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2022 Other Outputs Improved assembled genome of Cladocopium goreaui SCF055Chen, Yibi, Shah, Sarah, Dougan, Katherine E., van Oppen, Madeleine, J. H., Bhattacharya, Debashish and Chan, Cheong Xin (2022). Improved assembled genome of Cladocopium goreaui SCF055. The University of Queensland. (Dataset) |
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2022 Journal Article Transcriptome of the coralline alga Calliarthron tuberculosum (Corallinales, Rhodophyta) reveals convergent evolution of a partial lignin biosynthesis pathwayXue, Jan Y., Hind, Katharine R., Lemay, Matthew A., Mcminigal, Andrea, Jourdain, Emma, Chan, Cheong Xin and Martone, Patrick T. (2022). Transcriptome of the coralline alga Calliarthron tuberculosum (Corallinales, Rhodophyta) reveals convergent evolution of a partial lignin biosynthesis pathway. PLoS One, 17 (7) e0266892, 1-20. doi: 10.1371/journal.pone.0266892 |
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2022 Journal Article Genome-guided analysis of seven weed species reveals conserved sequence and structural features of key gene targets for herbicide developmentShah, Sarah, Lonhienne, Thierry, Murray, Cody-Ellen, Chen, Yibi, Dougan, Katherine E., Low, Yu Shang, Williams, Craig M., Schenk, Gerhard, Walter, Gimme H., Guddat, Luke W. and Chan, Cheong Xin (2022). Genome-guided analysis of seven weed species reveals conserved sequence and structural features of key gene targets for herbicide development. Frontiers in Plant Science, 13 909073. doi: 10.3389/fpls.2022.909073 |
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2022 Other Outputs Genomic resources of seven Australian weed species of national significanceShah, Sarah, Lonhienne, Thierry, Murray, Cody-Ellen, Chen, Yibi, Dougan, Katherine E., Low, Yu Shang, Williams, Craig M., Schenk, Gerhard, Walter, Gimme H., Guddat, Luke W. and Chan, Cheong Xin (2022). Genomic resources of seven Australian weed species of national significance. The University of Queensland. (Dataset) doi: 10.48610/c22c10c |
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2022 Journal Article Alignment-free analysis of whole-genome sequences from Symbiodiniaceae reveals different phylogenetic signals in distinct regionsLo, Rosalyn, Dougan, Katherine E., Chen, Yibi, Shah, Sarah, Bhattacharya, Debashish and Chan, Cheong Xin (2022). Alignment-free analysis of whole-genome sequences from Symbiodiniaceae reveals different phylogenetic signals in distinct regions. Frontiers in Plant Science, 13 815714, 1-13. doi: 10.3389/fpls.2022.815714 |
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2022 Other Outputs Genome data for Durusdinium trenchii CCMP2556 and SCF082Katherine E. Dougan, Anthony J. Bellantuono, Tim Kahlke, Raffaela M. Abbriano, Yibi Chen, Sarah Shah, Camila Granados-Cifuentes, Madeleine J. H. van Oppen, Debashish Bhattacharya, David J. Suggett, Mauricio Rodriguez-Lanetty and Cheong Xin Chan (2022). Genome data for Durusdinium trenchii CCMP2556 and SCF082. The University of Queensland. (Dataset) doi: 10.48610/27da3e7 |
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2022 Journal Article Genome-powered classification of microbial eukaryotes: focus on coral algal symbiontsDougan, Katherine E., González-Pech, Raúl A., Stephens, Timothy G., Shah, Sarah, Chen, Yibi, Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2022). Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts. Trends in Microbiology, 30 (9), 831-840. doi: 10.1016/j.tim.2022.02.001 |
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2022 Journal Article Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algaeRepetti, Sonja I., Iha, Cintia, Uthanumallian, Kavitha, Jackson, Christopher J., Chen, Yibi, Chan, Cheong Xin and Verbruggen, Heroen (2022). Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae. New Phytologist, 233 (5), 2144-2154. doi: 10.1111/nph.17926 |
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2022 Journal Article Tightly constrained genome reduction and relaxation of purifying selection during secondary plastid endosymbiosisUthanumallian, Kavitha, Iha, Cintia, Repetti, Sonja I, Chan, Cheong Xin, Bhattacharya, Debashish, Duchene, Sebastian and Verbruggen, Heroen (2022). Tightly constrained genome reduction and relaxation of purifying selection during secondary plastid endosymbiosis. Molecular Biology and Evolution, 39 (1) msab295. doi: 10.1093/molbev/msab295 |
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2022 Book Chapter Coral conservation from the genomic perspective on symbiodiniaceae diversity and function in the holobiontShah, Sarah, Dougan, Katherine E., Bhattacharya, Debashish and Chan, Cheong Xin (2022). Coral conservation from the genomic perspective on symbiodiniaceae diversity and function in the holobiont. Coral reefs of the world. (pp. 85-96) edited by Madeleine J. H. van Oppen and Manuel Aranda Lastra. Cham, Switzerland: Springer Cham. doi: 10.1007/978-3-031-07055-6_6 |
