Dr Nathan Kenny

2023

Journal - Research Article

Greenhough, H., Vignier, J., Peychers, C., Smith, K. F., Kenny, N. J., & Rolton, A. (2023). Exposure to Alexandrium spp. impairs the development of green-lipped mussel (Perna canaliculus) embryos and larvae. Harmful Algae, 127, 102465. doi: 10.1016/j.hal.2023.102465

Truchado-García, M., Perry, K. J., Cavodeassi, F., Kenny, N. J., Henry, J. Q., & Grande, C. (2023). A small change with a twist ending: A single residue in EGF-CFC drives bilaterian asymmetry. Molecular Biology & Evolution, 40(2), msac270. doi: 10.1093/molbev/msac270

Conference Contribution - Published proceedings: Abstract

Hawkes, M. K. N., Dearden, P. K., Gemmell, N. J., & Kenny, N. J. (2023). Evaluating the impacts of climate change at a cellular resolution through comparative single cell sequencing of kuku (green-lipped mussels). Proceedings of the Genetics Otago (GO) Annual Symposium & Workshops. Retrieved from https://blogs.otago.ac.nz/go

Kenny, N. (2023). Molecular mechanisms underlying resilience to climate change in the green lipped mussel (kuku) [Invited]. Proceedings of the Genetics Otago (GO) Annual Symposium & Workshops. Retrieved from https://blogs.otago.ac.nz/go

Null, R., Metzger, B., Álvarez-Campos, P., García-Castro, H., Salamanca-Diaz, D., Emill, E., … Kenny, N., … Özpolat, B. D. (2023). Automating the design of fluorescent in situ probes for big data sets. Proceedings of the Society for Developmental Biology 82nd Annual Meeting. (pp. 37). Retrieved from https://www.sdbonline.org

Conference Contribution - Poster Presentation (not in published proceedings)

Kenny, N. (2023, September). Tracing green-lipped mussel climate change resilience from genome to embryo. Poster session presented at the Company of Biologists Development Journal Meeting: Unconventional and emerging experimental organisms in cell and developmental biology, Dorking, UK.

Conference Contribution - Verbal presentation and other Conference outputs

Kenny, N. J., Gamlen-Greene, R., Stephens, J., Eason, C., & Foster, M. (2023, August). Tracing the diversity and phylogenetic inter-relationships of Kawakawa (Piper excelsum) using a transcriptome-based approach. Verbal presentation at the Kai mō Aotearoa Food Science Meeting [Queenstown Molecular Biology (QMB) Satellite], Queenstown, New Zealand.

Bailie, M., Elliot, A., Stephens, J., Eason, C., & Kenny, N. J. (2023, August). Advancing aquacultural aspirations through genomic sequencing. Verbal presentation at the Queenstown Molecular Biology (QMB) Genomics Satellite, Queenstown, New Zealand.

Kenny, N. (2023, September). Stretched mussels: Tracing the genetic basis of resilience to climate change and ocean acidification in cultured green-lipped mussels (kuku) from genome to embryo. Verbal presentation at the Frontiers in Molecular Zoology Symposium, Göttingen, Germany.

Kenny, N. (2023, August). Molecular mechanisms underlying resilience to climate change in kūtai. Verbal presentation at the New Zealand Ocean Acidification Conference & Climate Change Resilience in Aquaculture Symposium, Nelson, New Zealand.

Other Research Output

Kenny, N. (2023, October). Molecular mechanisms underlying resilience to climate change in the green lipped mussel (kuku). Department of Pathology Seminar Series, University of Otago, Dunedin, New Zealand. [Department Seminar].

