Abe H, Urao T, Seki M, Yamaguchi-Shinozaki S K. 2003. Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. The Plant Cell, 15, 63–78.
Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K. 1997. Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. The Plant Cell, 9, 1859–1868.
Altschul S F, Gish W, Miller W, Myers E W, Lipman D J. 1990. Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410.
Anders S, Huber W. 2012. Differential Expression of RNA-Seq Data at the Gene Level - the Deseq Package. European Molecular Biology Laboratory, Heidelberg.
Baerson S R, Rodriguez D J, Tran M, Feng Y, Biest N A, Dill G M. 2002. Identification of a mutation in the target enzyme 5-enolpyruvylshikimate-3-phosphate synthase. Plant Physiology, 129, 1265–1275.
Bao J, Corke H, Sun M. 2002. Microsatellites in starch-synthesizing genes in relation to starch physicochemical properties in waxy rice (Oryza sativa L.). Theoretical and Applied Genetics, 105, 898–905.
Bevilacqua A, Fiorenza M T, Mangia F. 2000. A developmentally regulated GAGA box-binding factor and Sp1 are required for transcription of the hsp70.1 gene at the onset of mouse zygotic genome activation. Development, 127, 1541–1551.
Bilaud T, Koering C E, Binet-Brasselet E, Ancelin K, Pollice A, Gasser S M, Gilson E. 1996. The telobox, a myb-related telomeric DNA binding motif found in proteins from yeast, plants and human. Nucleic Acids Research, 24, 1294–1303.
Bolger A M, Marc L, Bjoern U. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 15, 2114–2120.
Castillo-Davis C I. 2005. The evolution of noncoding DNA: How much junk, how much func? Trends in Genetics, 21, 533–536.
Croston G E, Kerrigan L A, Lira L M, Marshak D R, Kadonaga J T. 1991. Sequence-specific antirepression of histone H1-mediated inhibition of basal RNA polymerase II transcription. Science, 251, 643–649.
Dinelli G, Marotti I, Bonetti A, Minelli M, Catizone P, Barnes J. 2006. Physiological and molecular insight on the mechanisms of resistance to glyphosate in Conyza canadensis (L.) Cronq. Biotypes. Pesticide Biochemistry and Physiology, 86, 30–41.
Duke S O, Powles S B, Sammons R D. 2018. Glyphosate - how it became a once in a hundred year herbicide and its future. Outlooks on Pest Management, 29, 247–251.
Gaines T A, Zhang W, Wang D, Bukun B, Chisholm S T, Shaner D L, Nissen S J, Patzoldt W L, Tranel P J, Culpepper A S, Grey T L, Webster T M, Vencill W K, Sammons R D, Jiang J M, Preston C, Leach J E, Westra P. 2010. Gene amplification confers glyphosate resistance in Amaranthus palmeri. Proceedings of the National Academy of Sciences of the United States of America, 107, 1029–1034.
Gilmour S J, Sebolt A M, Salazar M P, Everard J D, Thomashow M F. 2000. Overexpression of the Arabidopsis CBF3 transcriptional activator mimics multiple biochemical changes associated with cold acclimation. Plant Physiology, 124, 1854–1865.
Grabherr M G, Haas B J, Yassour M, Levin J Z, Thompson D A, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q D. 2011. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature Biotechnology, 29, 644–652.
Heap I. 2021. The international survey of herbicide resistant weeds. [2021-01-09]. http://www.weedscience.org
Huang Z F, Wang G R, Huang H G, Wei S H, Zhou X X, Chen J Y, Zhang C X. 2015. Isolation and functional analysis of Convolvulus arvensis EPSPS promoter. Plant Molecular Biology Reporter, 33, 1–9.
Joshi-Saha A, Reddy K S. 2015. Repeat length variation in the 5´ UTR of myo-inositol monophosphatase gene is related to phytic acid content and contributes to drought tolerance in chickpea (Cicer arietinum L.). Journal of Experimental Botany, 6619, 5683–5690.
Kalluri U C, DiFazio S P, Brunner A M, Tuskan G A. 2007. Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. BMC Plant Biology, 7, 59.
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Research, 36, 480–484.
Kashi Y, King D, Soller M. 1997. Simple sequence repeats as a source of quantitative genetic variation. Trends in Genetics, 13, 74–78.
Kumar R, Tyagi A K, Sharma A K. 2011. Genome-wide analysis of auxin response factor (ARF) gene family from tomato and analysis of their role in flower and fruit development. Molecular Genetics and Genomics, 285, 245–260.
