Publications
2022
Vandepol N, Liber J, Yocca A, Matlock J, Edger P, Bonito G. Accepted. Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species. PLOS One. Accepted
2021
Wang W, Hejasebazzi A, Zheng J, Liu K. Build a better bootstrap and the RAWR shall beat a random path to your door: phylogenetic support estimation revisited. Bioinformatics. 2021; V37:111-119 DOI: doi.org/10.1093/bioinformatics/btab263
Mei Y, Liu C-Y, Li S-H, Guerin-Laguette A, Xiao Y-J, Tang P, Wan S-P, Bonito G, Wang Y. 2021. Phlebopus roseus, a new edible bolete from China, is associated with insects and plants. Mycologia. DOI: 10.1080/00275514.2020.1816781
Liao H-L, Bonito G, Hameed K, Wu SH, Chen K-H, Labbé J, Schadt CW, Tuskan GA, Martin F, Kuo A, Barry K, Grigoriev IV, Vilgalys R. 2021. Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root Fungi. Frontiers in Microbiology. DOI: 10.3389/fmicb.2021.680267
Liber JA, Bonito G, Benucci GMN. CONSTAX2: Improved taxonomic classification of environmental DNA markers. Bioinformatics. DOI: 10.1093/bioinformatics/btab347
2020
Zhu S, Bonito G, Chen Y, and Du Z. 2020. Oleaginous Fungi in Biorefineries. In “Reference Module in Life Sciences” (ISBN 9780128096338), DOI: 10.1016/B978-0-12-819990-9.00004-4.
Myers JM, Bonds AE, Simmons DR, Clemons RA, Thapa NA, Desiro A, Bonito G, Longcore JE, Stajich J, James TY. 2020. In vitro and in silico screenings of early-diverging lineages reveal abundant and diverse mycoviruses throughout kingdom Fungi. mSystems. doi: 10.1128/mBio.02027-20
Vandepol N, Liber J, Desiro A, Na H, Kennedy M, Barry K, Grigoriev IV, Miller A, O’Donnell K, Stajich J, Bonito G. 2020. Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics. Fungal Diversity. doi.org/10.1007/s13225-020-00455-5
Zhang K, Bonito G, Hsu CM, Hameed K, Vilgalys R, Liao HL. 2020. Mortierella elongata increases plant biomass among non-leguminous crop species. Agronomy, 10, 754. doi: 10.3390/agronomy10050754
Benucci GMN, Burnard D, Shepherd LD, Bonito G, Munkacsi A. 2020. Evidence for co-evolutionary history of early diverging Lycopodiaceae plants with fungi. Frontiers in Plant Biology. doi.org/10.3389/fmicb.2019.02944
2019
Banerjee A, Arnesen JA, Moser D, Motsa BB, Johnson SR, Hamberger B. Engineering modular diterpene biosynthetic pathways in Physcomitrella patens. Planta. 2019; 249(1):221-233. PubMed [journal] PMID: 30470899
Bonito G, Benucci GMN, Hameed K, Weighill D, Jones P, Chen KH, Jacobson D, Schadt C, Vilgalys R. Accepted. Fungal-bacterial networks in the Populus rhizobiome are impacted by soil properties and host genotype. Frontiers in Microbiology. 10:481 DOI: doi.org/10.3389/fmicb.2019.00481
Du Z-Y, Zienkiewicz K, Vande Pol N, Ostrom NE, Benning C, Bonito GM. 2019. Algal-fungal symbiosis leads to photosynthetic mycelium. eLife; 8:e47815 DOI: 10.7554/eLife.47815
Edger, P.P., T.J. Poorten, R. VanBuren, M.A. Hardigan, M. Colle, M.R. McKain, R.D. Smith, S. Teresi, A.D.L. Nelson, C.M. Wai, E.I. Alger, K.A. Bird, A.E. Yocca, N. Pumplin, S. Ou, G. Ben-Zvi, A. Brodt, K. Baruch, T. Swale, L. Shiue, C.B. Acharya, G.S. Cole, J.P. Mower, K.L. Childs, N. Jiang, E. Lyons, M. Freeling, J.R. Puzey, and S.J. Knapp. Origin and Evolution of the Octoploid Strawberry Genome. 2019. Nature Genetics. 51, 541-547.
