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1. 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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2. Additional file 16 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 16: Supplementary Table S14. 150 GO terms were significantly enriched in infected duck endothelial cells.

Published
2023
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3. 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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4. Additional file 14 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 14: Supplementary Table S12. 113 GO terms were significantly enriched in infected black swan endothelial cells.

Published
2023
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5. sj-pdf-1-eqs-10.1177_87552930231173446 – Supplemental material for A national seismic risk model for Canada: Methodology and scientific basis

Author

Hobbs, Tiegan E, Journeay, J Murray, Rao, Anirudh S, Kolaj, Michal, Martins, Luis, LeSueur, Philip, Simionato, Michele, Silva, Vitor, Pagani, Marco, Johnson, Kendra, Rotheram, Drew, and Chow, William

Subjects
FOS: Other engineering and technologies, 99999 Engineering not elsewhere classified
Abstract

Supplemental material, sj-pdf-1-eqs-10.1177_87552930231173446 for A national seismic risk model for Canada: Methodology and scientific basis by Tiegan E Hobbs, J Murray Journeay, Anirudh S Rao, Michal Kolaj, Luis Martins, Philip LeSueur, Michele Simionato, Vitor Silva, Marco Pagani, Kendra Johnson, Drew Rotheram and William Chow in Earthquake Spectra

Published
2023
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6. 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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7. Additional file 1 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 1: Supplementary Figure S1. Schematic overview of the process used to construct the black swan genome. Supplementary Figure S2. Schematic overview of the assembly pipeline version 1.5 of the vertebrate genome project used to construct the mute swan genome. Supplementary Figure S3. Hi-C contact maps for the black swan (a) and mute swan (b). Supplementary Figure S4. Schematic overview of the gene annotation pipeline. Supplementary Figure S5. The largest 34 chromosomes aligned between the black swan (left) and the mute swan (right). Supplementary Figure S6. Collinearity analysis of the Z chromosome between the mute swan (left) and black swan (right). Supplementary Figure S7. Black swan and duck synteny plot between the first chromosome. Supplementary Figure S8. MHC Class I (A) and MHC Class II (B) aligned regions of order-level consensus exons of the mute and black swan. Supplementary Figure S9. Relative locations of MHC complex and associated genes in black and mute swan chromosome 33. Supplementary Figure S10. TLR7 expression can be detected in ISO Seq analysis of the mute swan (A) but not the black swan (B). Supplementary Figure S11. IAV NP antigen distribution in tissues from a black swan naturally infected with A/Black swan/Akita/2/2016 (H5N6) in 2016 in Akita prefecture, Japan. Supplementary Figure S12. The successful culture of primary black swan endothelial cells confirmed by qRT-PCR, immunofluorescence and tube formation. Supplementary Figure S13. Differential regulation of DEGs linked to the “inactivation of MAPK” pathway in black swan endothelial cells in response to VN04 infection along with randomly selected GO terms.

Published
2023
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8. Additional file 10 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 10: Supplementary Table S8. Differentially expressed genes in infected black swan endothelial cells.

Published
2023
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9. Additional file 12 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 12: Supplementary Table S10. Differentially expressed genes in infected duck endothelial cells.

Published
2023
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10. 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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11. Additional file 17 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 17: Supplementary Table S15. Dual-specificity phosphatases in black swan, chicken and duck endothelial cells infected with VN04*.

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 15 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 15: Supplementary Table S13. 123 GO terms were significantly enriched in infected chicken endothelial cells.

Published
2023
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14. Additional file 18 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 18: Supplementary Table S16. Parameters used for the FALCON run. Length cut-off was detected automatically for seed-read length.

Published
2023
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15. Additional file 11 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 11: Supplementary Table S9. Differentially expressed genes in infected chicken endothelial cells.

Published
2023
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16. 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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17. 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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18. 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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19. Additional file 19 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 19: Review history.