2022

Chapter in Book - Research

Sollitto, M., Kenny, N. J., Greco, S., Tucci, C. F., Calcino, A. D., & Gerdol, M. (2022). Detecting structural variants and associated gene presence-absence variation phenomena in the genomes of marine organisms. In C. Verde & D. Giordano (Eds.), Marine genomics: Methods and protocols: Methods in molecular biology (Vol. 2498). (pp. 53-76). New York, NY: Springer. doi: 10.1007/978-1-0716-2313-8_4

Journal - Research Article

Leiva, C., Riesgo, A., Combosch, D., Arias, M. B., Giribet, G., Downey, R., Kenny, N. J., & Taboada, S. (2022). Guiding marine protected area network design with comparative phylogeography and population genomics: An exemplary case from the Southern Ocean. Diversity & Distributions, 28, 1891-1907. doi: 10.1111/ddi.13590

Conference Contribution - Published proceedings: Abstract

Achilleos, K., Smith, A. M., Kenny, N., & Brown, C. M. (2022). Transcriptome analysis of Cellaria immersa (Phylum: Bryozoa) provides insights into marine invertebrate biomineralizations and consequences of climatic changes. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

Hawkes, M., Kenny, N. J., & Itskovich, V. B. (2022). What's your poison? Differential transcriptomic responses to diverse stressors in the Lake Baikal sponge Lubomirskia baikalensis. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

Kenny, N. J. (2022). Stretched mussels: Tracing the genetic basis of resilience to climate change and ocean acidification in green-lipped mussels (kuku) from genome to embryo. Proceedings of the Malacological Society of Australasia (MSA) Molluscs Conference. Retrieved from http://www.malsocaus.org/

Kenny, N. J. (2022). Stretched mussels: Tracing the genetic basis of resilience to climate change and ocean acidification in green-lipped mussels (kuku) from genome to embryo [Invited]. Proceedings of the ComBio Conference. (pp. 80). Retrieved from https://combio.org.au/combio2022/

Conference Contribution - Poster Presentation (not in published proceedings)

Walker, L. A., Kenny, N. J., & Itskovich, V. B. (2022, August-September). To haline back: Investigating freshwater sponge hologenomes and mitgenomics using draft genomic sequencing. Poster session presented at the 31st Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.

Kenny, N. J., Arias-Baldrich, C., García-Castro, H., Emili, E., Mason, V., & Solana, J. (2022, August-September). Single cell RNAseq and ATACseq analysis uncovers the transcriptional landscape underpinning cell type specification in the flatworm Schmidtea mediterranea. Poster session presented at the 31st Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.

Kenny, N. J. (2022, August-September). Stretched mussels: Tracing the genetic basis of resilience to climate change and ocean acidification in cultured green-lipped mussels (kuku) from genome to embryo. Poster session presented at the 31st Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.

Hawkes, M., Kenny, N. J., & Itskovich, V. B. (2022, August-September). What's your poison? Differential transcriptomic responses to diverse stressors in the Lake Baikal sponge Lubomirskia baikalensis. Poster session presented at the 31st Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.

Greenhough, H. E., Smith, K. F., Vignier, J., Peychers, C., Rolton, A., & Kenny, N. J. (2022, August-September). Effect of Alexandrium spp. on the early life stages of Perna canaliculus. Poster session presented at the 31st Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.

Achilleos, K., Smith, A. M., Kenny, N., & Brown, C. M. (2022, August-September). Transcriptome analysis of Cellaria immersa (Phylum: Bryozoa) provides insights into marine invertebrate biomineralization and consequences of climatic changes. Poster session presented at the 31st Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.

Other Research Output

Kenny, N. (2022, October). Uncovering the transcriptional landscape underpinning cell type specification in whole animals using single cell RNAseq and ATACseq analysis. Department of Pathology Seminar Series, University of Otago, Dunedin, New Zealand. [Department Seminar].

Kenny, N. (2022, June). Genome evolution in the freshwater sponge Ephydatia muelleri (and the symbionts it has picked up along the way). Department of Microbiology and Immunology Research Seminar, University of Otago, Dunedin, New Zealand. [Department Seminar].

Kenny, N. (2022, May). The freshwater sponge Ephydatia muelleri: A multifaceted tool for tracing genome evolution across the Metazoa. College of Marine Life Sciences, Ocean University of China [Online]. [Research Presentation].