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2021 Journal Article Consensus guidelines for advancing coral holobiont genome and specimen voucher depositionVoolstra, Christian R., Quigley, Kate M., Davies, Sarah W., Parkinson, John Everett, Peixoto, Raquel S., Aranda, Manuel, Baker, Andrew C., Barno, Adam R., Barshis, Daniel J., Benzoni, Francesca, Bonito, Victor, Bourne, David G., Buitrago-López, Carol, Bridge, Tom C. L., Chan, Cheong Xin, Combosch, David J., Craggs, Jamie, Frommlet, Jörg C., Herrera, Santiago, Quattrini, Andrea M., Röthig, Till, Reimer, James D., Rubio-Portillo, Esther, Suggett, David J., Villela, Helena, Ziegler, Maren and Sweet, Michael (2021). Consensus guidelines for advancing coral holobiont genome and specimen voucher deposition. Frontiers in Marine Science, 8 701784, 1-12. doi: 10.3389/fmars.2021.701784 |
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2021 Journal Article Comparative genomics supports that Brazilian bioethanol Saccharomyces cerevisiae comprise a unified group of domesticated strains related to Cachaça spirit yeastsJacobus, Ana Paula, Stephens, Timothy G., Youssef, Pierre, González-Pech, Raul, Ciccotosto-Camp, Michael M., Dougan, Katherine E., Chen, Yibi, Basso, Luiz Carlos, Frazzon, Jeverson, Chan, Cheong Xin and Gross, Jeferson (2021). Comparative genomics supports that Brazilian bioethanol Saccharomyces cerevisiae comprise a unified group of domesticated strains related to Cachaça spirit yeasts. Frontiers in Microbiology, 12 644089, 644089. doi: 10.3389/fmicb.2021.644089 |
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2021 Journal Article Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus SymbiodiniumGonzalez-Pech, Raul A., Stephens, Timothy G., Chen, Yibi, Mohamed, Amin R., Cheng, Yuanyuan, Shah, Sarah, Dougan, Katherine E., Fortuin, Michael D. A., Lagorce, Remi, Burt, David W., Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2021). Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium. BMC Biology, 19 (1) 73, 73. doi: 10.1186/s12915-021-00994-6 |
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2021 Journal Article Genomic adaptations to an endolithic lifestyle in the coral-associated alga OstreobiumIha, Cintia, Dougan, Katherine E., Varela, Javier A., Avila, Viridiana, Jackson, Christopher J., Bogaert, Kenny A., Chen, Yibi, Judd, Louise M., Wick, Ryan, Holt, Kathryn E., Pasella, Marisa M., Ricci, Francesco, Repetti, Sonja I., Medina, Mónica, Marcelino, Vanessa R., Chan, Cheong Xin and Verbruggen, Heroen (2021). Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium. Current Biology, 31 (7), 1-10.e1–e5. doi: 10.1016/j.cub.2021.01.018 |
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2021 Book Chapter Inferring phylogenomic relationship of microbes using scalable alignment-free methodsBernard, Guillaume, Stephens, Timothy G., González-Pech, Raúl A. and Chan, Cheong Xin (2021). Inferring phylogenomic relationship of microbes using scalable alignment-free methods. Bacterial pangenomics: methods and protocols. (pp. 69-76) New York, United States: Humana Press. doi: 10.1007/978-1-0716-1099-2_5 |
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2021 Other Outputs Genome assemblies and the associated annotations for seven Symbiodinium isolatesGonzález-Pech, Raúl A., Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2021). Genome assemblies and the associated annotations for seven Symbiodinium isolates. The University of Queensland. (Dataset) doi: 10.14264/f1b3a11 |
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2020 Journal Article Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complexShah, Sarah, Chen, Yibi, Bhattacharya, Debashish and Chan, Cheong Xin (2020). Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex. Scientific Reports, 10 (1) 9792, 9792. doi: 10.1038/s41598-020-66429-4 |
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2020 Journal Article Dual RNA‐seq analyses of a coral and its native symbiont during the establishment of symbiosisMohamed, Amin R., Andrade, Natalia, Moya, Aurelie, Xin Chan, Cheong, Negri, Andrew P., Bourne, David G., Ying, Hua, Ball, Eldon E. and Miller, David J. (2020). Dual RNA‐seq analyses of a coral and its native symbiont during the establishment of symbiosis. Molecular Ecology, 29 (20), 3921-3937. doi: 10.1111/mec.15612 |
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2020 Journal Article Comparative transcriptomic analyses of Chromera and SymbiodiniaceaeMohamed, Amin R., Chan, Cheong Xin, Ragan, Mark A., Zhang, Jia, Cooke, Ira, Ball, Eldon E. and Miller, David J. (2020). Comparative transcriptomic analyses of Chromera and Symbiodiniaceae. Environmental Microbiology Reports, 12 (4), 435-443. doi: 10.1111/1758-2229.12859 |
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2020 Other Outputs Genomic adaptations to an endolithic lifestyle in the coral-associated alga OstreobiumIha, Cintia, Dougan, Katherine E., Varela, Javier A., Avila, Viridiana, Jackson, Christopher J., Bogaert, Kenny A., Chen, Yibi, Judd, Louise M., Wick, Ryan, Holt, Kathryn E., Pasella, Marisa M., Ricci, Francesco, Repetti, Sonja I., Medina, Mónica, Marcelino, Vanessa R., Chan, Cheong Xin and Verbruggen, Heroen (2020). Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium. doi: 10.1101/2020.07.21.211367 |
