@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{yow_bostan_young_valacchi_gillitt_perkins-veazie_xiang_iorizzo_2023, title={Identification of bromelain subfamily proteases encoded in the pineapple genome}, volume={13}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-023-38907-y}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Yow, Ashley G. and Bostan, Hamed and Young, Roberto and Valacchi, Giuseppe and Gillitt, Nicholas and Perkins-Veazie, Penelope and Xiang, Qiu-Yun and Iorizzo, Massimo}, year={2023}, month={Jul} }
 @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{mengist_bostan_de paola_teresi_platts_cremona_qi_mackey_bassil_ashrafi_et al._2022, title={Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum)}, volume={9}, ISSN={["1469-8137"]}, url={https://doi.org/10.1111/nph.18428}, DOI={10.1111/nph.18428}, abstractNote={Summary}, journal={NEW PHYTOLOGIST}, author={Mengist, Molla F. and Bostan, Hamed and De Paola, Domenico and Teresi, Scott J. and Platts, Adrian E. and Cremona, Gaetana and Qi, Xinpeng and Mackey, Ted and Bassil, Nahla V and Ashrafi, Hamid and et al.}, year={2022}, 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} }
 @article{hulse-kemp_bostan_chen_ashrafi_stoffel_sanseverino_li_cheng_schatz_garvin_et al._2021, title={An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids}, volume={6}, ISSN={["1940-3372"]}, DOI={10.1002/tpg2.20101}, abstractNote={Abstract}, journal={PLANT GENOME}, author={Hulse-Kemp, Amanda M. and Bostan, Hamed and Chen, Shiyu and Ashrafi, Hamid and Stoffel, Kevin and Sanseverino, Walter and Li, Linzhou and Cheng, Shifeng and Schatz, Michael C. and Garvin, Tyler and et al.}, year={2021}, month={Jun} }
 @article{qi_ogden_bostan_sargent_ward_gilbert_iorizzo_rowland_2021, title={High-Density Linkage Map Construction and QTL Identification in a Diploid Blueberry Mapping Population}, volume={12}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2021.692628}, abstractNote={Genotyping by sequencing approaches have been widely applied in major crops and are now being used in horticultural crops like berries and fruit trees. As the original and largest producer of cultivated blueberry, the United States maintains the most diverse blueberry germplasm resources comprised of many species of different ploidy levels. We previously constructed an interspecific mapping population of diploid blueberry by crossing the parent F1#10 (Vaccinium darrowiiFla4B × diploidV. corymbosumW85–20) with the parent W85–23 (diploidV. corymbosum). Employing the Capture-Seq technology developed by RAPiD Genomics, with an emphasis on probes designed in predicted gene regions, 117 F1progeny, the two parents, and two grandparents of this population were sequenced, yielding 131.7 Gbp clean sequenced reads. A total of 160,535 single nucleotide polymorphisms (SNPs), referenced to 4,522 blueberry genome sequence scaffolds, were identified and subjected to a parent-dependent sliding window approach to further genotype the population. Recombination breakpoints were determined and marker bins were deduced to construct a high density linkage map. Twelve blueberry linkage groups (LGs) consisting of 17,486 SNP markers were obtained, spanning a total genetic distance of 1,539.4 cM. Among 18 horticultural traits phenotyped in this population, quantitative trait loci (QTLs) that were significant over at least 2 years were identified for chilling requirement, cold hardiness, and fruit quality traits of color, scar size, and firmness. Interestingly, in 1 year, a QTL associated with timing of early bloom, full bloom, petal fall, and early green fruit was identified in the same region harboring the major QTL for chilling requirement. In summary, we report here the first high density bin map of a diploid blueberry mapping population and the identification of several horticulturally important QTLs.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Qi, Xinpeng and Ogden, Elizabeth L. and Bostan, Hamed and Sargent, Daniel J. and Ward, Judson and Gilbert, Jessica and Iorizzo, Massimo and Rowland, Lisa J.}, year={2021}, month={Jun} }
 @article{mengist_bostan_young_kay_gillitt_ballington_kay_ferruzzi_ashrafi_lila_et al._2021, title={High-density linkage map construction and identification of loci regulating fruit quality traits in blueberry}, volume={8}, ISSN={["2052-7276"]}, url={https://doi.org/10.1038/s41438-021-00605-z}, DOI={10.1038/s41438-021-00605-z}, abstractNote={Abstract}, number={1}, journal={HORTICULTURE RESEARCH}, author={Mengist, Molla F. and Bostan, Hamed and Young, Elisheba and Kay, Kristine L. and Gillitt, Nicholas and Ballington, James and Kay, Colin D. and Ferruzzi, Mario G. and Ashrafi, Hamid and Lila, Mary Ann and et al.}, year={2021}, month={Dec} }
 @article{mengist_burtch_debelo_pottorff_bostan_nunn_corbin_kay_bassil_hummer_et al._2020, title={Development of a genetic framework to improve the efficiency of bioactive delivery from blueberry}, volume={10}, ISSN={["2045-2322"]}, url={https://europepmc.org/articles/PMC7560831}, DOI={10.1038/s41598-020-74280-w}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Mengist, Molla F. and Burtch, Haley and Debelo, Hawi and Pottorff, Marti and Bostan, Hamed and Nunn, Candace and Corbin, Sydney and Kay, Colin D. and Bassil, Nahla and Hummer, Kim and et al.}, year={2020}, month={Oct} }
