Cochetel, Noe, Andrea Minio, Andrea Guarracino, Jadran F. Garcia, Rosa Figueroa-Balderas, Melanie Massonnet, Jason Londo, Erik Garrison, Brandon Gaut, and Dario Cantu. 2023. A Reference-Unbiased Super-Pangenome of the North American Wild Grape Species (Vitis Spp.) Reveals Genus-Wide Association with Adaptive Traits. bioRxiv. https://doi.org/10.1101/2023.06.27.545624. (Accepted)

Garcia, Jadran, Abraham Morales-Cruz, Noé Cochetel, Andrea Minio, Rosa Figueroa-Balderas, Philippe Rolshausen, Kendra Baumgartner, and Dario Cantu. 2023. Comparative Pangenomic Insights into the Distinct Evolution of Virulence Factors among Grapevine Trunk Pathogens. Molecular Plant-Microbe Interactions, November. https://doi.org/10.1094/MPMI-09-23-0129-R.

Minio, Andrea, Rosa Figueroa-Balderas, Stephen P Cohen, Shahin S Ali, Denny Carriel, Dahyana Britto, Conrad Stack, et al. 2023a. Clonal Reproduction of Moniliophthora Roreri and the Emergence of Unique Lineages with Distinct Genomes during Range Expansion. G3 Genes|Genomes|Genetics, June, jkad125. https://doi.org/10.1093/g3journal/jkad125.

Morales-Cruz, Abraham, Jonas Aguirre-Liguori, Mélanie Massonnet, Andrea Minio, Mirella Zaccheo, Noe Cochetel, Andrew Walker, et al. 2023. Multigenic Resistance to Xylella Fastidiosa in Wild Grapes (Vitis Sps.) and Its Implications within a Changing Climate. Communications Biology 6 (1): 1–15. https://doi.org/10.1038/s42003-023-04938-4.

Paineau, Manon, Andrea Minio, Pere Mestre, Frederic Fabre, Isabelle D. Mazet, Carole Couture, Fabrice Legeai, Thomas Dumartinet, Dario Cantu, and Francois Delmotte. 2023. An Effector Deletion Leads to the Breakdown of Partial Grapevine Resistance to Downy Mildew. bioRxiv. https://doi.org/10.1101/2023.08.17.553663. (Under Revision)

Solares, Edwin, Abraham Morales-Cruz, Rosa Figueroa Balderas, Eric Focht, Vanessa E T M Ashworth, Skylar Wyant, Andrea Minio, Dario Cantu, Mary Lu Arpaia, and Brandon S Gaut. 2023. Insights into the Domestication of Avocado and Potential Genetic Contributors to Heterodichogamy. G3 Genes|Genomes|Genetics 13 (2): jkac323. https://doi.org/10.1093/g3journal/jkac323.

Urra, Claudio, Dayan Sanhueza, Catalina Pavez, Patricio Tapia, Gerardo Núñez-Lillo, Andrea Minio, Matthieu Miossec, et al. 2023. Identification of Grapevine Clones via High-Throughput Amplicon Sequencing: A Proof-of-Concept Study. G3 Genes|Genomes|Genetics, July, jkad145. https://doi.org/10.1093/g3journal/jkad145.

Minio, A., Cochetel, N., Massonnet, M., Figueroa-Balderas R., Cantu D.. HiFi chromosome-scale diploid assemblies of the grape rootstocks 110R, Kober 5BB, and 101–14 Mgt. Sci Data 9, 660 (2022). https://doi.org/10.1038/s41597-022-01753-0

Minio, A., Cochetel, N., Vondras, AM., Massonnet, M., Cantu D. Assembly of complete diploid-phased chromosomes from draft genome sequences. G3 Genes|Genomes|Genetics. 2022 Jun 10;jkac143.

Morales-Cruz, A., Aguirre-Liguori, J., Massonnet M., Minio, A., Zaccheo, M. et al., 2022. Multigenic Resistance to Xylella Fastidiosa in Wild Grapes ( Vitis Sps.) and Its Implications within a Changing Climate’. Preprint. Genetics. https://doi.org/10.1101/2022.10.08.511428.

Massonnet M, Vondras AM, Cochetel N, Riaz S, Pap D, Minio A, et al. Haplotype-resolved powdery mildew resistance loci reveal the impact of heterozygous structural variation on NLR genes in Muscadinia rotundifolia. G3 Genes|Genomes|Genetics. 2022 Jun 13;jkac148.

Maestri S, Gambino G, Lopatriello G, Minio A, Perrone I, Cosentino E, et al. ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.). BMC Genomics. 2022 Dec;23(1):159.

Zou C, Massonnet M, Minio A, Patel S, Llaca V, Karn A, et al. Multiple independent recombinations led to hermaphroditism in grapevine. Proceedings of the National Academy of Sciences. 2021;118(15):e2023548118.

Vondras AM, Lerno L, Massonnet M, Minio A, Rowhani A, Liang D, et al. Rootstock influences the effect of grapevine leafroll‐associated viruses on berry development and metabolism via abscisic acid signalling. Mol Plant Pathol. 2021 Aug;22(8):984–1005.

Morales-Cruz A, Aguirre-Liguori JA, Zhou Y, Minio A, Riaz S, Walker AM, et al. Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation. Genome Biol. 2021 Dec;22(1):254.

Garcia JF, Lawrence DP, Morales-Cruz A, Travadon R, Minio A, Hernandez-Martinez R, et al. Phylogenomics of Plant-Associated Botryosphaeriaceae Species. Frontiers in Microbiology. 2021;12(March):1–18.