2021

Journal - Research Article

Pechmann, M., Kenny, N. J., Pott, L., Heger, P., Chen, Y.-T., Buchta, T., … Roth, S. (2021). Striking parallels between dorsoventral patterning in Drosophila and Gryllus reveal a complex evolutionary history behind a model gene regulatory network. eLIFE, 10, e68287. doi: 10.7554/eLife.68287

Calcino, A. D., Kenny, N. J., & Gerdol, M. (2021). Single individual structural variant detection uncovers widespread hemizygosity in molluscs. Philosophical Transactions of the Royal Society B, 376, 20200153. doi: 10.1098/rstb.2020.0153

Riesgo, A., Taboada, S., Kenny, N. J., Santodomingo, N., Moles, J., Leiva, C., … Maldonado, M. (2021). Recycling resources: Silica of diatom frustules as a source for spicule building in Antarctic siliceous demosponges. Zoological Journal of the Linnean Society, 192(2), 259-276. doi: 10.1093/zoolinnean/zlaa058

Kenny, N. J., & Itskovich, V. B. (2021). Phylogenomic inference of the interrelationships of Lake Baikal sponges. Systematics & Biodiversity, 19(2), 209-217. doi: 10.1080/14772000.2020.1827077

Plese, B., Kenny, N. J., Rossi, M. E., Cárdenas, P., Schuster, A., Taboada, S., … Riesgo, A. (2021). Mitochondrial evolution in the Demospongiae (Porifera): Phylogeny, divergence time, and genome biology. Molecular Phylogenetics & Evolution, 155, 107011. doi: 10.1016/j.ympev.2020.107011

Journal - Research Other

García-Castro, H., Kenny, N. J., Iglesias, M., Álvarez-Campos, P., Mason, V., Elek, A., … Solana, J. (2021). ACME dissociation: A versatile cell fixation-dissociation method for single-cell transcriptomics. Genome Biology, 22, 89. doi: 10.1186/s13059-021-02302-5

Other Research Output

Kenny, N. (2021, August). Polar porifera: Selection and novelty in Antarctic sponge gene complements. Department of Marine Science Seminar Series, University of Otago [Online]. [Department Seminar].

2020

Journal - Research Article

Kenny, N. J., Francis, W. R., Rivera-Vicéns, R. E., Juravel, K., de Mendoza, A., Díez-Vives, C., … Leys, S. P. (2020). Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri. Nature Communications, 11, 3676. doi: 10.1038/s41467-020-17397-w

Britstein, M., Cerrano, C., Burgsdorf, I., Zoccarato, L., Kenny, N. J., Riesgo, A., … Steindler, L. (2020). Sponge microbiome stability during environmental acquisition of highly specific photosymbionts. Environmental Microbiology, 22(8), 3593-3607. doi: 10.1111/1462-2920.15165

Journal - Research Other

Kenny, N. J., McCarthy, S. A., Dudchenko, O., James, K., Betteridge, E., Corton, C., … Williams, S. T. (2020). The gene-rich genome of the scallop Pecten maximus [Data Note]. GigaScience, 9(5), giaa037. doi: 10.1093/gigascience/giaa037

2019

Journal - Research Article

Sumner-Rooney, L., Kenny, N. J., Ahmed, F., & Williams, S. T. (2019). The utility of micro-computed tomography for the non-destructive study of eye microstructure in snails. Scientific Reports, 9, 15411. doi: 10.1038/s41598-019-51909-z

Kenny, N. J., Plese, B., Riesgo, A., & Itskovich, V. B. (2019). Symbiosis, selection, and novelty: Freshwater adaptation in the unique sponges of Lake Baikal. Molecular Biology & Evolution, 36(11), 2462-2480. doi: 10.1093/molbev/msz151

Kenny, N. J., Noreña, C., Damborenea, C., & Grande, C. (2019). Probing recalcitrant problems in polyclad evolution and systematics with novel mitochondrial genome resources. Genomics, 111(3), 343-355. doi: 10.1016/j.ygeno.2018.02.009

Leiva, C., Taboada, S., Kenny, N. J., Combosch, D., Giribet, G., Jombart, T., & Riesgo, A. (2019). Population substructure and signals of divergent adaptive selection despite admixture in the sponge Dendrilla antarctica from shallow waters surrounding the Antarctic Peninsula. Molecular Ecology, 28(13), 3151-3170. doi: 10.1111/mec.15135

Álvarez-Campos, P., Kenny, N. J., Verdes, A., Fernández, R., Novo, M., Giribet, G., & Riesgo, A. (2019). Delegating sex: Differential gene expression in stolonizing syllids uncovers the hormonal control of reproduction. Genome Biology & Evolution, 11(1), 295-318. doi: 10.1093/gbe/evy265

