Dr Cushla Metcalfe
Senior Research Assistant
Queensland Alliance for Agriculture and Food Innovation
Publications
Journal Articles
Healey, A. L., Garsmeur, O., Lovell, J. T., Shengquiang, S., Sreedasyam, A., Jenkins, J., Plott, C. B., Piperidis, N., Pompidor, N., Llaca, V., Metcalfe, C. J., Doležel, J., Cápal, P., Carlson, J. W., Hoarau, J. Y., Hervouet, C., Zini, C., Dievart, A., Lipzen, A., Williams, M., Boston, L. B., Webber, J., Keymanesh, K., Tejomurthula, S., Rajasekar, S., Suchecki, R., Furtado, A., May, G., Parakkal, P. ... D’Hont, A. (2024). The complex polyploid genome architecture of sugarcane. Nature, 628 (8009), 1-7. doi: 10.1038/s41586-024-07231-4
Metcalfe, Cushla J., Li, Jingchuan, Zheng, Bangyou, Stiller, Jiri, Healey, Adam, Piperidis, Nathalie and Aitken, Karen S. (2022). Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification. Theoretical and Applied Genetics, 135 (4), 1279-1292. doi: 10.1007/s00122-022-04030-1
Policarpo, Maxime, Bemis, Katherine E., Tyler, James C., Metcalfe, Cushla J., Laurenti, Patrick, Sandoz, Jean-Christophe, Rétaux, Sylvie and Casane, DIdier (2021). Evolutionary dynamics of the or gene repertoire in teleost fishes: evidence of an association with changes in olfactory epithelium shape. Molecular Biology and Evolution, 38 (9), 3742-3753. doi: 10.1093/molbev/msab145
Metcalfe, Cushla J., Li, Jingchuan, Giorgi, Debora, Dolezel, Jaroslav, Piperidis, Nathalie and Aitken, Karen S. (2019). Flow cytometric characterisation of the complex polyploid genome of Saccharum officinarum and modern sugarcane cultivarsa. Scientific Reports, 9 (1) 19362, 1-12. doi: 10.1038/s41598-019-55652-3
Castellanos-Gell, Jessy, Robainas-Barcia, Aymée, Pina-Amargós, Fabián, Chevalier-Monteagudo, Pedro, Metcalfe, Cushla, Molina, Wagner Franco, Casane, Didier and García-Machado, Erik (2016). Genetic diversity of reef fishes around Cuba: a multispecies assessment. Marine Biology, 163 (7) 165. doi: 10.1007/s00227-016-2935-6
Mies, Miguel, Van Sluys, M. A., Metcalfe, C. J. and Sumida, P. Y. G. (2016). Molecular evidence of symbiotic activity between Symbiodinium and Tridacna maxima larvae. Symbiosis, 72 (1), 13-22. doi: 10.1007/s13199-016-0433-8
Metcalfe, Cushla J., Oliveira, Sarah G., Gaiarsa, Jonas W., Aitken, Karen S., Carneiro, Monalisa S., Zatti, Fernanda and Van Sluys, Marie-Anne (2015). Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane. Journal of Experimental Botany, 66 (14), 4239-4250. doi: 10.1093/jxb/erv283
Ponce de León, José Luis, León, Gunnary, Rodríguez, Rodet, Metcalfe, Cushla J., Hernández, Damir, Casane, Didier and García-Machado, Erik (2014). Phylogeography of Cuban Rivulus: Evidence for allopatric speciation and secondary dispersal across a marine barrier. Molecular Phylogenetics and Evolution, 79, 404-414. doi: 10.1016/j.ympev.2014.07.007
