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Sampling the Waterhemp (Amaranthus tuberculatus) Genome Using Pyrosequencing Technology

Published online by Cambridge University Press:  20 January 2017

Ryan M. Lee
Affiliation:
Department of Crop Sciences, University of Illinois, 1201 W. Gregory Dr., Urbana, IL 61801
Jyothi Thimmapuram
Affiliation:
W. M. Keck Center for Comparative and Functional Genomics, University of Illinois, 1201 W. Gregory Dr., Urbana, IL 61801
Kate A. Thinglum
Affiliation:
Department of Crop Sciences, University of Illinois, 1201 W. Gregory Dr., Urbana, IL 61801
George Gong
Affiliation:
W. M. Keck Center for Comparative and Functional Genomics, University of Illinois, 1201 W. Gregory Dr., Urbana, IL 61801
Alvaro G. Hernandez
Affiliation:
W. M. Keck Center for Comparative and Functional Genomics, University of Illinois, 1201 W. Gregory Dr., Urbana, IL 61801
Chris L. Wright
Affiliation:
W. M. Keck Center for Comparative and Functional Genomics, University of Illinois, 1201 W. Gregory Dr., Urbana, IL 61801
Ryan W. Kim
Affiliation:
W. M. Keck Center for Comparative and Functional Genomics, University of Illinois, 1201 W. Gregory Dr., Urbana, IL 61801
Mark A. Mikel
Affiliation:
Roy J. Carver Biotechnology Center, University of Illinois, 1206 W. Gregory Dr., Urbana, IL 61801
Patrick J. Tranel
Affiliation:
Department of Crop Sciences, University of Illinois, 1201 W. Gregory Dr., Urbana, IL 61801
Corresponding
E-mail address:

Abstract

Recent advances in sequencing technologies (next-generation sequencing) offer dramatically increased sequencing throughput at a lower cost than traditional Sanger sequencing. This technology is changing genomics research by allowing large scale sequencing experiments in nonmodel systems. Waterhemp is an important weed in the midwestern United States with characteristics that makes it an interesting ecological model. However, very few genomic resources are available for this species. One half of a 70 by 75 picotiter plate of 454-pyrosequencing was performed on total DNA isolated from waterhemp, generating 158,015 reads of an average length of 271 bp, or a total of nearly 43 Mbp of sequence. Included in this sequence was a nearly complete sequence of the chloroplast genome, sequences of several important herbicide resistance genes, leads for simple sequence repeat (SSR) markers, and a sampling of the repeated elements (e.g., transposons) present in this species. Here we present the waterhemp genomic data gleaned from this sequencing experiment and illustrate the value of next-generation sequencing technology to weed science research.

Type
Physiology, Chemistry, and Biochemistry
Copyright
Copyright © Weed Science Society of America 

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