Dassanayake Lab
COMPARATIVE
FUNCTIONAL
& EVOLUTIONARY
GENOMICS
SELECTED PUBLICATIONS
* Equal contribution or † corresponding author from Dassanayake lab; Lab members in bold
A.W. Short, J.S. V. Sebastian, J. Huang, G. Wang, M. Dassanayake, P.M. Finnegan, J.D. Parker, K-F. Cao, A.K. S. Wee (2024), Comparative transcriptomics of the chilling stress response in two Asian mangrove species, Bruguiera gymnorhiza and Rhizophora apiculate. Tree Physiology. DOI: https://doi.org/10.1093/treephys/tpae019
K-N. Tran*, P. Pantha*, G. Wang*, N. Kumar*, C. Wijesinghege, D-H. Oh, S. Wimalagunasekara, N. Duppen, H. Li, H. Hong, J.C. Johnson, R. Kelt, M.G. Matherne, T.T. Nguyen, J.R. Garcia, A. Clement, D. Tran, C. Crain, et al, S. Barak & M.Dassanayake† (2023), Balancing growth amidst salt stress – lifestyle perspectives from the extremophyte model Schrenkiella parvula. The Plant Journal. DOI: https://doi.org/10.1111/tpj.16396
M.E. Mabry, R.S. Abrahams, I.A. Al-Shehbaz, W.J. Baker, S. Barak, M.S. Barker, R.L. Barrett, A.Beric, S.Bhattacharya, S.B. Carey, G.C. Conant, J.G. Conran, M. Dassanayake et al, A.E. Harkess (2023) Complementing model species with model clades. The Plant Cell. DOI: https://doi.org/10.1093/plcell/koad260
X. Huang, H. Tian, J. Park, D-H. Oh, J. Hu, R. Zentella, H. Qiao, M. Dassanayake & T-P. Sun (2023). The master growth regulator DELLA binding to histone H2A is essential for DELLA-mediated global transcription regulation. Nature Plants
DOI: https://doi.org/10.1038/s41477-023-01477-y
T. Bird, B. Nestor, P. Bayer, G. Wang, C. Gille, B. Soraru, K. Ranathunge, A. Severn-Ellis, R. Jost, W-R. Scheible, M. Dassanayake, J. Batley, D. Edwards, H. Lambers, P. Finnegan (2023). Delayed leaf greening involves a major shift in the expression of cytosolic and mitochondrial ribosomes to plastid ribosomes in the highly phosphorus-use-efficient Hakea prostrata (Proteaceae). Plant and Soil. DOI: https://doi.org/10.1007/s11104-023-06275-1
P. Pantha, D-H. Oh, David Longstreth, M. Dassanayake† (2022), Living with high potassium: balance between nutrient acquisition and K-induced salt stress signaling. Plant Physiology.
DOI: https://doi.org/10.1093/plphys/kiac564
C. Wijesinghege, G. Wang, P. Pantha, K-N. Tran, M. Dassanayake† (2022), Spatiotemporal gene expression atlas of the extremophyte Schrenkiella parvula. Preprint available on bioRxiv. DOI: https://doi.org/10.1101/2022.10.24.513627
C. Wijesinghege, K-N. Tran, M. Dassanayake† (2022), Alternative splicing preferentially increases transcript diversity associated with stress responses in the extremophyte Schrenkiella parvula. Preprint available on bioRxiv. DOI: https://doi.org/10.1101/2022.10.13.512046
G. Eshel, N. Duppen, G. Wang, D-H. Oh, Y. Kazachkova, P. Herzyk, A. Amtmann, M. Gordon, V. Chalifa-Caspi, M. Arland Oscar, S. Bar-David, A. Marshall-Colon, M. Dassanayake†, S. Barak (2022), Positive selection and heat-response transcriptomes reveal adaptive features of the Arabidopsis desert relative, Anastatica hierochuntica. New Phytologist. DOI: https://doi.org/10.1111/nph.18411
Y. Sun, D-H. Oh*, L Duan, P. Ramachandran, A. Ramirez, A. Bartlett, K-N. Tran, G. Wang, M. Dassanayake, J. R Dinneny (2022), Divergence in the ABA gene regulatory network underlies differential growth control. Nature Plants. DOI: https://doi.org/10.1038/s41477-022-01139-5
K-N. Tran, G. Wang, D-H. Oh, J.C. Larkin, A.P. Smith, M. Dassanayake† (2021), Multiple paths lead to salt tolerance - pre-adaptation vs dynamic responses from two closely related extremophytes. Preprint available on bioRxiv. DOI: https://doi.org/10.1101/2021.10.23.465591.
