@article{carbone_ramirez-prado_jakobek_horn_2007, title={Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster}, volume={7}, ISSN={["1471-2148"]}, DOI={10.1186/1471-2148-7-111}, abstractNote={The biosynthesis of aflatoxin (AF) involves over 20 enzymatic reactions in a complex polyketide pathway that converts acetate and malonate to the intermediates sterigmatocystin (ST) and O-methylsterigmatocystin (OMST), the respective penultimate and ultimate precursors of AF. Although these precursors are chemically and structurally very similar, their accumulation differs at the species level for Aspergilli. Notable examples are A. nidulans that synthesizes only ST, A. flavus that makes predominantly AF, and A. parasiticus that generally produces either AF or OMST. Whether these differences are important in the evolutionary/ecological processes of species adaptation and diversification is unknown. Equally unknown are the specific genomic mechanisms responsible for ordering and clustering of genes in the AF pathway of Aspergillus.To elucidate the mechanisms that have driven formation of these clusters, we performed systematic searches of aflatoxin cluster homologs across five Aspergillus genomes. We found a high level of gene duplication and identified seven modules consisting of highly correlated gene pairs (aflA/aflB, aflR/aflS, aflX/aflY, aflF/aflE, aflT/aflQ, aflC/aflW, and aflG/aflL). With the exception of A. nomius, contrasts of mean Ka/Ks values across all cluster genes showed significant differences in selective pressure between section Flavi and non-section Flavi species. A. nomius mean Ka/Ks values were more similar to partial clusters in A. fumigatus and A. terreus. Overall, mean Ka/Ks values were significantly higher for section Flavi than for non-section Flavi species.Our results implicate several genomic mechanisms in the evolution of ST, OMST and AF cluster genes. Gene modules may arise from duplications of a single gene, whereby the function of the pre-duplication gene is retained in the copy (aflF/aflE) or the copies may partition the ancestral function (aflA/aflB). In some gene modules, the duplicated copy may simply augment/supplement a specific pathway function (aflR/aflS and aflX/aflY) or the duplicated copy may evolve a completely new function (aflT/aflQ and aflC/aflW). Gene modules that are contiguous in one species and noncontiguous in others point to possible rearrangements of cluster genes in the evolution of these species. Significantly higher mean Ka/Ks values in section Flavi compared to non-section Flavi species indicate increased positive selection acting in the evolution of genes in OMST and AF gene clusters.}, journal={BMC EVOLUTIONARY BIOLOGY}, author={Carbone, Ignazio and Ramirez-Prado, Jorge H. and Jakobek, Judy L. and Horn, Bruce W.}, year={2007}, month={Jul} }
 @article{carbone_jakobek_ramirez-prado_horn_2007, title={Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus}, volume={16}, ISSN={["1365-294X"]}, DOI={10.1111/j.1365-294X.2007.03464.x}, abstractNote={Abstract}, number={20}, journal={MOLECULAR ECOLOGY}, author={Carbone, Ignazio and Jakobek, Judy L. and Ramirez-Prado, Jorge H. and Horn, Bruce W.}, year={2007}, month={Oct}, pages={4401–4417} }
 @article{ali_reddy_lindgren_jakobek_reddy_2003, title={Differential expression of genes encoding calmodulin-binding proteins in response to bacterial pathogens and inducers of defense responses}, volume={51}, ISSN={["0167-4412"]}, DOI={10.1023/A:1023001403794}, abstractNote={Calmodulin (CaM) plays an important role in sensing and transducing changes in cellular Ca2+ concentration in response to several biotic and abiotic stresses. Although CaM is implicated in plant-pathogen interactions, its molecular targets and their role in defense signaling pathway(s) are poorly understood. To elucidate the signaling pathways that link CaM to defense responses, we screened a cDNA library constructed from bean leaves undergoing a hypersensitive response (HR) with radiolabeled CaM isoforms. A total of 26 