title: Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression.
abstract: OBJECTIVE
  Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we describe 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. When 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 nonmodel 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 approximately estimate the genome-wide extent of introgression and to identify genes that have been exchanged between hybridizing taxa.
authors: Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana 47405, USA.
authors: Zhao
authors: Z
authors: Lai
authors: Nolan C
authors: NC
authors: Kane
authors: Alex
authors: A
authors: Kozik
authors: Kathryn A
authors: KA
authors: Hodgins
authors: Katrina M
authors: KM
authors: Dlugosch
authors: Michael S
authors: MS
authors: Barker
authors: Marta
authors: M
authors: Matvienko
authors: Qian
authors: Q
authors: Yu
authors: Kathryn G
authors: KG
authors: Turner
authors: Stephanie Anne
authors: SA
authors: Pearl
authors: Graeme D M
authors: GD
authors: Bell
authors: Yi
authors: Y
authors: Zou
authors: Chris
authors: C
authors: Grassa
authors: Alessia
authors: A
authors: Guggisberg
authors: Keith L
authors: KL
authors: Adams
authors: James V
authors: JV
authors: Anderson
authors: David P
authors: DP
authors: Horvath
authors: Richard V
authors: RV
authors: Kesseli
authors: John M
authors: JM
authors: Burke
authors: Richard W
authors: RW
authors: Michelmore
authors: Loren H
authors: LH
authors: Rieseberg
mesh_terms: D019659:Asteraceae / Q000235:genetics*; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D015723:Gene Library; D014644:Genetic Variation; D023281:Genomics / Q000379:methods*; D006824:Hybridization, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D018749:RNA, Plant / Q000235:genetics
chemical_list: D018076:DNA, Complementary; D018749:RNA, Plant