Cochetel N, Minio A, Massonnet M, Vondras AM, Figueroa-Balderas R, Cantu D. Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence. Morrell P, editor. G3 Genes|Genomes|Genetics. 2021 Apr 15;11(4):jkab033.

Morales-Cruz A, Ali SS, Minio A, Figueroa-Balderas R, García JF, Kasuga T, et al. Independent Whole-Genome Duplications Define the Architecture of the Genomes of the Devastating West African Cacao Black Pod Pathogen Phytophthora megakarya and Its Close Relative Phytophthora palmivora. G3 Genes|Genomes|Genetics. 2020;10(7):2241–55.

Massonnet M, Cochetel N, Minio A, Vondras AM, Lin J, Muyle A, et al. The genetic basis of sex determination in grapes. Nature communications. 2020 Dec;11(1):2902.

Zhou Y, Minio A, Massonnet M, Solares E, Lv Y, Beridze T, et al. The population genetics of structural variants in grapevine domestication. Nature Plants. 2019;5(9):965–79.

Vondras AM, Minio A, Blanco-Ulate B, Figueroa-Balderas R, Penn MA, Zhou Y, et al. The genomic diversification of grapevine clones. BMC genomics. 2019;20(1):972.

Minio A, Massonnet M, Figueroa-Balderas R, Vondras AM, Blanco-Ulate B, Cantu D. Iso-Seq allows genome-independent transcriptome profiling of grape berry development. G3: Genes, Genomes, Genetics. 2019 Jan;9(3):755–67.

Minio A, Massonnet M, Figueroa-Balderas R, Castro A, Cantu D. Diploid Genome Assembly of the Wine Grape Carménère. G3 Genes|Genomes|Genetics. 2019 May;9(5):1331–7.

Figueroa-Balderas R, Minio A, Morales-Cruz A, Vondras AM, Cantu D. Strategies for Sequencing and Assembling Grapevine Genomes. In: The Grape Genome. Springer, Cham; 2019. p. 77–88.

Barchi L, Pietrella M, Venturini L, Minio A, Toppino L, Acquadro A, et al. A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution. Scientific Reports. 2019;9(1):1–13.

Molin AD, Minio A, Griggio F, Delledonne M, Infantino A, Aragona M. The genome assembly of the fungal pathogen Pyrenochaeta lycopersici from Single-Molecule Real-Time sequencing sheds new light on its biological complexity. PLoS ONE. 2018;13(7):e0200217.

Massonnet M, Morales-Cruz A, Minio A, Figueroa-Balderas R, Lawrence DP, Travadon R, et al. Whole-genome resequencing and pan-transcriptome reconstruction highlight the impact of genomic structural variation on secondary metabolite gene clusters in the grapevine esca pathogen phaeoacremonium minimum. Frontiers in Microbiology. 2018;9(AUG):1784.

Minio A, Lin J, Gaut BS, Cantu D. How single molecule real-time sequencing and haplotype phasing have enabled reference-grade diploid genome assembly of wine grapes. Frontiers in Plant Science. 2017;8(May):1–6.

Lauritano C, De Luca D, Ferrarini A, Avanzato C, Minio A, Esposito F, et al. De novo transcriptome of the cosmopolitan dinoflagellate Amphidinium carterae to identify enzymes with biotechnological potential. Scientific Reports. 2017;7(1):1–12.

Donà M, Sabatini ME, Biggiogera M, Confalonieri M, Minio A, Delledonne M, et al. MtTdp1α-depleted Medicago truncatula plants show reduced cuticle permeability and altered expression of defense genes. Biologia Plantarum. 2017;61(1):192–6.

D’Esposito D, Ferriello F, Molin AD, Diretto G, Sacco A, Minio A, et al. Unraveling the complexity of transcriptomic, metabolomic and quality environmental response of tomato fruit. BMC Plant Biology. 2017;17(1):66.

Chitarra W, Perrone I, Avanzato CG, Minio A, Boccacci P, Santini D, et al. Grapevine grafting: Scion transcript profiling and defense-related metabolites induced by rootstocks. Frontiers in Plant Science. 2017;8:654.

Sabatini ME, Donà M, Leonetti P, Minio A, Delledonne M, Carboneral D, et al. Depletion of tyrosyl-DNA phosphodiesterase 1α (MtTdp1α) affects transposon expression in Medicago truncatula. Journal of integrative plant biology. 2016;58(7):618–22.

Bulgari D, Minio A, Casati P, Quaglino F, Delledonne M, Bianco PA. Curtobacterium sp. genome sequencing underlines plant growth promotion-related traits. Genome Announcements. 2014;2(4):e00592—-14.

Bellucci E, Bitocchi E, Ferrarini A, Benazzo A, Biagetti E, Klie S, et al. Decreased nucleotide and expression diversity and modified coexpression patterns characterize domestication in the common bean. Plant Cell. 2014;26(5):1901–12.

Aragona M, Minio A, Ferrarini A, Valente MT, Bagnaresi P, Orrù L, et al. De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici. BMC Genomics. 2014;15(1):313.

Venturini L, Ferrarini A, Zenoni S, Tornielli GB, Fasoli M, Santo SD, et al. De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity. BMC Genomics. 2013;14(1):41.

Donà M, Confalonieri M, Minio A, Biggiogera M, Buttafava A, Raimondi E, et al. RNA-Seq analysis discloses early senescence and nucleolar dysfunction triggered by Tdp1α depletion in Medicago truncatula. Journal of Experimental Botany. 2013;64(7):1941–51.

Da Silva C, Zamperin G, Ferrarini A, Minio A, Dal Molin A, Venturini L, et al. The high polyphenol content of grapevine cultivar tannat berries is conferred primarily by genes that are not shared with the reference genome. Plant Cell. 2013;25(12):4777–88.