Chris Jackson

Research Scientist (Bioinformatics)

Chris Jackson is a bioinformatician with a background in genomics, phylogenomics and endosymbiosis. His interests include the molecular-genetic evolution of algae and plants, ranging from single-celled dinoflagellate algae and glaucophytes through to multicellular seaweeds.

At the RBGV, Chris works with other Research Scientists on diverse projects including plant and fungal genome evolution, phylogenomics, and population genetics. In addition, Chris provides bioinformatics support for the Bioplatforms Australia project ‘Genomics for Australian Plants’, an initiative providing genomic resources for evolutionary and conservation studies of iconic Australian plants.


Refereed journal articles

Jackson, C., McLay, T., Schmidt-Lebuhn, A.N. (2023) hybpiper-nf and paragone-nf: Containerization and additional options for target capture assembly and paralog resolution. Appl Plant Sci. 11 (4):e11532. doi: 10.1002/aps3.11532

McLay. T.G.B., Murphy, D.J., Holmes, G.D., Mathews S, Brown GK, Cantrill, D.J., Udovicic, F., Allnutt, T.R., Jackson, C.J. (2022). A genome resource for Acacia, Australia's largest plant genus. PLoS One.17 (10):e0274267. doi: 10.1371/journal.pone.0274267

Repetti, S.I., Iha, C., Uthanumallian, K., Jackson, C.J., Chen, Y., Chan, C.X., Verbruggen, H. (2022). Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae. New Phytol. 233 (5): 2144 – 2154. doi: 10.1111/nph.17926

McLay, T.G.B., Birch JL, Gunn, B.F., Ning, W., Tate,  J.A,. Nauheimer, L., Joyce, E.M., Simpson, L., Schmidt-Lebuhn, A.N., Baker, W.J., Forest, F., Jackson, C.J. (2021). New targets acquired: Improving locus recovery from the Angiosperms353 probe set. Appl Plant Sci.  9 (7):10.1002/aps3.11420. doi: 10.1002/aps3.11420

Repetti, S.I., Jackson, C.J., Judd, L.M., Wick, R.R., Holt, K.E., Verbruggen, H. (2020). The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns. PeerJ.  8:e8273. doi: 10.7717/peerj.8273

Del Cortona. A., Jackson, C.J., Bucchini, F., Van Bel, M., D'hondt, S., Škaloud, P., Delwiche, C.F., Knoll, A.H., Raven, J.A., Verbruggen,  H., Vandepoele, K., De Clerck, O., Leliaert, F. (2020). Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds. Proc Natl Acad Sci U S A.  117 (5): 2551 – 2559. doi: 10.1073/pnas.1910060117

Davoodian, N., Jackson, C.J., Holmes, G.D., Lebel, T. 2020. Continental‐scale metagenomics, BLAST searches, and herbarium specimens: The Australian Microbiome Initiative and the National Herbarium of Victoria. Applications in Plant Sciences 8(9), e11392. DOI: 10.1002/aps3.11392

Wetherbee, R., Jackson, C., Repetti. S., Clementson, L., Costa, J., van de Meene, A., Crawford, S., and Verbgruggen, H. (2018) The golden paradox – a new heterokont lineage with chloroplasts surrounded by two membranes. J. Phycol. doi: 10.1111/jpy.12822

Oliveira, M.C., Repetti, S.I., Iha, C., Jackson, C.J., Díaz-Tapia, P., Lubiana, K.M.F., Cassano, V., Costa, J.F., Cremen, M.C.M., Marcelino, V.R., and Verbruggen, H. (2018) High-throughput sequencing for algal systematics. Eur. J. Phycol. 53 (3): 256–272. doi: 10.1080/09670262.2018.1441446

Figueroa-Martinez, F., Jackson, C., and Reyes-Prieto, A. (2018). Plastid genomes from diverse glaucophyte genera reveal a largely conserved gene content and limited architectural diversity. Genome Biol. Evol. 11 (1): 174–188. doi: 10.1093/gbe/evy268

Saunders, G.W., Jackson, C., and Salomaki, E.D. (2018) Phylogenetic analyses of transcriptome data resolve familial assignments for genera of the red-algal Acrochaetiales-Palmariales Complex (Nemaliophycidae). Mol. Phylogenet. Evol. 119: 151–159. doi: 10.1016/j.ympev.2017.11.002

