International Survey of Herbicide-Resistant Weeds

Countries Weeds Herbicides Mutations Graphs References Researchers

Genomic DNA Sequences that Encode for Herbicide Targets.

This database was created to (1) give quick access to the most common herbicide resistance genes across a wide range of weedy species and (2) provide a resource for researchers interested in discovering these gene sequences from weed species not listed here. See the notes below the table to find tools that may be useful for the latter objective.

Darci Giacomini is the curator of this information.  She is affiliated with the University of Illinois and Monsanto.
University of Illinois 320 ERML 1201 W. Gregory Drive Urbana, IL 61801 dagiac@illinois.edu

To add a new sequence, add further information to an existing case, point out an error, or just comment please click here.

SEE NOTES INCLUDING A DISCLAIMER AND T-COFFEE BELOW THE TABLE FOR A DEFINITION OF THE TARGETS

Click on the links in the table to see the full sequence and other details.
#SpeciesEPSPSGSACCaseALSHPPDPDSPPO (PPX1)
1 Abutilon theophrasticDNAcDNAcDNAcDNA cDNAcDNA 
2 Aegilops cylindricacDNA  cDNA    
3 Alnus glutinosacDNA cDNA     
4 Alopecurus japonicuscDNA  cDNA    
5 Alopecurus myosuroidescDNA  cDNAcDNA   
6 Amaranthus albuscDNA cDNA    cDNA
7 Amaranthus blitoidescDNA   cDNA   
8 Amaranthus chlorostachyscDNA cDNA cDNA   
9 Amaranthus graecizanscDNAcDNAcDNAcDNAcDNAcDNAcDNAcDNA
10 Amaranthus hybriduscDNAcDNAcDNAcDNAcDNAcDNAcDNAcDNA
11 Amaranthus hypochondriacus cDNA   cDNA   
12 Amaranthus lividuscDNAcDNAcDNAcDNAcDNA cDNAcDNA
13 Amaranthus palmericDNAcDNAcDNAcDNAcDNAcDNAcDNAcDNA
14 Amaranthus powelliicDNA   cDNA   
15 Amaranthus quitensiscDNA   cDNA   
16 Amaranthus retroflexuscDNA   cDNA   
17 Amaranthus rudiscDNAcDNAcDNAcDNAcDNAcDNAcDNAcDNA
18 Amaranthus spinosuscDNAcDNAcDNAcDNAcDNA cDNAcDNA
19 Amaranthus thunbergiicDNAcDNAcDNAcDNAcDNAcDNA cDNA
20 Amaranthus tuberculatuscDNAcDNA  cDNAcDNA  
21 Amaranthus viridiscDNAcDNAcDNAcDNAcDNAcDNAcDNAcDNA
22 Ambrosia artemisiifoliacDNAcDNAcDNA cDNA  cDNA
23 Ambrosia trifidacDNAcDNAcDNAcDNAcDNAcDNAcDNAcDNA
24 Anthemis cotulacDNA   cDNA   
25 Apera spica-venticDNA  cDNAcDNA   
26 Arabidopsis thalianacDNAcDNAcDNAcDNAcDNAcDNAcDNAcDNA
27 Avena fatuacDNA  cDNA    
