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 Citations (Scopus)

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

Fingerprint

Asteraceae
Expressed Sequence Tags
introgression
Genomics
expressed sequence tags
weed
genomics
Centaurea
weeds
Ambrosia
Metagenomics
Helianthus
Genetic Association Studies
Microarray Analysis
Gene Library
Transcriptome
hybridization
Economics
Genome
Costs and Cost Analysis

Keywords

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

ASJC Scopus subject areas

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

Cite this

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

In: American Journal of Botany, Vol. 99, No. 2, 02.2012, p. 209-218.

Research output: Contribution to journalArticle

Lai, Z, Kane, NC, Kozik, A, Hodgins, KA, Dlugosch, KM, Barker, MS, Matvienko, M, Yu, Q, Turner, KG, Pearl, SA, Bell, GDM, Zou, Y, Grassa, C, Guggisberg, A, Adams, KL, Anderson, JV, Horvath, DP, Kesseli, RV, Burke, JM, Michelmore, RW & Rieseberg, LH 2012, 'Genomics of compositae weeds: EST libraries, microarrays, and evidence of introgression', American Journal of Botany, vol. 99, no. 2, pp. 209-218. https://doi.org/10.3732/ajb.1100313
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. / Genomics of compositae weeds : EST libraries, microarrays, and evidence of introgression. In: American Journal of Botany. 2012 ; Vol. 99, No. 2. pp. 209-218.
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