L. Santiago‐Rosario, K. Harms, B. Elderd, P. Hart, M. Dassanayake (2021). No escape: The influence of substrate sodium on plant growth and tissue sodium responses. Ecology and Evolution. DOI: 10.1002/ece3.813
P. Issa, M. Garvey, S. Grimmell, P. Pantha, M. Dassanayake, B. Elderd (2021). Hitching a ride: examining the ability of a specialist baculovirus to translocate through its insect host’s food plant. Pathogens. DOI: 10.3390/pathogens10111500
D-H. Oh†, K.P. Kowalski, Q.N. Quach, C.Wijesinghege, P.Tanford, M. Dassanayake† and K.Clay (2021), Novel genome characteristics contribute to the invasiveness of Phragmites australis (common reed). Molecular Ecology. DOI: https://doi.org/10.1111/mec.16293
G. Wang, S. F. DiTusa, D-H. Oh, A. D. Herrmann, D. G. Mendoza-Cozatl, M. A. O'Neill, A. P. Smith, M. Dassanayake† (2021), Cross species multi-omics reveals cell wall sequestration and elevated global transcription as mechanisms of boron tolerance in plants. New Phytologist. DOI: https://doi.org/10.1111/nph.17295
P. Pantha, S. Chalivendra, D-H. Oh, B. D. Elderd, M. Dassanayake† (2021), A tale of two transcriptomic responses in agricultural pests via host defenses and viral replication. International Journal of Molecular Sciences. DOI: https://doi.org/10.3390/ijms22073568
P. Pantha, M. Dassanayake† (2020), Living with salt. The Innovation. DOI:https://doi.org/10.1016/j.xinn.2020.100050
P. S Young, J.-H. Choi, D.-H. Oh, J. C. Johnson, M. Dassanayake, D.-H. Jeong, and M.-H. Oh (2020) Genome-wide analysis of brassinosteroid responsive small RNAs in Arabidopsis thaliana. Genes & Genomics. DOI: https://doi.org/10.1007/s13258-020-00964-2
G. Wang, D-H. Oh, M. Dassanayake† (2020), GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. BMC Bioinformatics. DOI: https://doi.org/10.1186/s12859-020-3447-4
M.V. Cruz, G.M. Mori, D-H. Oh, M. Dassanayake, M.I. Zucchi, R.S. Oliveira, A.P. Souza# (2020), Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae). Molecular Ecology, 29:344-362, DOI: 10.1111/mec.15330.
M. Foroozani, S. Zahraeifard, D-H. Oh, G. Wang, M. Dassanayake, A. P. Smith (2020), Low-Phosphate Chromatin Dynamics Predict a Cell Wall Remodeling Network in Rice Shoots. Plant Physiology, 182:1494-1509, DOI: https://doi.org/10.1104/pp.19.01153.
M.V. Cruz, G.M. Mori, C.S. Müller, C.C. Silva, D-H. Oh, M. Dassanayake, M.I. Zucchi, R.S. Oliveira, A.P. Souza (2019), Local adaptation of a dominant coastal tree to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches. Scientific Reports, 9.1:1-15. doi.org/10.1038/s41598-019-56469-w.
M. Vithanage, P. Kumarathilaka, C. Oze, S. Karunatilake, M. Seneviratne, Z. Hseu, V. Gunarathne, M. Dassanayake, Y. Ok, J. Rinklebe (2019), Occurrence and cycling of trace elements in ultramafic soils and their impacts on human health: A critical review. Environment International, 131:104974-104993; doi.org/10.1016/j.envint.2019.104974
G. Wang, P. Pantha, K-N. Tran, D-H. Oh, and M. Dassanayake† (2019), Plant Growth and Agrobacterium Mediated Floral-dip Transformation of the Extremophyte Schrenkiella parvula. J. Vis. Exp. (143), e58544, doi:10.3791/58544.
