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17 results on '"Kuo, Richard I."'

1. The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Published
2023
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3. Corrigendum: The molecular basis of differential host responses to avian influenza viruses in avian species with differing susceptibility

Author

Morris, Katrina M., primary, Mishra, Anamika, additional, Raut, Ashwin A., additional, Gaunt, Eleanor R., additional, Borowska, Dominika, additional, Kuo, Richard I., additional, Wang, Bo, additional, Vijayakumar, Periyasamy, additional, Chingtham, Santhalembi, additional, Dutta, Rupam, additional, Baillie, Kenneth, additional, Digard, Paul, additional, Vervelde, Lonneke, additional, Burt, David W., additional, and Smith, Jacqueline, additional

Published
2023
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4. The molecular basis of differential host responses to avian influenza viruses in avian species with differing susceptibility

Author

Morris, Katrina M., primary, Mishra, Anamika, additional, Raut, Ashwin A., additional, Gaunt, Eleanor R., additional, Borowska, Dominika, additional, Kuo, Richard I., additional, Wang, Bo, additional, Vijayakumar, Periyasamy, additional, Chingtham, Santhalembi, additional, Dutta, Rupam, additional, Baillie, Kenneth, additional, Digard, Paul, additional, Vervelde, Lonneke, additional, Burt, David W., additional, and Smith, Jacqueline, additional

Published
2023
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5. Additional file 13 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 13: Supplementary Table S11. Differentially expressed cytokine or cytokine related genes in infected avian endothelial cells.

Published
2023
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6. Additional file 4 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 4: Supplementary Table S2. BUSCO analysis of the final genomes.

Published
2023
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7. Additional file 5 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 5: Supplementary Table S3. CEGMA analysis of the final genomes.

Published
2023
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8. Additional file 7 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 7: Supplementary Table S5. List of genes known to affect plumage colour in birds.

Published
2023
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9. Additional file 2 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 2: Supplementary Table S1. Heterozygosity, QV and completeness values for swan genomes.

Published
2023
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10. Additional file 6 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 6: Supplementary Table S4. GO biological process annotation of inverted genes in the Mallard duck (relative to the black swan).

Published
2023
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11. Additional file 3 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 3: Online Methods.

Published
2023
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12. Additional file 8 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 8: Supplementary Table S6. Immune gene families are contractive in black swans compared to mute swans. The number of genes in each immune gene sub-family identified is given in each column for the corresponding species.

Published
2023
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14. The swan genome and transcriptome: its not all black and white

Author

Karawita, Anjana C., primary, Cheng, Yuanyuan, additional, Chew, Keng Yih, additional, Challgula, Arjun, additional, Kraus, Robert, additional, Mueller, Ralf C., additional, Tong, Marcus Z. W., additional, Hulme, Katina D., additional, Beielefeldt-Ohmann, Helle, additional, Steele, Lauren E., additional, Wu, Melanie, additional, Sng, Julian, additional, Noye, Ellesandra, additional, Bruxner, Timothy J., additional, Au, Gough G., additional, Lowther, Suzanne, additional, Blommaert, Julie, additional, Suh, Alexander, additional, McCauley, Alexander J., additional, Kaur, Parwinder, additional, Dudchenko, Olga, additional, Aiden, Erez, additional, Fedrigo, Olivier, additional, Formenti, Giulio, additional, Mountcastle, Jacquelyn, additional, Chow, William, additional, Martin, Fergal J., additional, Ogeh, Denye N., additional, Thiaud-Nissen, Françoise, additional, Howe, Kerstin, additional, Collins, Joanna, additional, Tracey, Alan, additional, Smith, Jacqueline, additional, Kuo, Richard I., additional, Renfree, Marilyn B., additional, Kimura, Takashi, additional, Sakoda, Yoshihiro, additional, McDougall, Mathew, additional, Spencer, Hamish G., additional, Pyne, Michael, additional, Tolf, Conny, additional, Waldenström, Jonas, additional, Jarvis, Erich D., additional, Baker, Michelle L., additional, Burt, David W., additional, and Short, Kirsty R., additional

Published
2022
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15. A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

Author

Mueller, Ralf C, primary, Ellström, Patrik, additional, Howe, Kerstin, additional, Uliano-Silva, Marcela, additional, Kuo, Richard I, additional, Miedzinska, Katarzyna, additional, Warr, Amanda, additional, Fedrigo, Olivier, additional, Haase, Bettina, additional, Mountcastle, Jacquelyn, additional, Chow, William, additional, Torrance, James, additional, Wood, Jonathan M D, additional, Järhult, Josef D, additional, Naguib, Mahmoud M, additional, Olsen, Björn, additional, Jarvis, Erich D, additional, Smith, Jacqueline, additional, Eöry, Lél, additional, and Kraus, Robert H S, additional

Published
2021
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16. high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck).

Author

Mueller, Ralf C, Ellström, Patrik, Howe, Kerstin, Uliano-Silva, Marcela, Kuo, Richard I, Miedzinska, Katarzyna, Warr, Amanda, Fedrigo, Olivier, Haase, Bettina, Mountcastle, Jacquelyn, Chow, William, Torrance, James, Wood, Jonathan M D, Järhult, Josef D, Naguib, Mahmoud M, Olsen, Björn, Jarvis, Erich D, Smith, Jacqueline, Eöry, Lél, and Kraus, Robert H S

Subjects
PLANT chromosomes, AVIAN influenza A virus, AVIAN influenza, SEX chromosomes, GENOMES, DUCK plague, COMPLEMENTARY DNA
Abstract

Background The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome. Findings This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families. Conclusions This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses. [ABSTRACT FROM AUTHOR]

Published
2021
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17. nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

Author

Guizard, Sébastien, Miedzinska, Katarzyna, Smith, Jacqueline, Smith, Jonathan, Kuo, Richard I, Davey, Megan, Archibald, Alan, and Watson, Mick

Subjects
ANNOTATIONS, NUCLEOTIDE sequencing, GENES, GENOMES, TRANSCRIPTOMES
Abstract

Motivation Iso-Seq RNA long-read sequencing enables the identification of full-length transcripts and isoforms, removing the need for complex analysis such as transcriptome assembly. However, the raw sequencing data need to be processed in a series of steps before annotation is complete. Here, we present nf-core/isoseq, a pipeline for automatic read processing and genome annotation. Following nf-core guidelines, the pipeline has few dependencies and can be run on any of platforms. Availability and implementation The pipeline is freely available online on the nf-core website (https://nf-co.re/isoseq) and on GitHub (https://github.com/nf-core/isoseq) under MIT License (DOI: 10.5281/zenodo.7116979). [ABSTRACT FROM AUTHOR]

Published
2023
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