Johnson SR, Bhat WW, Bibik J, Turmo A, Hamberger B, Hamberger B. A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae). The Journal of biological chemistry. 2019; 294(4):1349-1362. PubMed [journal] PMID: 30498089, PMCID: PMC6349103
Johnson SR, Bhat WW, Sadre R, Miller GP, Garcia AS, Hamberger B. Promiscuous terpene synthases from Prunella vulgaris highlight the importance of substrate and compartment switching in terpene synthase evolution. The New Phytologist. 2019; PubMed [journal] PMID: 30843212Millet LJ, Aufrecht J, Labbé J, Uehling J, Vilgalys R, Estes ML, Guennoc CM, Deveau A, Olsson A, Bonito G, Doktycz MJ, Retterer ST. Fungal
Liao HL, Bonito G, Rojas JA, Hameed K, Wu S, Schadt CW, Labbé JL, Tuskan G, Martin FM, Greigoriev IV, Vilgalys R. 2019. Fungal endophytes of Populus trichocarpa alter host phenotype, gene expression and rhizobiome composition. Molecular Plant Microbial Interaction. 32: 853-864. https://doi.org/10.1094/MPMI-05-18-0133-R
Millet LJ, Aufrecht J, Labbé J, Uehling J, Vilgalys R, Estes ML, Guennoc CM, Deveau A, Olsson A, Bonito G, Doktycz MJ, Retterer ST. 2019. Increasing access to microfluidics for studying fungi and other branched biological structures. Fungal Biology and Biotechnology 6:1. doi: 10.1186/s40694-019-0071-z
Sadre R, Kuo P, Chen J, Yang Y, Banerjee A, Benning C, Hamberger B. Cytosolic lipid droplets as engineered organelles for production and accumulation of terpenoid biomaterials in leaves. Nature communications. 2019; 10(1):853. PubMed [journal] PMID: 30787273, PMCID: PMC6382807
2018
Benucci GMN, Bonito V, Bonito G. 2018. Fungal, Bacterial, and Archaeal Diversity in Soils Beneath Native and Introduced Plants in Fiji, South Pacific. Microbial Ecology. https://doiorg/101007/s00248-018-1266-1
Chang Y, Desirò A, Na H, Sandor L, Lipzen A, Clum A, Barry K, Grigoriev IV, Martin FM, Stajich JE, Smith ME, Bonito G, Spatafora JW. 2018. Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota. New Phytologist. doi:101111/nph15613. (I.F.=7.3)
Chen KH, Liao HL, Arnold AE, Bonito G, Lutzoni F. 2018. RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi. New Phytologist. doi.org/10.1111/nph.15092 (I.F.=7.3)
Desirò A, Hao Z, Julian L, Benucci G, Lowry D, Roberson R, Bonito G. 2018. Mortierellomycotina as model organisms to investigate the interaction between Mycoplasma-related endobacteria and their fungal hosts.ISME. https://doi.org/10.1038/s41396-018-0053-9 (I.F.=9.3)
Deveau A, Bonito G, Uehling J, Becker M, Bindschedler S, Paoletti M, Hacquard S, Hervé V, Labbé J, Lastovetsky O, Mieszkin S, Millet L, Vajna B, Bonfante P, van Elsas JD, Wick L. 2018. Bacterial – Fungal Interactions: ecology, mechanisms and challenges. FEMS Microbiology Reviews. (I.F.=12.2)
Edger PP, McKain MR, Bird KA and R. VanBuren. 2018. Subgenome assignment in allopolyploids: challenges and future directions. Current Opinion In Plant Biology 42: 76-80. (I.F. = 7.8).
Emery M, Willis MMS, Hao Y, Barry K, Oakgrove K, Peng Y, Schmutz J, Lyons E, Pires JC, Edger PP, Conant GC. 2018. Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. PloS Genetics 14: e1007267. (I.F. = 7.2).
Hao Y, Washburn JD, Rosenthal J, Nielsen B, Lyons E, Edger PP, Pires JC, Conant GC. 2018. Patterns of population variation in two paleopolyploid eudicot lineages suggest that dosage-based selection on homeologs is long-lived. Genome Biology and Evolution. 10: 999-1011. (I.F. = 3.9).
Hejase HA, Vande Pol N, Bonito GM, Liu KJ. 2018. FastNet: Fast and Accurate Statistical Inference of Phylogenetic Networks Using Large-Scale Genomic Sequence Data. In: Blanchette M., Ouangraoua A. (eds) Comparative Genomics. RECOMB-CG 2018. Lecture Notes in Computer Science, vol 11183. Pp.242-259. Springer, Cham.
Misztal, Pawel K., Despoina S. Lymperopoulou, Rachel I. Adams, Russell A. Scott, Steven E. Lindow, Thomas Bruns, John W. Taylor, GM Bonito, R Vilgalys, A Goldstein. 2018. Emission Factors of Microbial Volatile Organic Compounds from Environmental Bacteria and Fungi. Environmental Science & Technology 52 (15): 8272–82.
2017
Desirò A, Rimington W, Jacob A, Vande Pol N, Smith M, Trappe J, Bidartondo M, Bonito G. 2017. Multigene Phylogeny of Endogonales, an Early Diverging Lineage of Fungi Associated with Plants. IMA Fungus. 8 (2), 245-264.
Hejase H, VandePol N, Bonito G, Edger P, Liu K. 2017. Coal-Miner: A Statistical Method for GWA Studies of Quantitative Traits with Complex EvolutionaryOrigins. Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. 107-114. DOI: 10.1145/3107411.3107490
Zhi-Yan D, Alvaro J, Hyden B, Zienkiewicz K, Benning N, Zienkiewicz A, Bonito G, Benning C. 2017. Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata. Biotechnology for Biofuels. (I.F.=5.2)