González-Aravena, M., Kenny, N. J., Osorio, M., Font, A., Riesgo, A., & Cárdenas, C. A. (2019). Warm temperatures, cool sponges: The effect of increased temperatures on the Antarctic sponge Isodycta sp. PeerJ, 7, e8088. doi: 10.7717/peerj.8088

Journal - Research Other

Plese, B., Rossi, M. E., Kenny, N. J., Taboada, S., Koutsouveli, V., & Riesgo, A. (2019). Trimitomics: An efficient pipeline for mitochondrial assembly from transcriptomic reads in nonmodel species. Molecular Ecology Resources, 19(5), 1230-1239. doi: 10.1111/1755-0998.13033

2018

Journal - Research Article

Kenny, N. J., de Goeij, J. M., de Bakker, D. M., Whalen, C. G., Berezikov, E., & Riesgo, A. (2018). Towards the identification of ancestrally shared regenerative mechanisms across the metazoa: A transcriptomic case study in the demosponge Halisarca caerulea. Marine Genomics, 37, 135-147. doi: 10.1016/j.margen.2017.11.001

Taboada, S., Kenny, N. J., Riesgo, A., Wiklund, H., Paterson, G. L. J., Dahlgren, T. G., & Glover, A. G. (2018). Mitochondrial genome and polymorphic microsatellite markers from the abyssal sponge Plenaster craigi Lim & Wiklund, 2017: Tools for understanding the impact of deep-sea mining. Marine Biodiversity, 48, 621-630. doi: 10.1007/s12526-017-0786-0

Riesgo, A., Cavalcanti, F. F., Kenny, N. J., Ríos, P., Cristobo, J., & Lanna, E. (2018). Integrative systematics of clathrinid sponges: Morphological, reproductive and phylogenetic characterisation of a new species of Leucetta from Antarctica (Porifera, Calcarea, Calcinea) with notes on the occurrence of flagellated sperm. Invertebrate Systematics, 32(4), 827-841. doi: 10.1071/is17033

Schumann, I., Kenny, N., Hui, J., Hering, L., & Mayer, G. (2018). Halloween genes in panarthropods and the evolution of the early moulting pathway in Ecdysozoa. Royal Society Open Science, 5(9), 180888. doi: 10.1098/rsos.180888

2017

Journal - Research Article

Pechmann, M., Benton, M. A., Kenny, N. J., Posnien, N., & Roth, S. (2017). A novel role for Ets4 in axis specification and cell migration in the spider Parasteatoda tepidariorum. eLIFE, 6, e27590. doi: 10.7554/eLife.27590

2016

Journal - Research Article

Benton, M. A., Kenny, N. J., Conrads, K. H., Roth, S., & Lynch, J. A. (2016). Deep, staged transcriptomic resources for the novel coleopteran models Atrachya menetriesi and Callosobruchus maculatus. PLoS ONE, 11(12), e0167431. doi: 10.1371/journal.pone.0167431

Kenny, N. J., Truchado-García, M., & Grande, C. (2016). Deep, multi-stage transcriptome of the schistosomiasis vector Biomphalaria glabrata provides platform for understanding molluscan disease-related pathways. BMC Infectious Diseases, 16, 618. doi: 10.1186/s12879-016-1944-x

Kenny, N. J., Chan, K. W., Nong, W., Qu, Z., Maeso, I., Yip, H. Y., … Hui, J. H. L. (2016). Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs. Heredity, 116, 190-199. doi: 10.1038/hdy.2015.89

2015

Journal - Research Article

Kenny, N. J., Sin, Y. W., Hayward, A., Paps, J., Chu, K. H., & Hui, J. H. L. (2015). The phylogenetic utility and functional constraint of microRNA flanking sequences. Proceedings of the Royal Society B, 282(1803), 20142983. doi: 10.1098/rspb.2014.2983

Sin, Y. W., Kenny, N. J., Qu, Z., Chan, K. W., Chan, K. W. S., Cheong, S. P. S., … Hui, J. H. L. (2015). Identification of putative ecdysteroid and juvenile hormone pathway genes in the shrimp Neocaridina denticulata. General & Comparative Endocrinology, 214, 167-176. doi: 10.1016/j.ygcen.2014.07.018

