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Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression
Author(s) -
Lai Zhao,
Kane Nolan C.,
Kozik Alex,
Hodgins Kathryn A.,
Dlugosch Katrina M.,
Barker Michael S.,
Matvienko Marta,
Yu Qian,
Turner Kathryn G.,
Pearl Stephanie Anne,
Bell Graeme D. M.,
Zou Yi,
Grassa Chris,
Guggisberg Alessia,
Adams Keith L.,
Anderson James V.,
Horvath David P.,
Kesseli Richard V.,
Burke John M.,
Michelmore Richard W.,
Rieseberg Loren H.
Publication year - 2012
Publication title -
american journal of botany
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.218
H-Index - 151
eISSN - 1537-2197
pISSN - 0002-9122
DOI - 10.3732/ajb.1100313
Subject(s) - biology , introgression , dna microarray , genomics , genetics , genome , expressed sequence tag , sanger sequencing , dna sequencing , evolutionary biology , gene , gene expression
• Premise of 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 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.