28 Bacopa rotundifoliacDNA   cDNA   
29 Bidens subalternanscDNA   cDNA   
30 Brassica rapacDNA cDNA     
31 Bromus arvensiscDNA  cDNA    
32 Bromus diandrus cDNA  cDNA    
33 Bromus lanceolatuscDNA  cDNA    
34 Bromus secalinuscDNA  cDNA    
35 Bromus squarrosuscDNA  cDNA    
36 Bromus tectorumcDNA   cDNA   
37 Camelina microcarpacDNA   cDNA   
38 Camelina sativa cDNA   cDNA   
39 Capsella bursa-pastoriscDNA   cDNA   
40 Chenopodium albumcDNAcDNAcDNA cDNA   
41 Cirsium setosumcDNAcDNA      
42 Commelina diffusacDNAcDNAcDNAcDNA    
43 Convolvulus arvensiscDNAcDNAcDNA     
44 Conyza canadensiscDNAcDNAcDNAcDNAcDNAcDNAcDNAcDNA
45 Conyza sumatrensiscDNAcDNA      
46 Cyperus difformiscDNA   cDNA   
47 Dactylis glomeratacDNA  cDNA    
48 Dasypyrum villosumcDNA  cDNA    
49 Descurainia sophiacDNA   cDNA   
50 Digitaria ischaemumcDNA  cDNA    
51 Digitaria sanguinaliscDNAcDNAcDNAcDNA cDNA cDNA
52 Echinochloa crus-galli cDNA  cDNAcDNA   
53 Echinochloa phyllopogoncDNA   cDNA   
54 Eleusine indicacDNAcDNA      
55 Erigeron annuuscDNAcDNA      
56 Euphorbia heterophyllacDNAcDNAcDNAcDNAcDNAcDNA cDNA
57 Fallopia convolvuluscDNA   cDNA   
58 Festuca arundinaceacDNA  cDNA    
59 Galium spurium cDNA   cDNA   
60 Glycine maxcDNAcDNAcDNAcDNAcDNAcDNAcDNAcDNA
61 Gossypium hirsutumcDNAcDNA    cDNA 
62 Hordeum murinumcDNA   cDNA   
63 Kochia scopariacDNAcDNAcDNAcDNAcDNAcDNAcDNAcDNA
64 Lolium multiflorumcDNAcDNAcDNA cDNAcDNAcDNAcDNA
65 Lolium perennecDNA cDNA     
66 Lolium rigidumcDNAcDNA cDNA cDNA  
67 Medicago sativacDNA  cDNA    
68 Nicotiana benthamianacDNA     cDNA 
69 Nicotiana tabacumcDNAcDNAcDNA cDNA cDNAcDNA
70 Nymphaea albacDNAcDNA      
71 Oryza sativacDNAcDNAcDNA cDNAcDNAcDNAcDNA
72 Panicum capillarecDNA  cDNA    
73 Petunia x hybridacDNAcDNA      
74 Phalaris paradoxacDNA  cDNA    
75 Plantago lanceolatacDNAcDNA      
76 Poa annuacDNA  cDNA    
77 Polypogon fugaxcDNA  cDNA    
78 Raphanus raphanistrumcDNA   cDNA   
79 Setaria viridiscDNA  cDNAcDNA   
80 Sinapis arvensiscDNA   cDNA   
81 Solanum lycopersicumcDNAcDNAcDNAcDNAcDNAcDNAcDNAcDNA
82 Solanum tuberosumcDNA     cDNAcDNA
83 Sorghum halepensecDNAcDNA cDNA    
84 Tragus racemosuscDNA  cDNA    
85 Triticum aestivumcDNAcDNAcDNAcDNAcDNAcDNAcDNAcDNA
86 Xanthium strumariumcDNA  cDNA cDNA  
87 Zea mayscDNAcDNAcDNAcDNAcDNAcDNAcDNAcDNA