Kumar S, Bhatia S. 2016. A polymorphic (GA/CT)n-SSR influences promoter activity of Tryptophan decarboxylase gene in Catharanthus roseus L. Don. Scientific Reports, 6, 33280.
Langmead B, Salzberg S L. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357–366.
Lu Q, Wallrath L L, Granok H, Elgin S C. 1993. (CT)n (GA)n
repeats and heat shock elements have distinct roles in chromatin structure and transcriptional activation of the Drosophila hsp26 gene. Molecular and Cellular Biology, 13, 2802–2814.
Maeda H, Dudareva N. 2012. The shikimate pathway and aromatic amino acid biosynthesis in plants. Annual Review of Plant Biology, 63, 73–105.
Meister R J, Williams L A, Monfared M M, Gallagher T L, Kraft E A, Nelson C G, Gasser C S. 2004. Definition and interactions of a positive regulatory element of the Arabidopsis inner no outer promoter. Plant Journal, 37, 426–438.
Melfi R, Palla F, Di Simone P, Alessandro C, Cali L, Anello L, Spinelli G. 2000. Functional characterization of the enhancer blocking element of the sea urchin early histone gene cluster reveals insulator properties and three essential cis-acting sequences. Journal of Molecular Biology, 304, 753–763.
Mohammadparast S, Bayat H, Biglarian A, Ohadi M. 2014. Exceptional expansion and conservation of a CT-repeat complex in the core promoter of PAXBP1 in primates. American Journal of Primatology, 76, 747–756.
Ni M, James M, Tepperman J M, Quail P H. 1999. Binding of phytochrome B to its nuclear signalling partner PIF3 is reversibly induced by light. Nature, 400, 781–784.
Ni M, Tepperman J M, Quail P H. 1998. PIF3, a phytochrome interacting factor necessary for normal photo induced signal transduction is a novel basic helix-lop-helix protein. Cell, 95, 657–667.
Nole-Wilson S, Krizek B A. 2000. DNA binding properties of the Arabidopsis floral development protein AINTTGUMENTA. Nucleic Acids Research, 28, 4076–4082.
Ogo Y, Itai R N, Nakanishi H, Kobayashi T, Takahashi M, Mori S, Nishizawa N K. 2007. The rice bHLH protein OsIRO2 is an essential regulator of the genes involved in Fe uptake under Fe-deficient conditions. The Plant Journal, 51, 366–377.
Quattrocchio F, Wing J, Woude K V D, Souer E, Vetten N D, Mol J, Koes R. 1999. Molecular analysis of the anthocyanin2 gene of petunia and its role in the evolution of flower color. The Plant Cell, 11, 1433–1444.
Roberts A, Pachter L. 2013. Streaming fragment assignment for real-time analysis of sequencing experiments. Nature Methods, 10, 71–73.
Sammons D R, Gaines T A. 2014. Glyphosate resistance: State of knowledge. Pest Management Science, 70, 1367–1377.
Sangwan I, O’Brian M R. 2002. Identification of a soybean protein that interacts with GAGA element dinucleotide repeat DNA. Plant Physiology, 129, 1788–1794.
Santi L, Wang Y, Stile M R, Berendzen K, Wanke D, Roig C, Pozzi C, Müller K, Müller J, Rohde W, Salamini F. 2003. The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3. Plant Journal, 34, 813–826.
Shang Y, Yan L, Liu Z Q, Cao Z, Mei C, Xin Q, Wu F Q, Wang X F, Du S Y, Jiang T, Zhang X F, Zhao R, Sun H L, Liu R, Yu Y T, Zhang D P. 2010. The Mg-chelatase H subunit of Arabidopsis anta gonizes a group of WRKY transcription repressors to relieve ABA-responsive genes of inhibition. The Plant Cell, 22, 1909–1935.
Shanks C M, Hecker A, Cheng C Y, Brand L, Collani S, Schmid M, Schaller G, Wanke D, Harter K, Kieber J J. 2018. Role of BASIC PENTACYSTEINE transcription factors in a subset of cytokinin signaling responses. Plant Journal, 95, 458–473.
Sharkhuu A, Narasimhan M L, Merzaban J S, Bressan R A, Weller S, Gehring C. 2014. A red and far-red light receptor mutation confers resistance to the herbicide glyphosate. The Plant Journal, 78, 916–926.
Silva D R O, Vargas L, Agostinetto D, Santos F M. 2017. Photosynthetic performance of glyphosate resistant and glyphosate susceptible hairy fleabane under light intensity. Planta Daninha, 35, e017166275.
