PUBLICATIONS
Publications in peer-reviewed journals
17. The Mint Evolutionary Genomics Consortium (Authors in alphabetical order: Buell CR, Crisovan E, Dudareva N, Garcia N, Godden G, Henry L, Kates HR, Kilgore M, Kamileen MO, Lichman BR, Mavrodiev EV, Rodriguez C, O’Connor SE, Soltis D, Soltis P, Vaillancourt B, Wiegert-Rininger K, Zhao D), Phylogenomic mining of the mints: elucidating evolution in a chemically diverse clade. Provisionally accepted at Molecular Plant
16. Zhao D, Hamilton JP, Vaillancourt B, Zhang W, Eizenga GC, Cui Y, Jiang J, Buell CR, Jiang N (2018) The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum. Nucleic Acids Research. doi: 10.1093/nar/gky025
15. Hoopes G, Hamilton J, Kim J, Zhao D, Wiegert-Rininger K, Crisovan E, and Buell CR (2018) Genome assembly and annotation of the medicinal plant Calotropis gigantea, a producer of anti-cancer and anti-malarial cardenolides. G3: Genes, Genomes, Genetics 8(2): 385-391. doi: 10.1534/g3.117.300331.
14. Sherden NH, Lichman B, Caputi L, Zhao D, Kamileen MO, Buell CR, O’Connor SE (2017) Identification of iridoid synthases from Nepeta (catnip): Iridoid cyclization does not determine nepetalactone stereochemistry. Phytochemistry 145: 48-56
13. Zhao D, Hamilton JP, Pham GM, Crisovan E, Wiegert-Rininger K, Vaillancourt B, DellaPenna D, Buell CR (2017) De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin. GigaScience 6: 1-7 https://doi.org/10.1093/gigascience/gix065
12. Kamfwa K, Zhao D, Kelly JD, Cichy KA (2017) Transcriptome analysis of two recombinant inbred lines of common bean contrasting for symbiotic nitrogen fixation. PLoS One 12 (2), e0172141
11. Zhao D, Hamilton JP, Hardigan M, Yin D, He T, Vaillancourt B, Reynoso M, Pauluzzi G, Funkhouser S, Cui Y, Bailey-Serres J, Jiang J, Buell CR, Jiang N (2017) Analysis of ribosome-associated mRNAs in rice reveals the importance of transcript size and GC content in translation. G3: Genes, Genomes, Genetics 7 (1), 203-219
10. Gao D, Zhao D, Abernathy B, Iwata-Otsubo A, Herrera-Estrella A, Jiang N, Jackson SA (2016) Dynamics of a novel highly repetitive CACTA family in common bean (Phaseolus vulgaris). G3: Genes, Genomes, Genetics 6: 2091-2101
9. Zhao D, Ferguson A, and Jiang N (2016) What makes up plant genomes: the vanishing line between transposable elements and genes. BBA - Gene Regulatory Mechanisms 1859: 366-380
8. Zhao D, Ferguson A, and Jiang N (2015) Transposition of a rice Mutator-like transposable element in the yeast Saccharomyces cerevisiae. The Plant Cell 27: 132-148
7. Zhao D and Song GQ (2014) High-throughput sequencing as an effective approach in profiling small RNAs derived from a hairpin RNA expression vector in woody plants. Plant Science 228: 39-47
6. Zhao D and Song GQ (2014) Rootstock-to-scion transfer of transgene-derived small interfering RNAs and their effect on virus resistance in nontransgenic sweet cherry. Plant Biotechnology Journal 12: 1319-1328 doi: 10.1111/pbi.12243
5. Zhao D and Jiang N (2014) Nested insertions and accumulation of indels are negatively correlated with abundance of Mutator-like transposable elements in maize and rice. PLoS One 9 (1): e87069. doi:10.1371/journal.pone.0087069
4. Song GQ, Walworth A, Zhao D, Jiang N, and Hancock JF (2013) The Vaccinium corymbosum FLOWERING LOCUS T-like gene (VcFT): a flowering activator reverses photoperiodic and chilling requirements in blueberry. Plant Cell Reports 32: 1759-1769
3. Ferguson A, Zhao D, and Jiang N (2013) Selective acquisition and retention of genomic sequences by Pack-Mutator-like elements based on GC content and the breadth of expression. Plant Physiology 163(3): 1419-1432
2. Song GQ, Walworth A, Zhao D, Hildebrandt B, and Leasia M (2013) Constitutive expression of the K-domain of a Vaccinium corymbosum SOC1-like (VcSOC1-K) MADS-box gene is sufficient to promote flowering in tobacco. Plant Cell Reports 32: 1819-1826
1. Zhao D, Tian Q, Li L, and Zhang W (2007) Nitric oxide is involved in nitrate-induced inhibition of root elongation in Zea mays. Annals of Botany 100: 497-503
Manuscripts under review and submitted
Franke J, Kim J, Hamilton JP, Zhao D, Pham GM, Wiegert-Rininger K, Crisovan E, Newton LA, Vaillancourt B, Tatsis EC, Buell CR, O'Connor SE, Elucidating plant specialized metabolism using synteny. Submitted.
Conference abstracts and presentations
7. Zhao D (2018) Pack-Mutator-like transposable elements: Trash or hidden treasure? Invited Talk at Plant Biology Spring Seminar Series, MSU
6. Wang J, Zhao D, Buell CR, Childs K (2017) deFusion: a tool to improve predictions of tandemly duplicated genes created by the MAKER annotation pipeline. Genome Informatics Meeting at Cold Spring Harbor Laboratory
5. Zhao D (2015) Learn from practice: Detecting problems within your next-generation sequencing datasets. Applied Bioinformatics Seminar, MSU
4. Zhao D, Ferguson A, and Jiang N (2015) Transposition of a rice Mutator-like element in the yeast Saccharomyces cerevisiae. The 57th Annual Maize Genetics Conference Abstracts. 57:P336
3. Zhao D and Jiang N (2013) Nested insertions and accumulation of indels in coding-MULEs (Mutator-like transposable elements) are negatively correlated with abundance of MULEs in maize and rice. The 55th Annual Maize Genetics Conference Abstracts. 55:P340
2. Zhao D and Jiang N (2013) Nested insertions and accumulation of indels in coding-MULEs (Mutator-like transposable elements) are negatively correlated with abundance of MULEs in maize and rice. International Plant & Animal Genome Conference XXI Abstracts. P677
1. Zhao D, Moose S, and Jiang N (2011) The insertion polymorphism of Mutator-like elements (MULEs) and their influence on gene expression upon long-term selection in maize. The 53rd Annual Maize Genetics Conference Abstracts. 53:P294