NOTES

The targets are:

EPSPS - 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase is an enzyme that catalyzes the chemical reaction: phosphoenolpyruvate + 3-phosphoshikimate <----> phosphate + 5-enolpyruvylshikimate-3-phosphate (EPSP).

GS - Glutamine synthetase is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine: Glutamate + ATP + NH3 → Glutamine + ADP + phosphate

ACCase - Acetyl-CoA carboxylase is a biotin-dependent enzyme that catalyzes the irreversible carboxylation of acetyl-CoA to produce malonyl-CoA through its two catalytic activities, biotin carboxylase (BC) and carboxyltransferase (CT).

ALS - acetolactate synthase (ALS) enzyme (also known as acetohydroxy acid synthase, or AHAS) catalyzes the first step in the synthesis of the branched-chain amino acids (valine, leucine, and isoleucine).

HPPD - 4-Hydroxyphenylpyruvate dioxygenase is an enzyme found in both plants and animals which catalyzes the catabolism of the amino acid tyrosine.

PDS - Phytoene desaturase is an enzyme required in the biosynthesis of carotenoids which inturn play an important role in dissipating the oxidative energy of singlet O2 (1O2).

PPO - Protoporphyrinogen oxidase (PPG oxidase or Protox) is an enzyme of chlorophyll and heme biosynthesis catalyzing the oxidation of protoporphyrinogen IX (PPGIX) to protoporphyrin IX (PPIX).

T-Coffee (Tree-based Consistency Objective Function For alignment Evaluation) is a multiple sequence alignment software. It generates a library of pairwise alignments to guide the multiple sequence alignment. 

 

Please cite these results as: Giacomini,D., Heap, I., and Sammons, R.D. T-Coffee Alignments of Herbicide Target Genes.

 

Click on the following links to see T-Coffee alignment for these targets:

EPSPS_Tcoffee : GS_Tcoffee : ACCase_Tcoffee : ALS_Tcoffee : HPPD_Tcoffee : PDS_Tcoffee : PPO_Tcoffee


The sequences included in this database were collected from the USPTO Patent Full-Text Database (http://patft.uspto.gov/netahtml/PTO/index.html) and the NCBI nucleotide collection (http://www.ncbi.nlm.nih.gov/nuccore).

Some gene sequences were available in both the USPTO and NCBI databases. In these cases, the most complete sequence was included here.

Researchers interested in discovering these gene sequences from weed species not listed here may find the following tools and resources useful:

Designing degenerate primers – Instructions

A Primer for Designing Degenerate Primers http://cichlid.umd.edu/cichlidlabs/protocols/Basic/pcrdegenpri.html

Designing degenerate primers – Tools

SMS reverse translate (convert protein sequence to nucleotide sequence) http://www.bioinformatics.org/sms2/rev_trans.html

Genefisher2 (web-based program for designing degenerate primers) http://bibiserv2.cebitec.uni-bielefeld.de/genefisher2

CODEHOP (another web-based program for designing degenerate primers) http://blocks.fhcrc.org/codehop.html

HYDEN (downloadable batch program for designing degenerate primers) http://acgt.cs.tau.ac.il/hyden/

Additional Computational Links:

iPlant Collaborative: The iPlant Collaborative is a NSF-funded project that gives researchers in the plant sciences easy access to bioinformatics tools. Users can securely store terabytes of data and run this data quickly through iPlant's analysis tools and workflows without the need to go through a command-line interface. http://www.iplantcollaborative.org/

ConSurf: The ConSurf server allows users to align a set of nucleotide or protein sequences and estimate the evolutionary conservation of these residues. The conservation scores can be superimposed onto a crystal structure of the protein under investigation (if the structure is known) to visualize the protein in 3-D. http://consurf.tau.ac.il/

NCBI Blast: The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. http://blast.ncbi.nlm.nih.gov/Blast.cgi

To add a new sequence, add further information to an existing case, point out an error, or just comment please click here.

Disclaimer

A few entries contain only partial gene sequences or have a string of “N”s in the middle of their sequence. These “N” characters represent unknown nucleotides and are a result of sequence ambiguity at those positions. In cases where more than one allele per gene is documented per species, the most complete sequence was included. The sequences contained within this database are pulled directly from multiple public sources, including, but not limited to, GenBank, EMBL, USPTO, USPTO PSIPS, and EPO. Data from these sources have been prepared with a reasonable standard of care, but no guarantee of accuracy is made. If a more accurate sequence is available, but not currently shown on this site, please contact the database curator. Colorado State University and Monsanto lay no claim to the information provided within and all persons making use of this data are expected to adhere to the terms and conditions asserted by the authors/creators.

PERMISSION MUST BE OBTAINED FIRST if you intend to base a significant portion of a scientific paper on data derived from this site.
Cite this site as: Heap, I.  The International Survey of Herbicide Resistant Weeds.  Online.  Internet.  Sunday, July 23, 2017 .  Available  www.weedscience.org
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