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Characterization of an EST Database for the Perennial Weed Leafy Spurge: An Important Resource for Weed Biology Research

Published online by Cambridge University Press:  20 January 2017

James V. Anderson*
Affiliation:
USDA-ARS, Biosciences Research Laboratory, 1605 Albrecht Boulevard, Fargo, ND 58105
David P. Horvath
Affiliation:
USDA-ARS, Biosciences Research Laboratory, 1605 Albrecht Boulevard, Fargo, ND 58105
Wun S. Chao
Affiliation:
USDA-ARS, Biosciences Research Laboratory, 1605 Albrecht Boulevard, Fargo, ND 58105
Michael E. Foley
Affiliation:
USDA-ARS, Biosciences Research Laboratory, 1605 Albrecht Boulevard, Fargo, ND 58105
Alvaro G. Hernandez
Affiliation:
University of Illinois, W. M. Keck Center for Comparative and Functional Genomics, 1201 West Gregory Drive, Edward R. Madigan Laboratory, Urbana, IL 61801
Jyothi Thimmapuram
Affiliation:
University of Illinois, W. M. Keck Center for Comparative and Functional Genomics, 1201 West Gregory Drive, Edward R. Madigan Laboratory, Urbana, IL 61801
Lie Liu
Affiliation:
University of Illinois, W. M. Keck Center for Comparative and Functional Genomics, 1201 West Gregory Drive, Edward R. Madigan Laboratory, Urbana, IL 61801
George L. Gong
Affiliation:
University of Illinois, W. M. Keck Center for Comparative and Functional Genomics, 1201 West Gregory Drive, Edward R. Madigan Laboratory, Urbana, IL 61801
Mark Band
Affiliation:
University of Illinois, W. M. Keck Center for Comparative and Functional Genomics, 1201 West Gregory Drive, Edward R. Madigan Laboratory, Urbana, IL 61801
Ryan Kim
Affiliation:
University of Illinois, W. M. Keck Center for Comparative and Functional Genomics, 1201 West Gregory Drive, Edward R. Madigan Laboratory, Urbana, IL 61801
Mark A. Mikel
Affiliation:
University of Illinois, Department of Crop Sciences and Roy J. Carver Biotechnology Center, 1206 West Gregory Drive, 2610 Institute for Genomic Biology, Urbana, IL 61801
*
Corresponding author's E-mail: James.Anderson@ars.usda.gov.

Abstract

Genomics programs in the weed science community have not developed as rapidly as that of other crop, horticultural, forestry, and model plant systems. Development of genomic resources for selected model weeds are expected to enhance our understanding of weed biology, just as they have in other plant systems. In this report, we describe the development, characteristics, and information gained from an expressed sequence tag (EST) database for the perennial weed leafy spurge. ESTs were obtained using a normalized cDNA library prepared from a comprehensive collection of tissues. During the EST characterization process, redundancy was minimized by periodic subtractions of the normalized cDNA library. A sequencing success rate of 88% yielded 45,314 ESTs with an average read length of 671 nucleotides. Using bioinformatic analysis, the leafy spurge EST database was assembled into 23,472 unique sequences representing 19,015 unigenes (10,293 clusters and 8,722 singletons). Blast similarity searches to the GenBank nonredundant protein database identified 18,186 total matches, of which 14,205 were nonredundant. These data indicate that 77.4% of the 23,472 unique sequences and 74.7% of the 19,015 unigenes are similar to other known proteins. Further bioinformatics analysis indicated that 2,950, or 15.5%, of the unigenes have previously not been identified suggesting that some may be novel to leafy spurge. Functional classifications assigned to leafy spurge unique sequences using Munich Information Center for Protein or Gene Ontology were proportional to functional classifications for genes of arabidopsis, with the exception of unclassified or unknowns and transposable elements which were significantly reduced in leafy spurge. Although these EST resources have been developed for the purpose of constructing high-density leafy spurge microarrays, they are already providing valuable information related to sugar metabolism, cell cycle regulation, dormancy, terpenoid secondary metabolism, and flowering.

Type
Weed Biology and Ecology
Copyright
Copyright © Weed Science Society of America 

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References

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