 @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} }
 @article{becchimanzi_avolio_bostan_colantuono_cozzolino_mancini_chiusano_pucci_caccia_pennacchio_2020, title={Venomics of the ectoparasitoid wasp Bracon nigricans}, volume={21}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-019-6396-4}, abstractNote={Abstract}, number={1}, journal={BMC GENOMICS}, author={Becchimanzi, Andrea and Avolio, Maddalena and Bostan, Hamed and Colantuono, Chiara and Cozzolino, Flora and Mancini, Donato and Chiusano, Maria Luisa and Pucci, Pietro and Caccia, Silvia and Pennacchio, Francesco}, year={2020}, month={Jan} }
 @article{iorizzo_cavagnaro_bostan_zhao_zhang_simon_2019, title={A Cluster of MYB Transcription Factors Regulates Anthocyanin Biosynthesis in Carrot (Daucus carota L.) Root and Petiole}, volume={9}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2018.01927}, abstractNote={Purple carrots can accumulate large quantities of anthocyanins in their roots and –in some genetic backgrounds- petioles, and therefore they represent an excellent dietary source of antioxidant phytonutrients. In a previous study, using linkage analysis in a carrot F2 mapping population segregating for root and petiole anthocyanin pigmentation, we identified a region in chromosome 3 with co-localized QTL for all anthocyanin pigments of the carrot root, whereas petiole pigmentation segregated as a single dominant gene and mapped to one of these “root pigmentation” regions conditioning anthocyanin biosynthesis. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify candidate genes controlling anthocyanin pigmentation in the carrot root and petiole. Fine mapping was performed in four carrot populations with different genetic backgrounds and patterns of pigmentation. The regions controlling root and petiole pigmentation in chromosome 3 were delimited to 541 and 535 kb, respectively. Genome wide prediction of transcription factor families known to regulate the anthocyanin biosynthetic pathway coupled with orthologous and phylogenetic analyses enabled the identification of a cluster of six MYB transcription factors, denominated DcMYB6 to DcMYB11, associated with the regulation of anthocyanin biosynthesis. No anthocyanin biosynthetic genes were present in this region. Comparative transcriptome analysis indicated that upregulation of DcMYB7 was always associated with anthocyanin pigmentation in both root and petiole tissues, whereas DcMYB11 was only upregulated with pigmentation in petioles. In the petiole, the level of expression of DcMYB11 was higher than DcMYB7. DcMYB6, a gene previously suggested as a key regulator of carrot anthocyanin biosynthesis, was not consistently associated with pigmentation in either tissue. These results strongly suggest that DcMYB7 is a candidate gene for root anthocyanin pigmentation in all the genetic backgrounds included in this study. DcMYB11 is a candidate gene for petiole pigmentation in all the purple carrot sources in this study. Since DcMYB7 is co-expressed with DcMYB11 in purple petioles, the latter gene may act also as a co-regulator of anthocyanin pigmentation in the petioles. This study provides linkage-mapping and functional evidence for the candidacy of these genes for the regulation of carrot anthocyanin biosynthesis.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Iorizzo, Massimo and Cavagnaro, Pablo F. and Bostan, Hamed and Zhao, Yunyang and Zhang, Jianhui and Simon, Philipp W.}, year={2019}, month={Jan} }
 @article{bostan_senalik_simon_iorizzo_2019, title={Carrot Genetics, Omics and Breeding Toolboxes}, ISBN={["978-3-030-03388-0"]}, ISSN={["2199-479X"]}, DOI={10.1007/978-3-030-03389-7_13}, abstractNote={Today, researchers routinely generate and analyze large and complex omics, genetics and breeding datasets for both model and nonmodel crop species including carrot. This has resulted in the massive production and availability of omics data, which opened multiple challenges to store, organize and make those data available to the research and breeding communities. The value of these resources increases significantly when it is organized, annotated, effectively integrated with other data and made available to browse, query and analyze. In this chapter, we summarize the available omics, genetics and breeding resources for carrot and other Daucus species in different public and private databases. We also discuss the challenges for collecting, integrating and interpreting this data with a focus on the lack of dedicated, centralized and user-friendly bioinformatics platforms, breeding toolboxes and infrastructures for the carrot genome.}, journal={CARROT GENOME}, author={Bostan, Hamed and Senalik, Douglas and Simon, Philipp W. and Iorizzo, Massimo}, year={2019}, pages={225–245} }
 @article{ellison_senalik_bostan_iorizzo_simon_2017, title={Fine Mapping, Transcriptome Analysis, and Marker Development for Y-2, the Gene That Conditions beta-Carotene Accumulation in Carrot (Daucus carota L.)}, volume={7}, ISSN={["2160-1836"]}, DOI={10.1534/g3.117.043067}, abstractNote={Abstract}, number={8}, journal={G3-GENES GENOMES GENETICS}, author={Ellison, Shelby and Senalik, Douglas and Bostan, Hamed and Iorizzo, Massimo and Simon, Philipp}, year={2017}, month={Aug}, pages={2665–2675} }