Published
2023
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20. Segmental duplications

Author

Chaisson, Mark, Toh, Huishi, Stewart, Ron, Bukhman, Yury, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, and Thomson, James

Published
2022
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21. Heterozygosity spectrum

Author

Yang, Chentao, Zhang, Guojie, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, and Thomson, James

Abstract

Chentao Yang's heterozygosity spectrum analysis

Published
2022
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22. Comparison of house mouse gene complement to Nile rat using TOGA

Author

Bukhman, Yury, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Toh, Huishi, Chaisson, Mark, Stewart, Ron, Yang, Chentao, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, and Thomson, James

Published
2022
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23. Gene lists

Author

Bukhman, Yury, Toh, Huishi, Chaisson, Mark, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Raja, Kalpana, Yang, Chentao, Zhang, Guojie, Stewart, Ron, Formenti, Giulio, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, and Thomson, James

Published
2022
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24. Assembly quality

Author

Bukhman, Yury, Formenti, Giulio, Chaisson, Mark, Toh, Huishi, Yang, Chentao, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, Thomson, James, and Stewart, Ron

Abstract

Nile rat assembly quality metrics compared to other representative genomes of the Murinae

Published
2022
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25. Diversification selection

Author

Yang, Chentao, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, and Thomson, James

Abstract

Chentao Yang's dN/dS analysis of Nile rat vs. house mouse, Norway rat, and human

Published
2022
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26. GO term predictions

Author

Jain, Aashish, Kihara, Daisuke, Yang, Chentao, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, Thomson, James, and Chaisson, Mark

Published
2022
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27. Interesting genes

Author

Toh, Huishi, Yang, Chentao, Raja, Kalpana, Formenti, Giulio, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, Thomson, James, Stewart, Ron, Chaisson, Mark, and Bukhman, Yury

Published
2022
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28. Nile rat genome paper supplementary materials

Author

Toh, Huishi, Yang, Chentao, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, Thomson, James, Stewart, Ron, Chaisson, Mark, and Bukhman, Yury

Subjects
viruses, virus diseases, nervous system diseases
Abstract

Nile rat genome paper supplementary materials

Published
2022
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29. The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758

Author

Mead, Dan, Ogden, Rob, Meredith, Anna, Peniche, Gabriela, Smith, Michelle, Corton, Craig, Oliver, Karen, Skelton, Jason, Betteridge, Emma, Doulcan, Jale, Holmes, Nadine, Wright, Victoria, Loose, Matt, Quail, Michael A, McCarthy, Shane A, Howe, Kerstin, Chow, William, Torrance, James, Collins, Joanna, Challis, Richard, Durbin, Richard, Blaxter, Mark, Mead, Dan [0000-0001-7717-4330], Ogden, Rob [0000-0002-2831-0428], Doulcan, Jale [0000-0002-3551-1770], Wright, Victoria [0000-0002-9288-4338], Loose, Matt [0000-0002-5264-0929], McCarthy, Shane A [0000-0002-2715-4187], Howe, Kerstin [0000-0003-2237-513X], Torrance, James [0000-0002-6117-8190], Challis, Richard [0000-0002-3502-1122], Durbin, Richard [0000-0002-9130-1006], and Apollo - University of Cambridge Repository

Subjects
Aquila chrysaetos, genome sequence, European golden eagle, chromosomal
Abstract

We present a genome assembly from an individual female Aquila chrysaetos chrysaetos (the European golden eagle; Chordata; Aves; Accipitridae). The genome sequence is 1.23 gigabases in span. The majority of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the W and Z sex chromosomes.

Published
2021
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30. Towards complete and error-free genome assemblies of all vertebrate species

Author

Rhie, Arang, McCarthy, Shane A, Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Ko, Byung June, Chaisson, Mark, Gedman, Gregory L, Cantin, Lindsey J, Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C, Lama, Tanya M, Grutzner, Frank, Warren, Wesley C, Balakrishnan, Christopher N, Burt, Dave, George, Julia M, Biegler, Matthew T, Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Meyer, Axel, Kautt, Andreas F, Franchini, Paolo, Detrich, H William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin JP, Pippel, Martin, Malinsky, Milan, Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T, Pesout, Trevor, Houck, Marlys, Misuraca, Ann, Kingan, Sarah B, Hall, Richard, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E, Putnam, Nicholas H, Gut, Ivo, Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Wood, Jonathan, Dagnew, Robel E, Guan, Dengfeng, London, Sarah E, Clayton, David F, Mello, Claudio V, Friedrich, Samantha R, Lovell, Peter V, Osipova, Ekaterina, Al-Ajli, Farooq O, Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S, Makova, Kateryna D, Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P, Kwak, Woori, and Clawson, Hiram