D-H. Oh† and M Dassanayake† (2018), Landscape of gene transposition-duplication within the Brassicaceae family. DNA Research. doi: 10.1093/dnares/dsy035
Y. Kazachkova, G. Eshel, P. Pantha, J. Cheeseman, M. Dassanayake†, S. Barak (2018), Halophytism: What Have We Learnt From Arabidopsis Relative Model Systems?. Plant physiology, pp-00863. doi: 10.1104/pp.18.00863
B. Barkla, T. Rhodes, K-N. Tran, C. Wijesinghege, J. Larkin, M. Dassanayake (2018), Making epidermal bladder cells bigger: Developmental- and salinity-induced endopolyploidy in a model halophyte. Plant Physiology, pp.00033.2018; doi: 10.1104/pp.18.00033
L. Fan, G. Wang*, W. Hu, P. Pantha, K-N. Tran, H Zhang, L. An, M. Dassanayake†, Q. Qiu (2018), Transcriptomic view of survival during early seedling growth of the extremophyte Haloxylon ammodendron. Plant Physiology and Biochemistry. 132, pp475-489. doi.org/10.1016/j.plaphy.2018.09.024
S. Zahraeifard, M. Foroozani, A. Sepehri, D-H. Oh, G. Wang, V. Mangu, B. Chen, N. Baisakh, M. Dassanayake, A. Smith (2018), Rice H2A.Z negatively regulates genes responsive to nutrient starvation but promotes expression of key housekeeping genes. Journal of Experimental Botany, pp-4907–4919, doi: 10.1093/jxb/ery244
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Q. Zhang, D-H. Oh, S. DiTusa, M. Ramana Rao, N. Baisakh, M. Dassanayake†, A. Smith (2018), Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression. BMC Genomics. 19:97. do:10.1186/s12864-017-4397-8 Link
S. Shrestha, D-H. Oh, J. McKowen, M. Dassanayake, C. Hart (2018), 4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin. PLoS ONE, doi: 10.1371/journal.pone.0203843
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A. Gupta, R. Bedre, S. Thapa, A. Sabrin, G. Wang, M. Dassanayake, and A. Grove (2017),
Global Awakening of Cryptic Biosynthetic Gene Clusters in Burkholderia thailandensis. ACS Chemical Biology. doi: 10.1021/acschembio.7b00681
M. Dassanayake† and J. Larkin (2017), Making plants break a sweat: the structure, function, and evolution of plant salt glands. Frontiers in Plant Science. 8:406. doi: 10.3389/fpls.2017.00406.
J. Park, D. Oh, M. Dassanayake, K. T. Nguyen, J. Ogas, G. Choi, T. P. Sun TP (2017), Gibberellin signaling requires chromatin remodeler PICKLE to promote vegetative growth and phase transitions. Plant Physiology. pp.01471. doi: 10.1104/pp.16.01471.
B. Lambert, M. Dassanayake†, D. Oh, S. Garrett, S.Y. Lee, and G. S. Pettis (2016), A novel phase variant of the cholera pathogen shows stress-adaptive cryptic transcriptomic signatures. BMC Genomics. 17:914 doi: 10.1186/s12864-016-3233-x
R. DiMario, J. Quebedeaux, D. Longstreth, M. Dassanayake, M. Hartman, and J. Moroney (2016),The cytoplasmic carbonic anhydrases βCA2 and βCA4 are required for optimal plant growth at low CO2. Plant Physiology, 171(1):280-93. doi: 10. 1104/ pp. 15. 01990
N. Kumar, H. Harashima, S. Kalve, B. Sizani, K. Wang, R. Dale, J. Bramsiepe, L. Bertrand, M. Johnson, C. Faulk, L. Simmons, M. Churchman, K. Sugimoto, N. Kato, M. Dassanayake, G. Beemster, A. Schnittger, and J. Larkin (2015), Functional conservation in the SIAMESE-RELATED family of cyclin-dependent kinase inhibitors in land plants. Plant Cell, 27: 11 3065-3080. doi: http: 10.1105/tpc.15.00489
D-H. Oh, Barkla BJ, R Vera-estrella, O Pantoja, SY Lee, HJ Bohnert, M. Dassanayake† (2015) Cell type-specific responses to salinity – the epidermal bladder cell transcriptome of Mesembryanthemum crystallinum. New Phytologist 207: 627–644. doi: 10.1111/nph.13414
Q. Wang, C. Nowak, A. Korde, D-H. Oh, M. Dassanayake, and D. Donze (2014), Compromised RNA Polymerase III complex assembly leads to local alterations of intergenic RNA Polymerase II transcription in Saccharomyces cerevisiae, BMC Biology, 12:89. doi:10.1186/s12915-014-0089-x
D-H. Oh*, H. Hong*, D. Yun, S.Y. Lee, H. Bohnert, M. Dassanayake†(2014), Genome structures and transcriptomes signify niche adaptation for the multi-ion tolerant extremophyte Schrenkiella parvula, Plant Physiology 164-4. doi: 10. 1104/ pp. 113. 233551.
