Publications

More information at Google Scholar

2020

Yan H, Bombarely A, Li S (2020) DeepTE a computational method for de novo classification of transposons with convolutional neural network. Bioinformatics, btaa 519, https://doi.org/10.1093/bioinformatics/btaa519.

Huang L, Feng G, Yan H, Zhang Z, Bushman BS, Wang JP, Bombarely A, Li M, Yang Z, Nie G, Xie W, Xu L, Chen P, Zhao X, Jiang W, Zhang X (2020) Assembly of the orchardgrass genome provides insights into its genome evolution and flowering regulation. Plant biotechnology Journal 18 (2): 373-388 https://doi.org/10.1111/pbi.13205.

Pombo MA, Rosli HG Fernandez-Pozo N, Bombarely A (2020) The Nicotiana Genome Book, 231-247 – Compendium of Plant Genomes. Springer, Berlin, Heidelberg.

Jimenez-Ruiz J, Ramírez-Tejero JA, Fernandez-Pozo N, Leyva-Perez MO, Yan H, De la Rosa R, Belaj A, Montes E, Rodríguez-Ariza MO, Navarro F, Barroso JB, Beuzon CR, Valpuesta V, Bombarely A, Luque F (2020) The phenotypic diversity of the olive tree (Olea europaea L.) domestication is driven by transposon activity. The Plant Genome https://doi.org/10.1002/tpg2.20010.


2019

Talavera A, Soorni A, Bombarely A, Matas AJ, Hormaza JI (2019) Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana). Scientific reports 9 (1), 20137. doi:10.1038/s41598-019-56526-4

Gramazio P, Yan H, Hasing T, Vilanova S, Prohens J, Bombarely A (2019) Whole-genome resequencing of seven eggplant (Solanum melongena) and one wild relative (S. incanum) accessions provides new insights and breeding tools for eggplant enhancement. Frontiers in Plant Science 10:1220. doi:10.3389/fpls.2019.01220

Cui C, Herlihy JH, Bombarely A, McDowell JM, Haak DC (2019) Draft assembly of Phytopthora capsici from long-read sequencing uncovers complexity. Molecular Plant-Microbe Interactions https://doi.org/10.1094/MPMI-04-19-0103-TA.

Hasing T, Rinaldi E, Manrique S, Colombo L, Haak DC, Zaitlin D, Bombarely A (2019) Extensive phenotypic diversity in the cultivated Florist’s Gloxinia, Sinningia speciosa (Lodd.) Hiern, is derived from the domestication of a single founder population. Plants, People, Planet https://doi.org/10.1002/ppp3.10065

Yan H, Bombarely A, Xu B, Frazier TP, Zhang X, Chen J, Feng G, Wang C, Chen P, Cui C, Li Q, Zhao B, Huang L (2019) Autopolyploidization in switchgrass alters phenotype and flowering time via epigenetic and transcription regulation. Journal Experimental Botany erz325, https://doi.org/10.1093/jxb/erz325

Soorni A, Borna T, Alemardan A, Chakrabarti M, Hunt A, Bombarely A (2019) Transcriptome Landscape Variation in the Genus Thymus. Genes 10(8): 620. https://doi.org/10.3390/genes10080620

Jung H, Winefield C, Bombarely A, Prentis P, Waterhouse P (2019) Tools and strategies for long-read sequencing and de-novo assembly of plant genomes. Trend in Plant Science 24 (8): 700-724. https://doi.org/10.1016/j.tplants.2019.05.003

Manrique S, Friel J, Gramazio P, Hasing T, Ezquer I, Bombarely A (2019) Genetic Insights of the Modification of the Pre-Fertilization Mechanisms during Plant Domestication. Journal of Experimental Botany 70 (11), 3007-3019. https://doi.org/10.1093/jxb/erz231

