Characterization of <i>de novo</i> transcriptome for waterhemp (<i>Amaranthus tuberculatus</i>) using GS‐FLX 454 pyrosequencing and its application for studies of herbicide target‐site genes

Riggins, Chance W.; Peng, Yanhui; Stewart, C. Neal; Tranel, Patrick J.

doi:10.1002/ps.2006

Cited by 83 publications

(85 citation statements)

References 41 publications

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“…An altered target site was hypothesized to confer resistance in MCR as one of several potential mechanisms. In accord with our previous transcriptome study (Riggins et al, 2010), a single expressed HPPD gene was detected in waterhemp. The WCS HPPD coding sequence, which is 1,305 bp in length, is deposited in GenBank as accession JX259255.…”

Section: Hppd Target Site Analysessupporting

confidence: 88%

“…A nearly full-length HPPD sequence was first identified from the waterhemp transcriptome data set (Riggins et al, 2010). However, the 59 end was missing from this data set, so a full-length wild-type sequence from a mesotrionesensitive waterhemp individual was obtained by creating and screening a complementary DNA library using the Creator SMART cDNA library construction kit from Clontech.…”

Section: Hppd and Psba Gene Identificationmentioning

confidence: 99%

“…Primers for obtaining the full-length chloroplastic psbA gene in waterhemp were designed from shotgun genomic sequence data (Lee et al, 2009) and are listed in Supplemental Table S1. PCR protocols for amplifying and sequencing both genes are the same as provided by Riggins et al (2010).…”

Section: Hppd and Psba Gene Identificationmentioning

confidence: 99%

“…Molecular information regarding plant HPPD gene sequences and expression patterns is limited (for review, see Pallett, 2000;Kim and Petersen, 2002;Riechers and Stanford, 2002;Matringe et al, 2005), and only a single expressed HPPD gene was detected in waterhemp (Riggins et al, 2010). Herbicidal activity of mesotrione in sensitive plants is due to competitive inhibition of the HPPD enzyme, which is a key enzyme in the biosynthesis of tocopherols and plastoquinone.…”

mentioning

confidence: 99%

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Distinct Detoxification Mechanisms Confer Resistance to Mesotrione and Atrazine in a Population of Waterhemp

et al. 2013

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Previous research reported the first case of resistance to mesotrione and other 4-hydroxyphenylpyruvate dioxygenase (HPPD) herbicides in a waterhemp (Amaranthus tuberculatus) population designated MCR (for McLean County mesotrione-and atrazineresistant). Herein, experiments were conducted to determine if target site or nontarget site mechanisms confer mesotrione resistance in MCR. Additionally, the basis for atrazine resistance was investigated in MCR and an atrazine-resistant but mesotrione-sensitive population (ACR for Adams County mesotrione-sensitive but atrazine-resistant). A standard sensitive population (WCS for Wayne County herbicide-sensitive) was also used for comparison. Mesotrione resistance was not due to an alteration in HPPD sequence, HPPD expression, or reduced herbicide absorption. Metabolism studies using whole plants and excised leaves revealed that the time for 50% of absorbed mesotrione to degrade in MCR was significantly shorter than in ACR and WCS, which correlated with previous phenotypic responses to mesotrione and the quantity of the metabolite 4-hydroxy-mesotrione in excised leaves. The cytochrome P450 monooxygenase inhibitors malathion and tetcyclacis significantly reduced mesotrione metabolism in MCR and corn (Zea mays) excised leaves but not in ACR. Furthermore, malathion increased mesotrione activity in MCR seedlings in greenhouse studies. These results indicate that enhanced oxidative metabolism contributes significantly to mesotrione resistance in MCR. Sequence analysis of atrazine-resistant (MCR and ACR) and atrazine-sensitive (WCS) waterhemp populations detected no differences in the psbA gene. The times for 50% of absorbed atrazine to degrade in corn, MCR, and ACR leaves were shorter than in WCS, and a polar metabolite of atrazine was detected in corn, MCR, and ACR that cochromatographed with a synthetic atrazineglutathione conjugate. Thus, elevated rates of metabolism via distinct detoxification mechanisms contribute to mesotrione and atrazine resistance within the MCR population.

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Section: Hppd Target Site Analysessupporting

confidence: 88%

Section: Hppd and Psba Gene Identificationmentioning

confidence: 99%

Section: Hppd and Psba Gene Identificationmentioning

confidence: 99%

mentioning

confidence: 99%

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Distinct Detoxification Mechanisms Confer Resistance to Mesotrione and Atrazine in a Population of Waterhemp

et al. 2013

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“…To date, transcriptomes using next-generation sequencing of a few weedy species have been produced to aid the discovery of genes that contribute to herbicide resistance and other weediness traits, with most progress occurring in Conyza and Amaranthus spp. and Lolium rigidum (Lee et al, 2009;Peng et al, 2010;Riggins et al, 2010;Lai et al, 2012;Gaines et al, 2014).…”

mentioning

confidence: 99%

De Novo Genome Assembly of the Economically Important Weed Horseweed Using Integrated Data from Multiple Sequencing Platforms

et al. 2014

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Horseweed (Conyza canadensis), a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate. Horseweed, one of the most problematic weeds in the world, is a true diploid (2n = 2x = 18), with the smallest genome of any known agricultural weed (335 Mb). Thus, it is an appropriate candidate to help us understand the genetic and genomic bases of weediness. We undertook a draft de novo genome assembly of horseweed by combining data from multiple sequencing platforms (454 GS-FLX, Illumina HiSeq 2000, and PacBio RS) using various libraries with different insertion sizes (approximately 350 bp, 600 bp, 3 kb, and 10 kb) of a Tennessee-accessed, glyphosate-resistant horseweed biotype. From 116.3 Gb (approximately 3503 coverage) of data, the genome was assembled into 13,966 scaffolds with 50% of the assembly = 33,561 bp. The assembly covered 92.3% of the genome, including the complete chloroplast genome (approximately 153 kb) and a nearly complete mitochondrial genome (approximately 450 kb in 120 scaffolds). The nuclear genome is composed of 44,592 protein-coding genes. Genome resequencing of seven additional horseweed biotypes was performed. These sequence data were assembled and used to analyze genome variation. Simple sequence repeat and single-nucleotide polymorphisms were surveyed. Genomic patterns were detected that associated with glyphosate-resistant or -susceptible biotypes. The draft genome will be useful to better understand weediness and the evolution of herbicide resistance and to devise new management strategies. The genome will also be useful as another reference genome in the Compositae. To our knowledge, this article represents the first published draft genome of an agricultural weed.

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Corn‐Soybean and Rice‐Corn‐Soybean Cropping Systems

2023

Weed Science and Weed Management in Rice and Cereal‐Based Cropping Systems

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Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS‐FLX 454 pyrosequencing and its application for studies of herbicide target‐site genes

Cited by 83 publications

References 41 publications

Distinct Detoxification Mechanisms Confer Resistance to Mesotrione and Atrazine in a Population of Waterhemp

Distinct Detoxification Mechanisms Confer Resistance to Mesotrione and Atrazine in a Population of Waterhemp

De Novo Genome Assembly of the Economically Important Weed Horseweed Using Integrated Data from Multiple Sequencing Platforms

Corn‐Soybean and Rice‐Corn‐Soybean Cropping Systems

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