Genomics of compositae weeds: EST libraries, microarrays, and evidence of introgression

Zhao Lai, Nolan C. Kane, Alex Kozik, Kathryn A. Hodgins, Katrina M. Dlugosch, Michael S. Barker, Marta Matvienko, Qian Yu, Kathryn G. Turner, Stephanie Anne Pearl, Graeme D.M. Bell, Yi Zou, Chris Grassa, Alessia Guggisberg, Keith L. Adams, James V. Anderson, David P. Horvath, Richard V. Kesseli, John M. Burke, Richard W. MichelmoreLoren H. Rieseberg

Research output: Contribution to journalArticle

62 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)209-218
Number of pages10
JournalAmerican journal of botany
Volume99
Issue number2
DOIs
StatePublished - Feb 2012

Keywords

  • Asteraceae
  • Compositae
  • ESTs
  • Hybridization
  • Introgression
  • Invasive plants
  • Microarray development
  • Next-generation sequencing
  • Sequence assemblies
  • Transcriptome sequencing
  • Weeds

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Plant Science

Fingerprint Dive into the research topics of 'Genomics of compositae weeds: EST libraries, microarrays, and evidence of introgression'. Together they form a unique fingerprint.

  • Cite this

    Lai, Z., Kane, N. C., Kozik, A., Hodgins, K. A., Dlugosch, K. M., Barker, M. S., Matvienko, M., Yu, Q., Turner, K. G., Pearl, S. A., Bell, G. D. M., Zou, Y., Grassa, C., Guggisberg, A., Adams, K. L., Anderson, J. V., Horvath, D. P., Kesseli, R. V., Burke, J. M., ... Rieseberg, L. H. (2012). Genomics of compositae weeds: EST libraries, microarrays, and evidence of introgression. American journal of botany, 99(2), 209-218. https://doi.org/10.3732/ajb.1100313