de Setta, Nathalia, Monteiro-Vitorello, Cláudia Barros, Metcalfe, Cushla Jane, Cruz, Guilherme Marcelo Queiroga, Del Bem, Luiz Eduardo, Vicentini, Renato, Nogueira, Fábio Tebaldi Silveira, Campos, Roberta Alvares, Nunes, Sideny Lima, Turrini, Paula Cristina Gasperazzo, Vieira, Andreia Prata, Ochoa Cruz, Edgar Andrés, Corrêa, Tatiana Caroline Silveira, Hotta, Carlos Takeshi, de Mello Varani, Alessandro, Vautrin, Sonia, da Trindade, Adilson Silva, de Mendonça Vilela, Mariane, Lembke, Carolina Gimiliani, Sato, Paloma Mieko, de Andrade, Rodrigo Fandino, Nishiyama, Milton Yutaka, Cardoso-Silva, Claudio Benicio, Scortecci, Katia Castanho, Garcia, Antônio Augusto Franco, Carneiro, Monalisa Sampaio, Kim, Changsoo, Paterson, Andrew H, Bergès, Hélène ... Van Sluys, Marie-Anne (2014). Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics, 15 (1) 540. doi: 10.1186/1471-2164-15-540
Cruz, Guilherme M. Q., Metcalfe, Cushla J., de Setta, Nathalia, Cruz, Edgar A. O., Vieira, Andréia Prata, Medina, Rosario and Van Sluys, Marie-Anne (2014). Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons. PLoS ONE, 9 (5) e97099, e97099. doi: 10.1371/journal.pone.0097099
Metcalfe, Cushla J and Casane, Didier (2014). Modular organization and reticulate evolution of the ORF1 of Jockey superfamily transposable elements. Mobile DNA, 5 (1) 19, 19. doi: 10.1186/1759-8753-5-19
Debiais-Thibaud, Mélanie, Metcalfe, Cushla J., Pollack, Jacob, Germon, Isabelle, Ekker, Marc, Depew, Michael, Laurenti, Patrick, Borday-Birraux, Véronique and Casane, Didier (2013). Heterogeneous Conservation of Dlx Paralog Co-Expression in Jawed Vertebrates. PLoS ONE, 8 (6) e68182, e68182. doi: 10.1371/journal.pone.0068182
Metcalfe, Cushla J. and Casane, Didier (2013). Accommodating the load : The transposable element content of very large genomes. Mobile Genetic Elements, 3 (2) e24775, 1-8. doi: 10.4161/mge.24775
Metcalfe, C. J., Filee, J., Germon, I., Joss, J. and Casane, D. (2012). Evolution of the Australian Lungfish (Neoceratodus forsteri) Genome: A Major Role for CR1 and L2 LINE Elements. Molecular Biology and Evolution, 29 (11), 3529-3539. doi: 10.1093/molbev/mss159
Domingues, Douglas S, Cruz, Guilherme MQ, Metcalfe, Cushla J, Nogueira, Fabio TS, Vicentini, Renato, de S Alves, Cristiane and Van Sluys, Marie-Anne (2012). Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. BMC Genomics, 13 (1) 137. doi: 10.1186/1471-2164-13-137
Potter, Sally, Cooper, Steven J.B., Metcalfe, Cushla J., Taggart, David A. and Eldridge, Mark D.B. (2012). Phylogenetic relationships of rock-wallabies, Petrogale (Marsupialia: Macropodidae) and their biogeographic history within Australia. Molecular Phylogenetics and Evolution, 62 (2), 640-652. doi: 10.1016/j.ympev.2011.11.005
García-Machado, Erik, Hernández, Damir, García-Debrás, Alfredo, Chevalier-Monteagudo, Pedro, Metcalfe, Cushla, Bernatchez, Louis and Casane, Didier (2011). Molecular phylogeny and phylogeography of the Cuban cave-fishes of the genus Lucifuga: Evidence for cryptic allopatric diversity. Molecular Phylogenetics and Evolution, 61 (2), 470-483. doi: 10.1016/j.ympev.2011.06.015
Eldridge, M. D. B., Heckenberg, K., Neaves, L. E., Metcalfe, C. J., Hamilton, S., Johnson, P. M. and Close, R. L. (2011). Genetic differentiation and introgression amongst Thylogale (pademelons) taxa in eastern Australia. Australian Journal of Zoology, 59 (2), 103-117. doi: 10.1071/zo11022