Subjects
Sex Chromosomes, Genome, General Science & Technology, Human Genome, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, DNA, Genomics, Mitochondrial, Birds, Haplotypes, Genome Size, Vertebrates, Genetics, Animals, Generic health relevance, Sequence Alignment, Sequence Analysis, Gene Library, Biotechnology
Abstract

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Published
2021

31. The genome sequence of the brown trout, Salmo trutta Linnaeus 1758

Author

Hansen, Tom, Fjelldal, Per Gunnar, Lien, Sigbjørn, Smith, Michelle, Corton, Craig, Oliver, Karen, Skelton, Jason, Betteridge, Emma, Doulcan, Jale, Fedrigo, Olivier, Mountcastle, Jacquelyn, Jarvis, Erich, McCarthy, Shane A, Chow, William, Howe, Kerstin, Torrance, James, Wood, Jonathan, Sims, Ying, Haggerty, Leanne, Challis, Richard, Threlfall, Jonathan, Mead, Daniel, Durbin, Richard, Blaxter, Mark, Hansen, Tom [0000-0002-4784-5014], Doulcan, Jale [0000-0002-3551-1770], Fedrigo, Olivier [0000-0002-6450-7551], Mountcastle, Jacquelyn [0000-0003-1078-4905], Howe, Kerstin [0000-0003-2237-513X], Torrance, James [0000-0002-6117-8190], Wood, Jonathan [0000-0002-7545-2162], Challis, Richard [0000-0002-3502-1122], Threlfall, Jonathan [0000-0001-8599-4320], Mead, Daniel [0000-0001-7717-4330], Durbin, Richard [0000-0002-9130-1006], Blaxter, Mark [0000-0003-2861-949X], and Apollo - University of Cambridge Repository

Subjects
brown trout, animal diseases, genome sequence, Salmo trutta, chromosomal
Abstract

We present a genome assembly from an individual female Salmo trutta (the brown trout; Chordata; Actinopteri; Salmoniformes; Salmonidae). The genome sequence is 2.37 gigabases in span. The majority of the assembly is scaffolded into 40 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 43,935 protein coding genes.

Published
2021

32. The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769

Author

Howe, Kerstin, Dwinell, Melinda, Shimoyama, Mary, Corton, Craig, Betteridge, Emma, Dove, Alexander, Quail, Michael A, Smith, Michelle, Saba, Laura, Williams, Robert W, Chen, Hao, Kwitek, Anne E, McCarthy, Shane A, Uliano-Silva, Marcela, Chow, William, Tracey, Alan, Torrance, James, Sims, Ying, Challis, Richard, Threlfall, Jonathan, Blaxter, Mark, Howe, Kerstin [0000-0003-2237-513X], Saba, Laura [0000-0001-9649-1294], Williams, Robert W [0000-0001-8924-4447], Kwitek, Anne E [0000-0003-1024-4116], Tracey, Alan [0000-0002-4805-9058], Torrance, James [0000-0002-6117-8190], Challis, Richard [0000-0002-3502-1122], Threlfall, Jonathan [0000-0001-8599-4320], Blaxter, Mark [0000-0003-2861-949X], and Apollo - University of Cambridge Repository

Subjects
genome sequence, chromosomal, Rattus norvegicus, reference genome, Norway rat
Abstract

We present a genome assembly from an individual male Rattus norvegicus (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled. This genome assembly, mRatBN7.2, represents the new reference genome for R. norvegicus and has been adopted by the Genome Reference Consortium.

Published
2021

33. Genomic consequences of domestication of the Siamese fighting fish

Author

Kwon, Young Mi, Vranken, Nathan, Hoge, Carla, Lichak, Madison R, Francis, Kerel X, Camacho-Garcia, Julia, Bista, Iliana, Wood, Jonathan, McCarthy, Shane, Chow, William, Tan, Heok Hui, Howe, Kerstin, Bandara, Sepalika, von Lintig, Johannes, Rüber, Lukas, Durbin, Richard, Svardal, Hannes, and Bendesky, Andres

