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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 ,
Jyothi Thimmapuram ,
Kate A. Thinglum ,
George Gong ,
Alvaro G. Hernandez ,
Chris L. Wright ,
Ryan W. Kim ,
Mark A. Mikel  and
Patrick J. Tranel
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 author's E-mail: [email protected]
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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.

Keywords

Common waterhemp, Amaranthus tuberculatus (Moq.) Sauer var. rudis (Sauer) Costea and Tardif AMATUTall waterhemp, Amaranthus tuberculatus (Moq.) Sauer var. tuberculatus (Sauer) Costea and Tardif AMATU.Herbicide resistancepyrosequencingnext-generation sequencinggenomicsDNA sequenceSSR
Type
Physiology, Chemistry, and Biochemistry
Information
Weed Science , Volume 57 , Issue 5 , October 2009 , pp. 463 - 469
Copyright
Copyright © Weed Science Society of America 

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References

Literature Cited

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403–410.Google Scholar
Arabidopsis Genome Initiative 2000. Analysis of the genome of the flowering plant Arabidopsis thaliana . Nature. 408:796–815.Google Scholar
Ashburner, M., Ball, C. A., Blake, J. A., et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25:25–29.Google Scholar
Bennetzen, J. L. 2000. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42:251–269.Google Scholar
Doyle, J. J. and Doyle, J. L. 1990. Isolation of plant DNA from fresh tissue. Focus. 12:13–15.Google Scholar
Finnegan, D. J. 1992. Transposable elements. Curr. Opin. Genet. Dev. 2:861–867.Google Scholar
Foes, M. J., Liu, L., Tranel, P. J., Wax, L. M., and Stoller, E. W. 1998. A biotype of common waterhemp (Amaranthus rudis) resistant to triazine and ALS herbicides. Weed Sci. 46:514–520.Google Scholar
Hager, A. G., Wax, L. M., Stoller, E. W., and Bollero, G. A. 2002. Common waterhemp (Amaranthus rudis) interference in soybean. Weed Sci. 50:607–610.Google Scholar
Heap, I. 2008. International Survey of Herbicide Resistant Weeds. www.weedscience.com. Accessed: December 15, 2008.Google Scholar
Kubo, T., Nishizawa, S., Sugawara, A., Itchoda, N., Estiati, A., and Mikami, T. 2000. The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNA(Cys)(GCA). Nucleic Acids Res. 28:2571–2576.Google Scholar
Lee, J. R., Hong, G. Y., Dixit, A., et al. 2008. Characterization of microsatellite loci developed for Amaranthus hypochondriacus and their cross-amplifications in wild species. Conserv. Genet. 9:243–246.Google Scholar
Legleiter, T. R. and Bradley, K. W. 2008. Glyphosate and multiple herbicide resistance in common waterhemp (Amaranthus rudis) populations from Missouri. Weed Sci. 56:582–587.Google Scholar
Lomsadze, A., Ter-Hovhannisyan, V., Chernoff, Y. O., and Borodovsky, M. 2005. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res. 33:6494–6506.Google Scholar
Lonsdale, D. M., Hodge, T. P., Howe, C. J., and Stern, D. B. 1983. Maize mitochondrial DNA contains a sequence homologous to the ribulose-1,5-bisphosphate carboxylase large subunit gene of chloroplast DNA. Cell. 34:1007–1014.Google Scholar
Mallory, M. A., Hall, R. V., McNabb, A. R., Pratt, D. B., Jellen, E. N., and Maughan, P. J. 2008. Development and characterization of microsatellite markers for the grain amaranths. Crop Sci. 48:1098–1106.Google Scholar
Mallory-Smith, C. A. and Retzinger, E. J. Jr. 2003. Revised classification of herbicides by sites of action for weed resistance management strategies. Weed Technol. 17:605–619.Google Scholar
Margulies, M., Egholm, M., Altman, W. E., et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 437:376–380.Google Scholar
Maughan, P. J., Sisneros, N., Luo, M., Kudrna, D., Ammiraju, J. S. S., and Wing, R. A. 2008. Construction of an Amaranthus hypochondriacus bacterial artificial chromosome library and genomic sequencing of herbicide target genes. Crop Sci. 48:S85–S94.Google Scholar
McClintock, B. 1951. Chromosome organization and genic expression. Cold Spring Harbor Symp. Quant. Biol. 16:13–47.Google Scholar
McClintock, B. 1984. The significance of responses of the genome to challenge. Science. 226:792–801.Google Scholar
Notsu, Y., Masood, S., Nishikawa, T., Kubo, N., Akiduki, G., Nakazono, M., Hirai, A., and Kadowaki, K. 2002. The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol. Genet. Genomics. 268:434–445.Google Scholar
Palmer, J. D., Adams, K. L., Cho, Y., Parkinson, C. L., Qiu, Y. L., and Song, K. 2000. Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proc. Natl. Acad. Sci. USA. 97:6960–6966.Google Scholar
Patzoldt, W. L., Hager, A. G., McCormick, J. S., and Tranel, P. J. 2006. A codon deletion confers resistance to herbicides inhibiting protoporphyrinogen oxidase. Proc. Natl. Acad. Sci. USA. 103:12329–12334.Google Scholar
Patzoldt, W. L., Tranel, P. J., and Hager, A. G. 2005. A waterhemp (Amaranthus tuberculatus) biotype with multiple resistance across three herbicide sites of action. Weed Sci. 53:30–36.Google Scholar
Rayburn, A. L., McCloskey, R., Tatum, T. C., Bollero, G. A., Jeschke, M. R., and Tranel, P. J. 2005. Genome size analysis of weedy Amaranthus species. Crop Sci. 45:2557–2562.Google Scholar
Rounsley, S., Marri, P. R., Yu, Y., et al. 2009. De novo next generation sequencing of plant genomes. Rice. 2:35–43.Google Scholar
Sanger, F., Air, G. M., Barrell, B. G., Brown, N. L., Coulson, A. R., Fiddes, C. A., Hutchison, C. A., Slocombe, P. M., and Smith, M. 1977. Nucleotide sequence of bacteriophage phi X174 DNA. Nature. 265:687–695.Google Scholar
SanMiguel, P., Gaut, B. S., Tikhonov, A., Nakajima, Y., and Bennetzen, J. L. 1998. The paleontology of intergene retrotransposons of maize. Nat. Genet. 20:43–45.Google Scholar
SanMiguel, P., Tikhonov, A., Jin, Y. K., et al. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science. 274:765–768.Google Scholar
Schmitz-Linneweber, C., Maier, R. M., Alcaraz, J. P., Cottet, A., Herrmann, R. G., and Mache, R. 2001. The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plant Mol. Biol. 45:307–315.Google Scholar
Sugiura, M. 2003. History of chloroplast genomics. Photosynth. Res. 76:371–377.Google Scholar
Turcotte, K., Srinivasan, S., and Bureau, T. 2001. Survey of transposable elements from rice genomic sequences. Plant J. 25:169–179.Google Scholar
Unseld, M., Marienfeld, J. R., Brandt, P., and Brennicke, A. 1997. The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nat Genet. 15:57–61.Google Scholar
Vera, J. C., Wheat, C. W., Fescemyer, H. W., Frilander, M. J., Crawford, D. L., Hanski, I., and Marden, J. H. 2008. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol. Ecol. 17:1636–1647.Google Scholar
Vitte, C. and Bennetzen, J. L. 2006. Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. Proc. Natl. Acad. Sci. USA. 103:17638–17643.Google Scholar