Qu, Z., Kenny, N. J., Lam, H. M., Chan, T. F., Chu, K. H., Bendena, W. G., … Hui, J. H. L. (2015). How did arthropod sesquiterpenoids and ecdysteroids arise? Comparison of hormonal pathway genes in noninsect arthropod genomes. Genome Biology & Evolution, 7(7), 1951-1959. doi: 10.1093/gbe/evv120

Kenny, N. J., Shen, X., Chan, T. T. H., Wong, N. W. Y., Chan, T. F., Chu, K. H., … Hui, J. H. L. (2015). Genome of the rusty millipede, Trigoniulus corallinus, illuminates diplopod, myriapod, and arthropod evolution. Genome Biology & Evolution, 7(5), 1280-1295. doi: 10.1093/gbe/evv070

Kenny, N. J., Namigai, E. K. O., Marlétaz, F., Hui, J. H. L., & Shimeld, S. M. (2015). Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida). Marine Genomics, 24, 139-146. doi: 10.1016/j.margen.2015.07.004

2014

Journal - Research Article

Kenny, N. J., Sin, Y. W., Shen, X., Zhe, Q., Wang, W., Chan, T. F., … Hui, J. H. L. (2014). Genomic sequence and experimental tractability of a new decapod shrimp model, Neocaridina denticulata. Marine Drugs, 12(3), 1419-1437. doi: 10.3390/md12031419

Grande, C., Martín-Durán, J. M., Kenny, N. J., Truchado-García, M., & Hejnol, A. (2014). Evolution, divergence and loss of the nodal signalling pathway: New data and a synthesis across the Bilateria. International Journal of Developmental Biology, 58, 521-532. doi: 10.1387/ijdb.140133cg

Kenny, N. J., Namigai, E. K. O., Dearden, P. K., Hui, J. H. L., Grande, C., & Shimeld, S. M. (2014). The lophotrochozoan TGF-β signalling cassette: Diversification and conservation in a key signalling pathway. International Journal of Developmental Biology, 58, 533-549. doi: 10.1387/ijdb.140080nk

Chipman, A. D., Ferrier, D. E. K., Brena, C., Qu, J., Hughes, D. S. T., Schröder, R., … Dearden, P. K., … Duncan, E. J., … Kenny, N. J., … Richards, S. (2014). The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima. PLoS Biology, 12(11), e1002005. doi: 10.1371/journal.pbio.1002005

Wilson, M. J., Kenny, N. J., & Dearden, P. K. (2014). Components of the dorsal-ventral pathway also contribute to anterior-posterior patterning in honeybee embryos (Apis mellifera). EvoDevo, 5, 11. doi: 10.1186/2041-9139-5-11

Journal - Research Other

Namigai, E. K. O., Kenny, N. J., & Shimeld, S. M. (2014). Right across the tree of life: The evolution of left-right asymmetry in the Bilateria. Genesis, 52(6), 458-470. doi: 10.1002/dvg.22748

2013

Journal - Research Article

Kenny, N. J., & Dearden, P. K. (2013). NMDA receptor expression and C terminus structure in the rotifer Brachionus plicatilis and long-term potentiation across the Metazoa. Invertebrate Neuroscience, 13, 125-134. doi: 10.1007/s10158-013-0154-0

Journal - Research Other

Kenny, N. J., Quah, S., Holland, P. W. H., Tobe, S. S., & Hui, J. H. L. (2013). How are comparative genomics and the study of microRNAs changing our views on arthropod endocrinology and adaptations to the environment? General & Comparative Endocrinology, 188, 16-22. doi: 10.1016/j.ygcen.2013.02.013

2012

Journal - Research Article

Kenny, N. J., & Shimeld, S. M. (2012). Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida; Serpulidae) reveals annelid trochophore transcription factor cassette. Development Genes & Evolution, 222, 325-339. doi: 10.1007/s00427-012-0416-6

2009

Conference Contribution - Verbal presentation and other Conference outputs

Kenny, N. (2009, November). Getting nervous? The neural architecture of the Rotifer Brachionus plicatilis. Verbal presentation at the Genetics Otago Postgraduate Symposium, Dunedin, New Zealand.