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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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2. Lipoprotein lipase reaches the capillary lumen in chickens despite an apparent absence of GPIHBP1

Author

He, Cuiwen, Hu, Xuchen, Jung, Rachel S, Larsson, Mikael, Tu, Yiping, Duarte-Vogel, Sandra, Kim, Paul, Sandoval, Norma P, Price, Tara R, Allan, Christopher M, Raney, Brian, Jiang, Haibo, Bensadoun, André, Walzem, Rosemary L, Kuo, Richard I, Beigneux, Anne P, Fong, Loren G, and Young, Stephen G

Subjects
Cardiovascular, Adipose Tissue, Animals, Antibodies, Capillaries, Chickens, Endothelial Cells, Female, Goats, Heart, Heparin, Humans, Immunoglobulin G, Lipid Metabolism, Lipoprotein Lipase, Lipoproteins, Male, Mice, Receptors, Lipoprotein, Triglycerides
Abstract

In mammals, GPIHBP1 is absolutely essential for transporting lipoprotein lipase (LPL) to the lumen of capillaries, where it hydrolyzes the triglycerides in triglyceride-rich lipoproteins. In all lower vertebrate species (e.g., birds, amphibians, reptiles, fish), a gene for LPL can be found easily, but a gene for GPIHBP1 has never been found. The obvious question is whether the LPL in lower vertebrates is able to reach the capillary lumen. Using purified antibodies against chicken LPL, we showed that LPL is present on capillary endothelial cells of chicken heart and adipose tissue, colocalizing with von Willebrand factor. When the antibodies against chicken LPL were injected intravenously into chickens, they bound to LPL on the luminal surface of capillaries in heart and adipose tissue. LPL was released rapidly from chicken hearts with an infusion of heparin, consistent with LPL being located inside blood vessels. Remarkably, chicken LPL bound in a specific fashion to mammalian GPIHBP1. However, we could not identify a gene for GPIHBP1 in the chicken genome, nor could we identify a transcript for GPIHBP1 in a large chicken RNA-seq data set. We conclude that LPL reaches the capillary lumen in chickens - as it does in mammals - despite an apparent absence of GPIHBP1.

Published
2017

6. 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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7. 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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8. 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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9. 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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10. 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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11. 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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12. 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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13. 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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14. 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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15. 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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17. 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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18. 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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19. Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap

Author

Giuffra, Elisabetta, Tuggle, Christopher K., Archibald, A.L., ACLOQUE, Hervé, Chamberlain, Amanda J., Cochrane, Guy, Daetwyler, Hans D., Djebali Quelen, Sarah, Eory, Lel, Foissac, Sylvain, Goddard, Michael E., Groenen, Martien A.M., Halstead, Michelle, Harrison, Peter W., Hayes, B.J., Kern, Colin, Khatib, Hassan, Kuo, Richard I., MacHugh, David E., MacLeod, I.M., Madsen, Ole, Reecy, Mark James, Ross, Pablo, J., Watson, Mick, Wells, Jerry M., Zhou, H.J., Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Iowa State University (ISU), University of Edinburgh, Dept Econ Dev Jobs Transport & Resources, European Molecular Biology Laboratory European Bioinformatics Institute, La Trobe University, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Melbourne, Wageningen University and Research Centre (WUR), University of California [Davis] (UC Davis), University of California, University of Queensland [Brisbane], University of Wisconsin-Madison, University College Dublin (UCD), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Epigenomics, 0301 basic medicine, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], domesticated animal, Genotype, Genomics, Computational biology, Animal Breeding and Genomics, Biology, Genome, genomic selection, 03 medical and health sciences, Annotation, Genome editing, functional genomic, Genetics, Animals, genome editing, Fokkerij en Genomica, Epigenetics, Gene Editing, 2. Zero hunger, epigenetics, General Veterinary, 0402 animal and dairy science, Molecular Sequence Annotation, 04 agricultural and veterinary sciences, genotype-to-phenotype, 040201 dairy & animal science, Chromatin, Phenotype, 030104 developmental biology, domesticated animals, Animals, Domestic, DNA methylation, WIAS, Animal Science and Zoology, functional genomics, Functional genomics, epigenetic, Biotechnology
Abstract

International audience; Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics is deficient in such annotation. To address this, the FAANG (Functional Annotation of Animal Genomes) Consortium is producing genome-wide data sets on RNA expression, DNA methylation, and chromatin modification, as well as chromatin accessibility and interactions. In addition to informing our understanding of genome function, including comparative approaches to elucidate constrained sequence or epigenetic elements, these annotation maps will improve the precision and sensitivity of genomic selection for animal improvement. A scientific community-driven effort has already created a coordinated data collection and analysis enterprise crucial for the success of this global effort. Although it is early in this continuing process, functional data have already been produced and application to genetic improvement reported. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal species.

Published
2019

20. A 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, Olsen, Björn, Jarvis, Erich D., Smith, Jacqueline, Eory, Lel, Kraus, Robert H. S., 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, Olsen, Björn, Jarvis, Erich D., Smith, Jacqueline, Eory, Lel, and Kraus, Robert H. S.

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.

Published
2021
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21. Additional file 2 of Illuminating the dark side of the human transcriptome with long read transcript sequencing

Author

Kuo, Richard I., Yuanyuan Cheng, Runxuan Zhang, Brown, John W. S., Smith, Jacqueline, Archibald, Alan L., and Burt, David W.

Subjects
ComputingMethodologies_PATTERNRECOGNITION
Abstract

Additional file 2: Table S1. Table of long read datasets information on number of mapped reads, reference annotation, and genome assembly scaffold numbers.

Published
2020
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22. A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duckAythya 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, 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 HS, additional

Published
2021
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23. Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human

Author

Kuo, Richard I, Tseng, Elizabeth, Eory, Lel, Paton, Ian R, Archibald, Alan L, and Burt, David W

Subjects
PacBio, Avian, lcsh:QH426-470, lcsh:Biotechnology, Iso-Seq, Gallus gallus, Single molecule long read sequencing, Coding RNA, RNAseq, Chicken, lcsh:Genetics, lcsh:TP248.13-248.65, Transcriptome sequencing, Non-coding RNA, Genome annotation
Abstract

BACKGROUND: Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read RNAseq data. While previous studies have used single molecule long read sequencing for transcript discovery, they did not perform RNA normalization and 5'-cap selection which may have resulted in lower transcriptome coverage and truncated transcript sequences.RESULTS: We sequenced normalised chicken brain and embryo RNA libraries with Pacific Bioscience Iso-Seq. 5' cap selection was performed on the embryo library to provide methodological comparison. From these Iso-Seq sequencing projects, we have identified 60 k transcripts and 29 k genes within the chicken transcriptome. Of these, more than 20 k are novel lncRNA transcripts with ~3 k classified as sense exonic overlapping lncRNA, which is a class that is underrepresented in many vertebrate annotations. The relative proportion of alternative transcription events revealed striking similarities between the chicken and human transcriptomes while also providing explanations for previously observed genomic differences.CONCLUSIONS: Our results indicate that the chicken transcriptome is similar in complexity compared to human, and provide insights into other vertebrate biology. Our methodology demonstrates the potential of Iso-Seq sequencing to rapidly expand our knowledge of transcriptomics.

Published
2017

24. 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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26. 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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