Hu Y, Resende M, Bombarely A, Brym M, Bassil E, Chambers A (2019) Genomics-Based diversity analysis of Vanilla species using a Vanilla planifolia draft genome and genotyping by sequencing. Scientific reports 9 (1), 3416. https://doi.org/10.1038/s41598-019-40144-1


2018

Bally J, Jung H, Mortimer C, Naim F, Philips JG, Hellens R, Bombarely A, Goodin MM, Waterhouse PM (2018) The Rise and Rise of Nicotiana benthamiana: A Plant for All Reasons. Annual Review of Phytopathology 56:405-426, https://doi.org/10.1146/annurev-phyto-080417-050141

Yan H, Bombarely A, Xu B, Fraizer TP, Wang C, Cheng P, Chen J, Hasing T, Cui C, Zhang XZ, Zhao B, Huang L (2018) SiRNA regulates DNA methylation that interferes gene and lncRNA expression in the heterozygous polyploid switchgrass. Biotechnology for Biofuels 11:208, https://doi.org/10.1186/s13068-018-1202-0.

Bombarely A (2018) Roses for Darwin. Nature Plants – News & Views. Published: 15 June 2018. 10.1038/s41477-018-0195-9

Blankers T. Oh KP, Bombarely A, Shaw KL. (2018) Evolution of the Genomic Architecture in a Rapid Island Radiation: Mapping Chromosomal Rearrangements and Recombination Rate Variation. Genetics August 2018 209: 1329-1344. https://doi.org/10.1534/genetics.118.300894

Foerster H, Bombarely A, Battey JND, Sierro N, Ivanov NV, Mueller LA. (2018) SolCyc: A database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases. Database volume 2018 01/01/2018 bay035 https://doi.org/10.1093/database/bay035.

Montero-Pau J, Blanca J, Bombarely A, Ziarsolo P, Esteras C, Martí-Gómez C, Ferriol M, Gómez P, Jamilena M, Mueller L, Picó B, Cañizares J. (2018). De-novo assembly of zucchini genome: a whole genome duplication associated with the origin of the Cucurbita Plant Biotechnology 16 (6): 1161-1171 DOI: 10.1111/pbi.12860


2017

Soorni A, Fatahi R, Haak D, Salami SA, Bombarely A. (2017). Assessment of Genetic Diversity and Population Structure in Iranian Cannabis Germplasm by Genotyping-By-Sequencing Data. Scientific Reports 7:15668 doi:10.1038/s41598-017-15816-5

Sanchez-Sevilla JF, Vallarino JG, Osorio S, Bombarely A, Pose D, Merchante C, Botella MA, Amaya I, Valpuesta V. (2017) Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa). Scientific Reports 7:13737 doi:10.1038/s41598-017-14239-6

Carlson KD, Fernandez-Pozo N, Bombarely A, Mueller LM, Madlung A (2017) Genomic and transcriptomic natural variation in two populations of the allopolyploid Arabidopsis suecica. BMC Genomics 18 (1), 653; doi: 1186/s12864-017-4067-x

Villarino G, Hu Q, Scanlon M, Mueller LA, Bombarely A, Mattson N. (2017) Dissecting tissue-specific transcriptomic responses from leaf and roots under salt stress in Petunia hybrida Mitchell. Genes 8(8), 195; doi:10.3390/genes8080195.

Zhao C, Lasses T, Bako L, Kong D, Zhao B, Chanda B, Bombarely A, Cruz-Ramírez A, Scheres B, Brunner A, Beers E (2017) XYLEM NAC DOMAIN1: A potential angiosperm innovation regulating xylem differentiation through multiple conserved linear motifs interacting with RETINOBLASTOMA-RELATED. New Phytologist doi:10.1111/nph.14704.

Sherman-Broyles S, Bombarely A, Doyle JJ. (2017). Characterizing the allopolyploid species among the wild relatives of soybean: Utility of reduced representation genotyping methodologies. Journal of Systematics and Evolution 55: 365–376. doi:10.1111/jse.12268.

