@article{filichkin_wu_busov_meilan_lanz-garcia_groover_goldfarb_ma_dharmawardhana_brunner_et al._2006, title={Enhancer trapping in woody plants: Isolation of the ET304 gene encoding a putative AT-hook motif transcription factor and characterization of the expression patterns conferred by its promoter in transgenic Populus and Arabidopsis}, volume={171}, ISSN={["0168-9452"]}, DOI={10.1016/j.plantsci.2006.03.011}, abstractNote={Enhancer trapping is a useful tool in isolation of novel genes and functional characterization of promoters directing tissue-specific expression in trees. Using an enhancer trap approach we isolated a novel gene ET304 from Populus (Populus: aspens and cottonwoods). Both ET304 enhancer trap line and putative ET304 promoter fused to a GUS reporter gene conferred strongly root-predominant expression patterns and directed expression to specific root tissue and cell types. GUS activity was detected in lateral root primordia, root apical meristem, elongation zone and cortex. ET304 promoter sequence contained a canonic auxin response element (AuxRE) located upstream of the enhancer trap insertion site. In a synchronized lateral root induction system ET304 promoter conferred an auxin-responsive expression in newly emerging lateral roots of both poplar and Arabidopsis. A detailed histochemical examination of poplar transgenics showed that ET304 promoter was highly active in actively growing lateral roots, their primordia and to a lesser extent—in secondary meristems of aerial organs rich in free endogenous auxin. These results were consistent with the expression profiling of ET304 mRNA in various tissues of mature poplar trees. The analysis of Populus genomic sequence suggested that ET304 represents a large family of putative transcription factors containing a conserved AT-hook motif and DNA binding domain.}, number={2}, journal={PLANT SCIENCE}, author={Filichkin, Sergei A. and Wu, Qian and Busov, Victor and Meilan, Richard and Lanz-Garcia, Carmen and Groover, Andrew and Goldfarb, Barry and Ma, Caiping and Dharmawardhana, Palitha and Brunner, Amy and et al.}, year={2006}, month={Aug}, pages={206–216} }
 @article{busov_johannes_whetten_sederoff_spiker_lanz-garcia_goldfarb_2004, title={An auxin-inducible gene from loblolly pine ( Pinus taeda L.) is differentially expressed in mature and juvenile-phase shoots and encodes a putative transmembrane protein}, volume={218}, ISSN={0032-0935 1432-2048}, url={http://dx.doi.org/10.1007/s00425-003-1175-4}, DOI={10.1007/s00425-003-1175-4}, abstractNote={We have isolated a gene from loblolly pine, 5NG4, that is highly and specifically induced by auxin in juvenile loblolly pine shoots prior to adventitious root formation, but substantially down-regulated in physiologically mature shoots that are adventitious rooting incompetent. 5NG4 was highly auxin-induced in roots, stems and hypocotyls, organs that can form either lateral or adventitious roots following an auxin treatment, but was not induced to the same level in needles and cotyledons, organs that do not form roots. The deduced amino acid sequence shows homology to the MtN21 nodulin gene from Medicago truncatula. The expression pattern of 5NG4 and its homology to a protein from Medicago involved in a root-related process suggest a possible role for this gene in adventitious root formation. Homology searches also identified similar proteins in Arabidopsis thaliana and Oryza sativa. High conservation across these evolutionarily distant species suggests essential functions in plant growth and development. A 38-member family of genes homologous to 5NG4 was identified in the A. thaliana genome. The physiological significance of this redundancy is most likely associated with functional divergence and/or expression specificity of the different family members. The exact biochemical function of the gene is still unknown, but sequence and structure predictions and 5NG4::GFP fusion protein localizations indicate it is a transmembrane protein with a possible transport function.}, number={6}, journal={Planta}, publisher={Springer Science and Business Media LLC}, author={Busov, Victor B. and Johannes, Eva and Whetten, Ross W. and Sederoff, Ronald R. and Spiker, Steven L. and Lanz-Garcia, Carmen and Goldfarb, Barry}, year={2004}, month={Apr}, pages={916–927} }
 @article{goldfarb_lanz-garcia_lian_whetten_2003, title={Aux/IAA gene family is conserved in the gymnosperm, loblolly pine (Pinus taeda)}, volume={23}, ISSN={0829-318X 1758-4469}, url={http://dx.doi.org/10.1093/treephys/23.17.1181}, DOI={10.1093/treephys/23.17.1181}, abstractNote={We isolated five members of the Aux/IAA gene family in loblolly pine (Pinus taeda L.). Degenerate primers complementary to conserved regions of angiosperm Aux/IAA genes were used to amplify fragments that were, in turn, used as probes to screen a cDNA library constructed from auxin-treated hypocotyls. The five unique clones, named PTIAA1-5, contain the four highly conserved domains that are characteristic of the Aux/IAA proteins. All clones contain the bipartite nuclear localization signal (NLS) between Domains I and II that is predicted in most angiosperm Aux/IAA genes, but only one, PTIAA2, contains the conserved NLS in Domain IV. The five invariant residues in Domain II that have been found to constitute part of a protein destabilization element in Arabidopsis thaliana (L.) Heynh. are conserved in all the PTIAAs. A postulated phosphorylation site located between Domains I and II and proximal to the conserved bipartite NLS was conserved in 20 out of 36 genes in this analysis, including the pine genes. Transcripts of all five PTIAAs accumulated specifically in the hypocotyls in response to exogenous auxin treatment and were induced by all auxins tested. Transcript abundance above basal levels in response to 1-naphthaleneacetic acid treatment was first detected after 10 min (PTIAA3) to 3 h (PTIAA2) in the different genes and remained above basal levels throughout 7 days. Induction of PTIAA2 was inhibited by the protein synthesis inhibitor cycloheximide, indicating that PTIAA2 is a secondary response gene. Phylogenetic analysis showed that all five pine genes clustered within a single class (Class I) of the dendrogram. Clone PTIAA2 has a sequence that is relatively distinct from the other four and is the most closely related to the angiosperm genes of Class I. Class I contains both primary and secondary auxin response genes, suggesting that it is the original lineage and that other gene classes have evolved subsequent to the angiosperm/gymnosperm divergence.}, number={17}, journal={Tree Physiology}, publisher={Oxford University Press (OUP)}, author={Goldfarb, B. and Lanz-Garcia, C. and Lian, Z. and Whetten, R.}, year={2003}, month={Dec}, pages={1181–1192} }
 @inbook{goldfarb_lian_lanz-garcia_whetten_1997, title={Auxin-induced gene expression during rooting of loblolly pine stem cuttings}, ISBN={0306457067}, DOI={10.1007/978-1-4615-5403-5_31}, booktitle={Biology of Root Formation and Development}, publisher={New York: Plenum Press}, author={Goldfarb, B. and Lian, Z. and Lanz-Garcia, C. and Whetten, R. K.}, editor={A. Altman and Waisel, Y.Editors}, year={1997}, pages={163–167} }