@article{surzenko_bastidas_reid_curaba_zhang_bostan_wilson_dominique_roberson_ignacio_et al._2024, title={Functional recovery following traumatic brain injury in rats is enhanced by oral supplementation with bovine thymus extract}, volume={38}, ISSN={["1530-6860"]}, DOI={10.1096/fj.202301859R}, abstractNote={Abstract}, number={3}, journal={FASEB JOURNAL}, author={Surzenko, Natalia and Bastidas, Johana and Reid, Robert W. and Curaba, Julien and Zhang, Wei and Bostan, Hamed and Wilson, Mickey and Dominique, Ashley and Roberson, Julia and Ignacio, Glicerio and et al.}, year={2024}, month={Feb} }
 @article{d'amelia_curaba_abid_esposito_cavagnaro_carputo_iorizzo_2023, title={Functional characterization of DcMYB11, an R2R3 MYB associated with the purple pigmentation of carrot petiole}, volume={258}, ISSN={["1432-2048"]}, DOI={10.1007/s00425-023-04200-5}, number={3}, journal={PLANTA}, author={D'Amelia, Vincenzo and Curaba, Julien and Abid, Muhammad Ali and Esposito, Salvatore and Cavagnaro, Pablo and Carputo, Domenico and Iorizzo, Massimo}, year={2023}, month={Sep} }
 @article{coe_bostan_rolling_turner-hissong_macko-podgorni_senalik_liu_seth_curaba_mengist_et al._2023, title={Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots}, volume={9}, ISSN={["2055-0278"]}, url={https://doi.org/10.1038/s41477-023-01526-6}, DOI={10.1038/s41477-023-01526-6}, abstractNote={Abstract}, journal={NATURE PLANTS}, author={Coe, Kevin and Bostan, Hamed and Rolling, William and Turner-Hissong, Sarah and Macko-Podgorni, Alicja and Senalik, Douglas and Liu, Su and Seth, Romit and Curaba, Julien and Mengist, Molla Fentie and et al.}, year={2023}, month={Sep} }
 @article{yow_bostan_castanera_ruggieri_mengist_curaba_young_gillitt_iorizzo_2022, title={Improved High-Quality Genome Assembly and Annotation of Pineapple (Ananas comosus) Cultivar MD2 Revealed Extensive Haplotype Diversity and Diversified FRS/FRF Gene Family}, volume={13}, ISSN={["2073-4425"]}, url={https://doi.org/10.3390/genes13010052}, DOI={10.3390/genes13010052}, abstractNote={Pineapple (Ananas comosus (L.) Merr.) is the second most important tropical fruit crop globally, and ‘MD2’ is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. Here, PacBio and Hi-C data were used to develop a new high-quality MD2 assembly and gene prediction. Compared to the previous MD2 assembly, major improvements included a 26.6-fold increase in contig N50 length, phased chromosomes, and >6000 new genes. The new MD2 assembly also included 161.6 Mb additional sequences and >3000 extra genes compared to the F153 genome. Over 48% of the predicted genes harbored potential deleterious mutations, indicating that the high level of heterozygosity in this species contributes to maintaining functional alleles. The genome was used to characterize the FAR1-RELATED SEQUENCE (FRS) genes that were expanded in pineapple and rice. Transposed and dispersed duplications contributed to expanding the numbers of these genes in the pineapple lineage. Several AcFRS genes were differentially expressed among tissue-types and stages of flower development, suggesting that their expansion contributed to evolving specialized functions in reproductive tissues. The new MD2 assembly will serve as a new reference for genetic and genomic studies in pineapple.}, number={1}, journal={GENES}, author={Yow, Ashley G. and Bostan, Hamed and Castanera, Raul and Ruggieri, Valentino and Mengist, Molla F. and Curaba, Julien and Young, Roberto and Gillitt, Nicholas and Iorizzo, Massimo}, year={2022}, month={Jan} }