Jackson, C., Knoll, A.H., Chan, C.X., and Verbruggen, H. (2018) Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids. Sci. Rep. 8 (1): 1523. doi: 10.1038/s41598-017-18805-w

Verbruggen, H., Marcelino, V.R., Guiry, M.D., Cremen, M.C.M., and Jackson, C.J. (2017) Phylogenetic position of the coral symbiont Ostreobium (Ulvophyceae) inferred from chloroplast genome data. J. Phycol. 53 (4): 790–803. doi: 10.1111/jpy.12540

Jackson, C., Salomaki, E., Lane, C.E., Saunders, G.W. (2017) Kelp transcriptomes provide robust support for interfamilial relationships and revision of the little know Arthrothamnaceae (Laminariales). J. Phycol. 53 (1): 1–6. doi: 10.1111/jpy.12465

Marcelino, V.R., Cremen, M.C., Jackson, C.J., Larkum, A.A., and Verbruggen, H. (2016) Evolutionary dynamics of chloroplast genomes in low light : a case study of the endolithic green alga Ostreobium quekettii. Genome Biol. Evol 8 (9): 2939–2951. doi: 10.1093/gbe/evw206

Jackson, C., Claydon, S. and Reyes-Prieto, A. (2015) The Glaucophyta: the blue-green plants in a nutshell. Acta Societatis Botanicorum Poloniae 84 (2). doi: 10.5586/asbp.2015.020

Jackson, C.J. and Reyes-Prieto, A. (2014) The mitochondrial genomes of the glaucophytes Gloeochaete wittrockiana and Cyanoptyche gloeocystis: multi-locus phylogenetics suggests a monophyletic Archaeplastida. Genome Biol. Evol. 6 (10): 2774–2785. doi: 10.1093/gbe/evu218

Smith, D.R., Jackson, C.J., Reyes-Prieto, A. (2014) Nucleotide substitution analyses of the glaucophyte Cyanophora suggest an ancestrally lower mutation rate in plastid vs mitochondrial DNA for the Archaeplastida. Mol. Phylogenet. Evol. 79: 380–384. doi: 10.1016/j.ympev.2014.07.001

Chong, J., Jackson, C.J., Kim, J.I., Yoon, H.S., Reyes-Prieto, A. (2014) Molecular markers from different genomic compartments reveal cryptic diversity within glaucophyte species. Mol. Phylogenet. Evol. 76: 181–188. doi: 10.1016/j.ympev.2014.03.019

Jackson, C.J. and Waller, R.F. (2013) A widespread and unusual RNA trans-splicing type in dinoflagellate mitochondria. PloS ONE 8 (2). doi: 10.1371/journal.pone.0056777

Jackson, C.J., Gornik, S.G. and Waller, R.F. (2012) A tertiary plastid gains RNA editing in its new host. Mol. Biol. Evol. 30 (4):788–92. doi: 10.1093/molbev/mss270

Jackson, C.J., Gornik, S.G. and Waller, R.F. (2012) The mitochondrial genome and transcriptome of the basal dinoflagellate Hematodinium sp.: character evolution within the highly derived mitochondrial genomes of dinoflagellates. Genome Biol. Evol. 4 (1): 59–72. doi: 10.1093/gbe/evr122

Burger, G., Jackson, C.J. and Waller, R.F. (2012) Unusual mitochondrial genomes and genes. In: Organelle Genetics (ed. Charles Bullerwell) Springer, New York, USA. Pp 41–77

Waller, R.F. and Jackson, C.J. (2009) Dinoflagellate mitochondrial genomes: stretching the rules of molecular biology. Bioessays 31 (2): 237–245. doi: 10.1002/bies.200800164

Jackson, C.J., Norman, J.E., Schnare, M.N., Gray, M.W., Keeling, P.K., Waller, R.F. (2007) Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria. BMC Biol 5: 41. doi: 10.1186/1741-7007-5-41

GitHub repositories

Chris Jackson Bioinformatics Repository.

Matt Johnson (Texas Tech University) and Chris Jackson (Royal Botanic Gardens Victoria, Melbourne), co-developed HybPiper 2 Repository.