Metcalfe, Cushla J, Bulazel, Kira V, Ferreri, Gianni C, Schroeder-Reiter, Elizabeth, Wanner, Gerhard, Rens, Willem, Obergfell, Craig, Eldridge, Mark D B and O'Neill, Rachel J (2007). Genomic Instability Within Centromeres of Interspecific Marsupial Hybrids. Genetics, 177 (4), 2507-2517. doi: 10.1534/genetics.107.082313
Debiais‐Thibaud, Mélanie, Borday‐Birraux, Véronique, Germon, Isabelle, Bourrat, Frank, Metcalfe, Cushla Jane, Casane, Didier and Laurenti, Patrick (2007). Development of oral and pharyngeal teeth in the medaka (Oryzias latipes): comparison of morphology and expression of eve1 gene. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 308B (6), 693-708. doi: 10.1002/jez.b.21183
Metcalfe, C.J., Eldridge, M.D.B. and Johnston, P.G. (2007). Mapping the distribution of the telomeric sequence (T2AG3)n in the Macropodoidea (Marsupialia) by fluorescence in situ hybridization. II. The ancestral 2n = 22 macropodid karyotype. Cytogenetic and Genome Research, 116 (3), 212-217. doi: 10.1159/000098189
Bulazel, Kira, Metcalfe, Cushla, Ferreri, Gianni C, Yu, Jingwei, Eldridge, Mark D B and O'Neill, Rachel J (2006). Cytogenetic and Molecular Evaluation of Centromere-Associated DNA Sequences From a Marsupial (Macropodidae:Macropus rufogriseus) X Chromosome. Genetics, 172 (2), 1129-1137. doi: 10.1534/genetics.105.047654
O'Neill, R. J., Eldridge, M. D. B. and Metcalfe, C. J. (2004). Centromere Dynamics and Chromosome Evolution in Marsupials. Journal of Heredity, 95 (5), 375-381. doi: 10.1093/jhered/esh063
Metcalfe, C. J., Eldridge, M. D. B. and Johnston, P. G. (2004). Mapping the Distribution of the Telomeric Sequence (T2AG3) n in the 2n = 14 Ancestral Marsupial Complement and in the Macropodines (Marsupialia: Macropodidae) by fluorescence in situ hybridization. Chromosome Research, 12 (4), 405-414. doi: 10.1023/b:chro.0000034133.77878.88
Metcalfe, C.J., Eldridge, M.D.B. and Johnston, P.G. (2002). Mapping the distribution of the telomeric sequence (T2AG3)n in rock wallabies, Petrogale (Marsupialia: Macropodidae), by fluorescence in situ hybridization: II. The lateralis complex. Cytogenetic and Genome Research, 96 (1-4), 169-175. doi: 10.1159/000063037
Eldridge, M. D. B., Wilson, A. C. C., Metcalfe, C. J., Dollin, A. E., Bell, J. N., Johnson, P. M., Johnston, P. G. and Close, R. L. (2001). Taxonomy of rock-wallabies, Petrogale (Marsupialia : Macropodidae). III. Molecular data confirms the species status of the purple-necked rock-wallaby (Petrogale purpureicollis Le Souef). Australian Journal of Zoology, 49 (4), 323-343. doi: 10.1071/zo00082
Metcalfe, C. J., Eldridge, M. D. B., Toder, R. and Johnston, P. G. (1998). Mapping the distribution of the telomeric sequence (T2AG3)n in the Macropodoidea (Marsupialia), by fluorescence in situ hybridization. I. The swamp wallaby, Wallabia bicolor. Chromosome Research, 6 (8), 603-610. doi: 10.1023/a:1009249325574
Metcalfe, C.J., Eldridge, M.D.B., McQuade, L.R. and Johnston, P.G. (1997). Mapping the distribution of the telomeric sequence (T2AG3)n in rock-wallabies, Petrogale (Marsupialia: Macropodidae), by fluorescence in situ hybridization. I. The penicillata complex Available. Cytogenetic and Genome Research, 78 (1), 74-80. doi: 10.1159/000134634