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2022 Journal Article Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximumZhang, Jia, Richards, Zoe T, Adam, Arne A S, Chan, Cheong Xin, Shinzato, Chuya, Gilmour, James, Thomas, Luke, Strugnell, Jan M, Miller, David J and Cooke, Ira (2022). Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum. Molecular Biology and Evolution, 39 (10) msac201, 1-18. doi: 10.1093/molbev/msac201 |
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2022 Journal Article Improved Cladocopium goreaui genome assembly reveals features of a facultative coral symbiont and the complex evolutionary history of dinoflagellate genesChen, Yibi, Shah, Sarah, Dougan, Katherine E., van Oppen, Madeleine J. H., Bhattacharya, Debashish and Chan, Cheong Xin (2022). Improved Cladocopium goreaui genome assembly reveals features of a facultative coral symbiont and the complex evolutionary history of dinoflagellate genes. Microorganisms, 10 (8) 1662, 1-20. doi: 10.3390/microorganisms10081662 |
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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 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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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, 1. doi: 10.1093/molbev/msab295 |
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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 Conference Publication PATTERNS OF ADAPTIVE SELECTION ON SYMBIOTIC DINOFLAGELLATE LINEAGES WITHIN THE GENUS <i>SYMBIODINIUM</i>Dougan, Katherine, Bhattacharya, Debashish and Chan, Cheong Xin (2021). PATTERNS OF ADAPTIVE SELECTION ON SYMBIOTIC DINOFLAGELLATE LINEAGES WITHIN THE GENUS SYMBIODINIUM. ABINGDON: TAYLOR & FRANCIS LTD. |
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2021 Conference Publication THE GENOME AS A TAXONOMIC MARKER: INSIGHTS GAINED FROM DINOFLAGELLATES OF THE FAMILY SYMBIODINIACEAE AND GENUS <i>SYMBIODINIUM</i>Dougan, Katherine E., Gonzalez-Pech, Raul A., Stephens, Timothy G., Shah, Sarah, Chen, Yibi, Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2021). THE GENOME AS A TAXONOMIC MARKER: INSIGHTS GAINED FROM DINOFLAGELLATES OF THE FAMILY SYMBIODINIACEAE AND GENUS SYMBIODINIUM. ABINGDON: TAYLOR & FRANCIS LTD. |
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2021 Conference Publication <i>DE NOVO</i> GENOMES OF THE DINOFLAGELLATE <i>EFFRENIUM VORATUM</i> REVEAL HALLMARKS OF FREE-LIVING LIFESTYLE IN SYMBIODINIACEAEShah, Sarah, Bhattacharya, Debashish, Chen, Yibi, Dougan, Katherine, Rai, Subash and Chan, Cheong Xin (2021). DE NOVO GENOMES OF THE DINOFLAGELLATE EFFRENIUM VORATUM REVEAL HALLMARKS OF FREE-LIVING LIFESTYLE IN SYMBIODINIACEAE. ABINGDON: TAYLOR & FRANCIS LTD. |
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2021 Conference Publication REVISED GENOME ASSEMBLY OF THE CORAL SYMBIONT <i>CLADOCOPIUM GOREAUI</i> REVEALS GENES WITH INTRICATE EVOLUTIONARY HISTORIESChen, Yibi, Shah, Sarah, Dougan, Katherine, Bhattacharya, Debashish and Chan, Cheong Xin (2021). REVISED GENOME ASSEMBLY OF THE CORAL SYMBIONT CLADOCOPIUM GOREAUI REVEALS GENES WITH INTRICATE EVOLUTIONARY HISTORIES. ABINGDON: TAYLOR & FRANCIS LTD. |
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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 |