Edwards K, Fernandez-Pozo N, Drake-Stowe K, Humphry M, Evans A, Bombarely A, Allen F, Hurst R, White B, Kernodle S, Bromley J, Sanchez-Tamburrino J.P., Lewis R, Mueller LA (2017) Map-based cloning of homeologous loci implicated in nitrogen utilization efficiency enabled by an improved Nicotiana tabacum genome assembly. BMC Genomics 18:448. doi:10.1186/s12864-017-3791-6.

Zimmers J, Thomas M, Yang L, Bombarely A, Mancuso M, Wojciechowski M, Smith J. (2017) Species Boundaries in the Astragalus cusickii Complex Delimited using Molecular Phylogenetic Techniques. Molecular Phylogenetics and Evolution 114 :93-110. doi:10.1016/j.ympev.2017.06.004.

Mizzotti C, Galliani B, Dreni L, Sommer H, Bombarely A, Masiero S (2017) ERAMOSA controls lateral branching in snapdragon revealing the molecular evolution of meristem control in higher plants. Scientific Reports 7:41319 doi:10.1038/srep41319.

Soorni A, Haak D, Zaitlin D, Bombarely A (2017) Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data. BMC Genomics 18 (1):49 doi:10.1186/s12864-016-3412-9.

Jiménez-Ruiz J, Leyva-Pérez MO, Schilirò E, Barroso JB, Bombarely A, Mueller LM, Mercado-Blanco J, Luque F (2017) Transcriptomic analysis of the olive (Olea europaea L.)-Verticillium dahliae interaction during early root infection process. The Plant Genome DOI: doi:10.3835/plantgenome2016.07.0060.


2016

Frazier TP, Palmer NA, Xie F, Tobias CM, Donze-Reiner T, Bombarely A, Childs K, Shu S, Jenkins J, Schmutz J, Zhang B, Sarath G, Zhao B (2016) Identification, Characterization, and Gene Expression Analysis of Nucleotide Binding Site (NB)-Type Resistance Gene Homologues in Switchgrass. BMC Genomics 17 (1): 892. doi:10.1186/s12864-016-3201-5.

Coate J, Song M, Bombarely A, Doyle JJ (2016) Expression-level support for gene dosage sensitivity in three Glycine subgenus Glycine polyploids and their diploid progenitors. New Phytologist 212 (4), 1083-1093. doi:10.1111/nph.14090.

Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS, Bliek M, Boersma M, Borghi L, Bruggmann R, Bucher M, D’Agostino N, Davies K, Druege U, Dudareva N, Egea-Cortines M, Delledonne M, Fernandez-Pozo N, Franken P, Grandont L, Heslop-Harrison JS, Hintzsche J, Johns M, Koes R, Lv X, Lyons E, Malla D, Martinoia E, Mattson NS, Morel P, Mueller LA, Muhlemann J, Nouri E, Passeri V, Qi Q, Reinhardt D, Rich M, Richert-Pöggeler K, Robbins TP, Schatz MC, Schranz E, Schuurink RC, Schwarzacher T, Spelt K, Tang H, Urbanus SL, Vandenbusschen M, Vijverberg K, Villarino GH, Warner RM, Weiss J, Yue Z, Zethof J, Quattrocchio F, Sims TL, Kuhlemeier C (2016) Whole genome sequences of the wild parents of the garden petunia give insights into the evolution of Solanaceae genomes. Nature Plants 2: 16074 doi:10.1038/nplants.2016.74.


2015

Castro JC, Maddox JD, Cobos M, Requena D, Zimic M, Bombarely A, Imán SA, Cerdeira LA, Medina AE (2015) De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis. BMC Genomics 16 (1): 997. doi: 1186/s12864-015-2225-6

Vallarino JG, Osorio S, Bombarely A, Casañal A, Cruz‐Rus E, Sánchez‐Sevilla JF, Amaya I, Giavalisco P, Fernie AR, Botella MA, Valpuesta V (2015) Central role of FaGAMYB in the transition of the strawberry receptacle from development to ripening. New Phytologist 208 (2):482-496. doi:10.1111/nph.13463.