G. Batelli, D-H. Oh, M.P. D’Urzo, F. Orsini, M. Dassanayake, J.K. Zhu, H.J. Bohnert, R.A. Bressan, A. Maggio, (2014). Using Arabidopsis-related model species (ARMS): growth, genetic transformation, and comparative genomics. Methods in Molecular Biology, 1062, 27–51. doi:10.1007/978-1-62703-580-4_2
D-H. Oh, M. Dassanayake, H. Hong, S. George, S. Paeng, A. Kropornika, S. Lee, R. A. Bressan, D. J. Yun, J. M. Cheeseman, H. J. Bohnert (2013), “Genomics of Plant Abiotic Stress Tolerance” in: Plant Abiotic Stress, 2nd edition, eds. M. Jenks, P. M. Hasegawa. ISBN: 978-1-118-41217-6.
R. A. Bressan, H. C. Park, F. Orsini, D-H. Oh, M. Dassanayake, G. Inan, D. Yun, H. J. Bohnert, A. Maggio (2013), "Biotechnology for mechanisms that counteract salt stress in extremophile species: a genome-based view", Plant Biotechnology Reports, 7-1, pp 27-37
Published before 2013 when Dassanayake was in the labs of Drs. Hans Bohnert or John Cheeseman
H. Wu*, Z. Zhang*, J. Wang*, D-H. Oh*, M. Dassanayake*, B. Liu*, Q. Huang*, H. Sun, R. Xia, Y. Wu, Y. Wang, Z. Yang, Y. Liu, W. Zhang, H. Zhang, J. Chu, C. Yan, S. Fang, J. Zhang, Y. Wang, F. Zhan, G. Wang, S. Lee, J. Cheeseman, B. Yang,B. Li, J. Min, L. Yang, J. Wang, C. Chu, S. Chen, H. Bohnert, J. Zhu, X. Wang, Q. Xie, (2012), Gene Complement and Small RNA Complexity Support the Abiotic Stress Tolerance Phenotype of Thellungiella salsuginea – a Genome-based View. Proceedings of the National Academy of Sciences, 109(30), pp12219-24.
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D-H. Oh*, M. Dassanayake*, H. J. Bohnert, and J. M. Cheeseman. (2012) Life in the extreme: Lessons from the Genome. Genome Biology, 13(3), pp241-249.
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M. Dassanayake*, D-H. Oh*, J. Haas, A. Hernandez, H. Hong, S. Ali, D. Yun, R. Bressan, J. Zhu, J. M. Cheeseman, and H. J. Bohnert. (2011), The Genome of an extremophile Arabidopsis-relative: Thellungiella parvula. Nature Genetics, 43, pp913–918.\
M. Dassanayake, D-H. Oh, D. Yun, R. Bressan, J. M. Cheeseman, H. J. Bohnert. (2011) “The Scope of Things to come - new Paradigms in Biotechnology” in: Plant Biotechnology and Agriculture: Prospects for the 21st Century, eds. A. Altman and M. Hasegawa, Elsevier. ISBN: 978-0-12-381466-1.
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M. Dassanayake, D-H. Oh, H. Hong, H. J. Bohnert, and J. M. Cheeseman (2011), Transcription strength and halophytic lifestyle, Trends in plant science, 16(1), pp1-3.
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D-H. Oh*, M. Dassanayake*, J. Haas, A. Kropornika, C. Wright, M. Urzo, H. Hong, S. Ali, A. Hernandez, G. Lambert, G. Inan, D. Galbraith, R. Bressan, D. Yun, J. Zhu, J. Cheeseman, H. Bohnert. (2010), Genome Structures and Halophyte-Specific Gene Expression of the Extremophile Thellungiella parvula in Comparison with Thellungiella salsuginea (Thellungiella halophila) and Arabidopsis, Plant Physiology, 154, pp1040-1052.
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M. Dassanayake, J. Haas, H. J. Bohnert, J. M. Cheeseman (2010), Comparative Transcriptomics for Mangrove Species: An Expanding Resource, Functional and Integrative Genomics, 10(4), pp523-32.
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M. Dassanayake, J. Haas, H. J. Bohnert, J. M. Cheeseman (2009), Shedding Light on an Extremophile Lifestyle through Transcriptomics, New Phytologist, 183(3), pp764-775.