putative CBPs were identified. Sequencing of the cDNAs revealed that they represent 8 different genes. They are homologues of previously identified CaM-binding proteins (CBPs) in other systems. However, some CBPs are novel members of known CBP families. The proteins encoded by these clones bound CaM in a Ca2+-dependent manner. To determine if these CBPs are involved in plant defense responses, we analyzed their expression in bean leaves inoculated with compatible, incompatible and nonpathogenic bacterial strains. Expression of three CBPs including an isoform of cyclic nucleotide-gated channels (PvCNGC-A) and two hypothetical proteins (PvCBP60-C and PvCBP60-D) was induced whereas the expression of two other isoforms of CNGCs (PvCNGC-B and PvCNGC-C) was repressed in response to incompatible pathogens. The expression of the rest, a small auxin up RNA (PvSAUR1) and two hypothetical proteins (PvCBP60-A and PvCBP60-B), was not changed. The expression of most of the pathogen-regulated genes was also affected by salicylic acid, jasmonic acid, hydrogen peroxide and a fungal elicitor, which are known to induce defense responses. Our results strongly suggest that at least five bean CBPs are involved in plant defense responses.}, number={6}, journal={PLANT MOLECULAR BIOLOGY}, author={Ali, GS and Reddy, VS and Lindgren, PB and Jakobek, JL and Reddy, ASN}, year={2003}, month={Apr}, pages={803–815} }
 @article{jakobek_lindgren_2002, title={Expression of a bean acid phosphatase cDNA is correlated with disease resistance}, volume={53}, ISSN={["1460-2431"]}, DOI={10.1093/jexbot/53.367.387}, abstractNote={A cDNA clone, designated Hra28 (for hypersensitive reaction associated), was identified corresponding to an RNA transcript that accumulates in bean during the hypersensitive reaction. The Hra28 cDNA is 1084 nucleotides in length and is predicted to encode an acid phosphatase of 264 amino acids. Northern analysis demonstrated that the Hra28 transcript accumulated differentially in response to bacteria which induce a hypersensitive response (HR), a bacterium which causes disease, and a Hrp(-) mutant which does not elicit an HR or cause disease. In contrast, the Hra28 transcript did not accumulate in response to wounding. Thus, the Hra28 gene is induced by multiple stimuli and appears to be regulated in a complex manner.}, number={367}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Jakobek, JL and Lindgren, PB}, year={2002}, month={Feb}, pages={387–389} }
 @article{sullivan_jakobek_lindgren_2001, title={Cloning and characterization of a bean UDP-glucosyltransferase cDNA expressed during plant-bacterial interactions}, volume={14}, ISSN={["0894-0282"]}, DOI={10.1094/MPMI.2001.14.1.90}, abstractNote={ A cDNA clone, which corresponds to an RNA transcript that accumulates in bean during the hypersensitive reaction, was isolated and designated Hra25 (for hypersensitive reaction associated). Hra25 is predicted to encode a UDP-glucosyltransferase. Northern analysis was used to study Hra25 transcript accumulation in bean in response to incompatible and compatible strains of Pseudomonas syringae, an Hrp¯ mutant, and wounding. Our data suggest that the Hra25 transcript is activated in response to specific avr-derived signals as well as non-avr, general signals. }, number={1}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Sullivan, TA and Jakobek, JL and Lindgren, PB}, year={2001}, month={Jan}, pages={90–92} }
 @article{jakobek_lindgren_1993, title={GENERALIZED INDUCTION OF DEFENSE RESPONSES IN BEAN IS NOT CORRELATED WITH THE INDUCTION OF THE HYPERSENSITIVE REACTION}, volume={5}, ISSN={["1040-4651"]}, DOI={10.2307/3869427}, number={1}, journal={PLANT CELL}, author={JAKOBEK, JL and LINDGREN, PB}, year={1993}, month={Jan}, pages={49–56} }
 @article{jakobek_smith_lindgren_1993, title={Suppression of bean defense responses by Pseudomonas syringae}, volume={5}, DOI={10.2307/3869428}, number={1}, journal={Plant Cell}, author={Jakobek, J. L. and Smith, J. A. and Lindgren, P. B.}, year={1993}, pages={57} }