the development of
 genomic tools and resources for 11 weeds from the Compositae family that
 will serve as a basis for subsequent population and comparative genomic
 analyses. Because hybridization has been suggested as a stimulus for the
 evolution of invasiveness, we also analyze these genomic data for evidence
 of hybridization. METHODS: We generated 22 expressed sequence tag (EST)
 libraries for the 11 targeted weeds using Sanger, 454, and Illumina
 sequencing, compared the coverage and quality of sequence assemblies, and
 developed NimbleGen microarrays for expression analyses in five taxa.
 Where possible, we also compared the distributions of Ks values between
 orthologs of congeneric taxa to detect and quantify hybridization and
 introgression. RESULTS: Gene discovery was enhanced by sequencing from
 multiple tissues, normalization of cDNA libraries, and especially greater
 sequencing depth. However, assemblies from short sequence reads sometimes
 failed to resolve close paralogs. Substantial introgression was detected
 in Centaurea and Helianthus, but not in Ambrosia and Lactuca. CONCLUSIONS:
 Transcriptome sequencing using next generation platforms has greatly
 reduced the cost of genomic studies of non-model organisms, and the ESTs
 and microarrays reported here will accelerate evolutionary and molecular
 investigations of Compositae weeds. Our study also shows how ortholog
 comparisons can be used to quantify the genome-wide extent of
 introgression and to identify genes that have been exchanged between
 hybridizing taxa.
description: SAW-3Collection ID: SAW-3 |
 Taxon: Helianthus annuus L. | Common name: Common sunflower | Collection
 locality: Port Augusta, Australia (latitude 32.29, longitude 137.47) |
 Plant tissues employed for EST library development: Seedlings | Library
 type: Normalized | Sequence type: Illumina280808-2Collection ID: 280808-2 | Taxon: Cirsium arvense (L.) Scop. | Common name: Canada thistle | Collection locality: Female plant, Lugoj, Romania (latitude 45.65, longitude 21.95) | Plant tissues employed for EST library development: Leaves | Library type: Standard | Sequence type: IlluminaAA8-20Collection ID: AA8-20 | Taxon: Ambrosia artemisiifolia | Common name: Common ragweed | Collection locality: Russell, MN, USA (latitude 44.19, longitude -95.57) | Plant tissues employed for EST library development: Leaves | Library type: Normalized, Size-selected | Sequence type: 454AR-13-24Collection ID: AR-13-24 | Taxon: Centaurea solstitialis L. | Common name: Yellow starthistle | Collection locality: Santa Rosa, Argentina (latitude -37.39, longitude -64.08) | Plant tissues employed for EST library development: Leaves | Library type: Normalized, double-stranded | Sequence type: 454DK_TR001-1LCollection ID: DK_TR001-1L | Taxon: Centaurea diffusa Lam. | Common name: Diffuse knapweed | Collection locality: Kirklarelì, Turkey (latitude 41.45, longitude 27.14) | Plant tissues employed for EST library development: Leaves | Library type: Normalized, double-stranded | Sequence type: 454DK_US022-31ECollection ID: DK_US022-31E | Taxon: Centaurea diffusa Lam. | Common name: Diffuse knapweed | Collection locality: Roosevelt, WA, USA (latitude 45.44, longitude -120.12) | Plant tissues employed for EST library development: Leaves | Library type: Normalized, double-stranded | Sequence type: 454GNV8ASA01Collection ID: GNV8ASA01 | Taxon: Ambrosia trifida L. | Common name: Giant ragweed | Collection locality: Jilin, Jilin, China (latitude 43.50, longitude 126.32) | Plant tissues employed for EST library development: Roots, Leaves, Flower buds, Mature Flowers | Library type: Normalized, double-stranded | Sequence type: 454GNV8ASA02Collection ID: GNV8ASA02 | Taxon: Ambrosia trifida L. | Common name: Giant ragweed | Collection locality: Dengta, Liaoning, China (latitude 41.25, longitude 123. 20) | Plant tissues employed for EST library development: Roots, Leaves, Flower buds, Mature Flowers | Library type: Normalized, double-stranded | Sequence type: 454GNV8ASA03Collection ID: GNV8ASA03 | Taxon: Ambrosia trifida L. | Common name: Giant ragweed | Collection locality: Kampsville, IL, USA (latitude 39.16, longitude 90.37) | Plant tissues employed for EST library development: Roots, Leaves, Flower buds, Mature Flowers | Library type: Normalized, double-stranded | Sequence type: 454GNV8ASA04Collection ID: GNV8ASA04 | Taxon: Ambrosia trifida L. | Common name: Giant ragweed | Collection locality: Bloomington, IN, USA (latitude 39.92, longitude 86.31) | Plant tissues employed for EST library development: Roots, Leaves, Flower buds, Mature Flowers | Library type: Normalized, double-stranded | Sequence type: 454Hann_ISICollection ID: Hann_ISI | Taxon: Helianthus annuus L. | Common name: Common sunflower | Collection locality: Ma'ayan Tzvi, Israel (latitude 32.33, longitude 34.56) | Plant tissues employed for EST library development: Seedlings | Library type: Normalized, double-stranded | Sequence type: 454HU1-11Collection ID: HU1-11 | Taxon: Ambrosia artemisiifolia L. | Common name: Common ragweed | Collection locality: Biatorbagy, Hungary (latitude 47.46, longitude 18.81) | Plant tissues employed for EST library development: Leaves | Library type: Normalized, Size-selected | Sequence type: 454KN-ONCollection ID: KN-ON | Taxon: Cirsium arvense (L.) Scop. | Common name: Canada thistle | Collection locality: Male plant, Richmond Hill, ON, Canada (latitude 43.95, longitude -79.56) | Plant tissues employed for EST library development: Leaves | Library type: Standard | Sequence type: IlluminaNW-22-1-MCollection ID: NW-22-1-M | Taxon: Cirsium arvense (L.) Scop. | Common name: Canada thistle | Collection locality: Female plant, Fargo, ND, USA (latitude 46.93, longitude -96.86) | Plant tissues employed for EST library development: Roots, Leaves, Flower buds, Mature flowers | Library type: Normalized, double-stranded | Sequence type: 454PI407602Collection ID: PI407602 | Taxon: Carthamus oxyacanthus M. Bieb. | Common name: Jeweled distaff thistle | Collection locality: 38 km north of crossroad just west of Mardin, Turkey | Plant tissues employed for EST library development: Roots, Leaves, Mature Flowers | Library type: Normalized, double-stranded | Sequence type: 454