Simar-Blanchet A E, Legraverend C, Thissen J P, Cam A L. 1998. Transcription of the rat serine protease inhibitor 2.1 gene in vivo: Correlation with GAGA box promoter occupancy and mechanism of cytokinemediated down-regulation. Molecular Endocrinology, 12, 391–404.
Singh K B. 1998. Transcriptional regulation in plants: The importance of combinatorial control. Plant Physiology, 118, 1111–1120.
Sreenivasulu M, Ramesh P, Damodharam T. 2015. Effect of glyphosate on chlorophyll and carotenoids in weed species. International Journal of Advanced Scientific and Technical Research, 5, 2249–2254.
Sweeney M T, Thomson M J, Pfeil B E, McCouch S. 2006. Caught red-Handed: Rc encodes a basic helix-lop-helix protein conditioning red pericarp in rice. The Plant Cell, 18, 283–294.
Trapnell C, Williams B A, Petea G, Mortazavi A, Kwan G, Baren M J V, Salzberg S L, Wold B J, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 28, 511–515.
Trifonov E N. 2004. Tuning function of tandemly repeating sequences: A molecular device for fast adaptation. In: Wasser S P, ed., Evolutionary Theory and Processes: Modern Horizons. Springer, Dordrecht. pp. 115–138.
Tsukiyama T, Becker P B, Wu C. 1994. ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor. Nature, 367, 525–532.
Tsukiyama T, Wu C. 1995. Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell, 83, 1011–1020.
Tzin V, Galili G. 2010. New insights into the shikimate and aromatic amino acids biosynthesis pathways in plants. Molecular Plant, 3, 956–972.
Viana A A, Fragoso R R, Guimarães L M, Pontes N, Oliveira-neto O B, Artico S Nardeli S M, Alves-Ferreira M, Batista J A N, Silva M C M, Grossi-de-Sa M F. 2011. Isolation and functional characterization of a cotton ubiquitination-related promoter and 5´UTR that drives high levels of expression in root and flower tissues. BMC Biotechnology, 11, 115.
Vinces M D, Legendre M, Caldara M, Hagihara M, Verstreoen K J. 2009. UnsTable tandem repeats in promoters center transcriptional evolvability. Science, 324, 1213–1216.
Wiersma A T, Gaines T A, Preston C, Hamilton J P, Giacomini D, Buell C R, Leach J E, Westra P. 2015. Gene amplification of 5-enol-pyruvylshikimate-3-phosphate synthase in glyphosate-resistant Kochia scoparia. Planta, 41, 463–474.
Wyse B D, Linas S L, Thekkumkara T J. 2000. Functional role of a novel cis-acting element (GAGA box) in human type-1 angiotensin II receptor gene transcription. Journal of Molecular Endocrinology, 25, 97–108.
Ye J, Zhang Y, Cui H, Liu J, Wu Y, Cheng Y, Xu H, Huang X, Li S, Zhou A, Zhang X, Bolund L, Chen Q, Wang J, Yang H, Fang L, Shi C. 2018. WEGO 2.0: A web tool for analyzing and plotting GO annotations. Nucleic Acids Research, 46, W71–W75.
Yu Q, Jalaludin A, Han H, Chen M, Sammons R D, Powles S B. 2015. Evolution of a double amino acid substitution in the 5-enolpyruvylshikimate-3-phosphate synthase in Eleusine indica conferring high-level glyphosate resistance. Plant Physiology, 167, 1440–1447.
Yuan C I, Chaing M Y, Chen Y M. 2002. Triple mechanisms of glyphosate-resistance in a naturally occurring glyphosate-resistant plant Dicliptera chinensis. Plant Science, 163, 543–554.
Zhang C, Feng L, He T T, Yang C H, Chen G Q, Tian X S. 2015. Investigating the mechanisms of glyphosate resistance in goosegrass (Eleusine indica) population from South China. Journal of Integrative Agriculture, 14, 714–723.
Zhang C, Feng L, Tian X S. 2018. Alterations in the 5´ untranslated region of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene influence EPSPS overexpression in glyphosate-resistant Eleusine indica. Pest Management Science, 74, 2561–2568.
Zhang T J, Feng L, Tian X S, Yang C H, Gao J D. 2015. Use of chlorophyll fluorescence and P700 absorbance to rapidly detect glyphosate resistance in goosegrass (Eleusine indica). Journal of Integrative Agriculture, 14, 714–723.
Zhou J, Li F, Wang J L, Ma Y, Chong K, Xu Y Y. 2009. Basic helix-loop-helix transcription factor from wild rice (OrbHLH2) improves tolerance to salt- and osmotic stress in Arabidopsis. Journal of Plant Physiology, 166, 1296–1306.
|