Soliman SSM, Greenwood JS, Bombarely A, Mueller LA, Tsao R, Mosser DD, Raizada MN (2015) An Endophyte Constructs Fungicide-Containing Extracellular Barriers for Its Host Plant. Current Biology. 25 (19):2570-2576. doi:10.1016/j.cub.2015.08.027.

Duran I, Csukasi F, Taylor SP, Krakow D, Becerra J, Bombarely A, Marí-Beffa M (2015) Collagen duplicate genes of bone and cartilage participate during regeneration of zebrafish fin skeleton. Gene Expression Patterns 19 (1): 60-69 doi:10.1016/j.gep.2015.07.004.

Strickler SR, Bombarely A, Munkvold JD, Menda N, Martin GB, Mueller LA (2015) Comparative genomics and phylogenetic discordance of cultivated tomato and its nearest wild relatives. 3, e793. doi:10.7717/peerj.793.

Fernandez-Pozo N, Menda N, Edwards JD, Saha S, Tecle IY, Strickler SR, Bombarely A, Fisher-York T, Pujar A, Foerster H, Yan A, Mueller LA (2015) The Sol Genomics Network (SGN)—from genotype to phenotype to breeding. Nucleic Acids Research. 43 (D1), D1036-D1041; doi: 10.1093/nar/gku1195


2014

Kang YJ , Kim S, Kim MY , Lestari P, Kim KH, Ha BK, Jun TH, Hwang WJ, Lee T, Lee J, Shim S, Yoon MY, Jang YE, Han KS, Taeprayoon P, Yoon N, Somta P, Tanya P, Kim KS, Gwag JG, Moon JK, Lee YH, Park BS, Bombarely A, Doyle J, Jackson S, Schafleitner R, Srinives P, Varshney R. (2014) Genome sequence of mungbean and insights into evolution within Vigna species. Nature Communications. 5: 5443 doi:10.1038/ncomms6443.

Menda N, Stricker SR, Edwards JD, Bombarely A, Dunham DM, Martin GB, Mejia L, Hutton SF, Havey MJ, Maxwell DP, Mueller LA. (2014) Analysis of introgressions in the genome of a begomovirus-resistant tomato inbred uncovers origins of its wild ancestors. BMC Plant Biology 14 (1): 287. doi:10.1186/s12870-014-0287-2.

Sherman-Broyles S, Bombarely A, Powell AF, Doyle JL, Egan AN, Coate JE, Doyle JJ (2014) The wild side of a major crop: Soybean’s perennial cousins from Down Under. American Journal of Botany 101:1651-1665. doi:10.3732/ajb.1400121.

Sherman-Broyles S, Bombarely A, Grimwood J, Schmutz J, Doyle JJ (2014) Complete Plastome Sequences from Glycine syndetika, and Six Additional Perennial Wild Relatives of Soybean. G3: Genes| Genomes| Genetics, g3. 114.012690. doi:10.1534/g3.114.012690.

Bombarely A, Coate JE, Doyle JJ (2014) Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex. PeerJ 2, e391. doi: 7717/peerj.391.

Villarino GH, Bombarely A, Giovannoni JJ, Scanlon MJ, Mattson NS (2014) Transcriptomic Analysis of Petunia hybrida in Response to Salt Stress Using High Throughput RNA Sequencing. PloS One 9 (4), e94651. doi:10.1371/journal.pone.0099146.

Jung S, Ficklin S, Lee T, Cheng CH, Blenda A, Zheng P, Yu J, Bombarely A, Cho, IH, Yu S, Evans K, Peace C, Abbott A, Mueller LA, Olmstead M, Main D. (2014) The Genome Database for Rosaceae (GDR): Year 10 Update. Nucleic Acid Research 42 (D1), D1237-D1244. doi:10.1093/nar/gkt1012

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