 @misc{iorizzo_curaba_pottorff_ferruzzi_simon_cavagnaro_2020, title={Carrot Anthocyanins Genetics and Genomics: Status and Perspectives to Improve Its Application for the Food Colorant Industry}, volume={11}, ISSN={["2073-4425"]}, DOI={10.3390/genes11080906}, abstractNote={Purple or black carrots (Daucus carota ssp. sativus var. atrorubens Alef) are characterized by their dark purple- to black-colored roots, owing their appearance to high anthocyanin concentrations. In recent years, there has been increasing interest in the use of black carrot anthocyanins as natural food dyes. Black carrot roots contain large quantities of mono-acylated anthocyanins, which impart a measure of heat-, light- and pH-stability, enhancing the color-stability of food products over their shelf-life. The genetic pathway controlling anthocyanin biosynthesis appears well conserved among land plants; however, different variants of anthocyanin-related genes between cultivars results in tissue-specific accumulations of purple pigments. Thus, broad genetic variations of anthocyanin profile, and tissue-specific distributions in carrot tissues and organs, can be observed, and the ratio of acylated to non-acylated anthocyanins varies significantly in the purple carrot germplasm. Additionally, anthocyanins synthesis can also be influenced by a wide range of external factors, such as abiotic stressors and/or chemical elicitors, directly affecting the anthocyanin yield and stability potential in food and beverage applications. In this study, we critically review and discuss the current knowledge on anthocyanin diversity, genetics and the molecular mechanisms controlling anthocyanin accumulation in carrots. We also provide a view of the current knowledge gaps and advancement needs as regards developing and applying innovative molecular tools to improve the yield, product performance and stability of carrot anthocyanin for use as a natural food colorant.}, number={8}, journal={GENES}, author={Iorizzo, Massimo and Curaba, Julien and Pottorff, Marti and Ferruzzi, Mario G. and Simon, Philipp and Cavagnaro, Pablo F.}, year={2020}, month={Aug} }
 @article{curaba_bostan_cavagnaro_senalik_mengist_zhao_simon_iorizzo_2020, title={Identification of an SCPL Gene Controlling Anthocyanin Acylation in Carrot (Daucus carota L.) Root}, volume={10}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2019.01770}, abstractNote={Anthocyanins are natural health promoting pigments that can be produced in large quantities in some purple carrot cultivars. Decoration patterns of anthocyanins, such as acylation, can greatly influence their stability and biological properties and use in the food industry as nutraceuticals and natural colorants. Despite recent advances made toward understanding the genetic control of anthocyanin accumulation in purple carrot, the genetic mechanism controlling acylation of anthocyanin in carrot root have not been studied yet. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify the genetic factor conditioning the accumulation of non-acylated (Cy3XGG) versus acylated (Cy3XFGG and Cy3XSGG) cyanidin derivatives, in three carrot populations. Segregation and mapping analysis pointed to a single gene with dominant effect controlling anthocyanin acylation in the root, located in a 576kb region containing 29 predicted genes. Orthologous and phylogenetic analyses enabled the identification of a cluster of three SCPL-acyltransferases coding genes within this region. Comparative transcriptome analysis indicated that only one of these three genes, DcSCPL1, was always expressed in association with anthocyanin pigmentation in the root and was co-expressed with DcMYB7, a gene known to activate anthocyanin biosynthetic genes in carrot. DcSCPL1 sequence analysis, in root tissue containing a low level of acylated anthocyanins, demonstrated the presence of an insertion causing an abnormal splicing of the 3rd exon during mRNA editing, likely resulting in the production of a non-functional acyltransferase and explaining the reduced acylation phenotype. This study provides strong linkage-mapping and functional evidences for the candidacy of DcSCPL1 as a primary regulator of anthocyanin acylation in carrot storage root.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Curaba, Julien and Bostan, Hamed and Cavagnaro, Pablo F. and Senalik, Douglas and Mengist, Molla Fentie and Zhao, Yunyang and Simon, Philipp W. and Iorizzo, Massimo}, year={2020}, month={Jan} }