Subjects
570 Life sciences, biology
Abstract

Siamese fighting fish, commonly known as betta, are among the world’s most popular and morphologically diverse pet fish, but the genetic processes leading to their domestication and phenotypic diversification are largely unknown. We assembled de novo the genome of a wild Betta splendens and whole-genome sequenced multiple individuals across five species within the B. splendens species complex, including wild populations and domesticated ornamental betta. Given our estimate of the mutation rate from pedigrees, our analyses suggest that betta were domesticated at least 1,000 years ago, centuries earlier than previously thought. Ornamental betta individuals have variable contributions from other Betta species and have also introgressed into wild populations of those species. We identify dmrt1 as the main sex determination gene in ornamental betta but not in wild B. splendens, and find evidence for recent directional selection at the X-allele of the locus. Furthermore, we find genes with signatures of recent, strong selection that have large effects on color in specific parts of the body, or the shape of individual fins, and are almost all unlinked. Our results demonstrate how simple genetic architectures paired with anatomical modularity can lead to vast phenotypic diversity generated during animal domestication, and set the stage for using betta as a modern system for evolutionary genetics.

Published
2021
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34. The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861)

Author

Bista, Iliana, McCarthy, Shane A, Wood, Jonathan, Ning, Zemin, Detrich Iii, H William, Desvignes, Thomas, Postlethwait, John, Chow, William, Howe, Kerstin, Torrance, James, Smith, Michelle, Oliver, Karen, Vertebrate Genomes Project Consortium, Miska, Eric A, Durbin, Richard, Bista, Iliana [0000-0002-6155-3093], McCarthy, Shane A [0000-0002-2715-4187], Wood, Jonathan [0000-0002-7545-2162], Detrich Iii, H William [0000-0002-0783-4505], Desvignes, Thomas [0000-0001-5126-8785], Howe, Kerstin [0000-0003-2237-513X], Torrance, James [0000-0002-6117-8190], and Apollo - University of Cambridge Repository

Subjects
channel bull blenny, genome assembly chromosomal, Cottoperca gobio, Notothenioidei
Abstract

We present a genome assembly for Cottoperca gobio (channel bull blenny, (Günther, 1861)); Chordata; Actinopterygii (ray-finned fishes), a temperate water outgroup for Antarctic Notothenioids. The size of the genome assembly is 609 megabases, with the majority of the assembly scaffolded into 24 chromosomal pseudomolecules. Gene annotation on Ensembl of this assembly has identified 21,662 coding genes.

Published
2020
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36. MOESM1 of Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome

Author

Wentao Shi, Massaia, Andrea, Louzada, Sandra, Handsaker, Juliet, Chow, William, McCarthy, Shane, Collins, Joanna, Hallast, Pille, Howe, Kerstin, Church, Deanna, Fengtang Yang, Yali Xue, and Tyler-Smith, Chris

Abstract

Additional file 1: Figure S1. Tandem duplication in HG01097. Figure S2. Tandem duplication in HG04131. Figure S3. Tandem duplication in NA18953. Figure S4. Fiber-FISH results for HG00707, HG01031 and HG00982. (PDF 689 kb)

Published
2019
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40. Towards complete and error-free genome assemblies of all vertebrate species

Author

Rhie, Arang, McCarthy, Shane A, Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Ko, Byung June, Chaisson, Mark, Gedman, Gregory L, Cantin, Lindsey J, Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C, Lama, Tanya M, Grutzner, Frank, Warren, Wesley C, Balakrishnan, Christopher N, Burt, Dave, George, Julia M, Biegler, Matthew T, Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Meyer, Axel, Kautt, Andreas F, Franchini, Paolo, Detrich, H William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin JP, Pippel, Martin, Malinsky, Milan, Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T, Pesout, Trevor, Houck, Marlys, Misuraca, Ann, Kingan, Sarah B, Hall, Richard, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E, Putnam, Nicholas H, Gut, Ivo, Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Wood, Jonathan, Dagnew, Robel E, Guan, Dengfeng, London, Sarah E, Clayton, David F, Mello, Claudio V, Friedrich, Samantha R, Lovell, Peter V, Osipova, Ekaterina, Al-Ajli, Farooq O, Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S, Makova, Kateryna D, Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P, Kwak, Woori, Clawson, Hiram, Diekhans, Mark, Nassar, Luis, Paten, Benedict, Kraus, Robert HS, Crawford, Andrew J, Gilbert, M Thomas P, Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W, Koepfli, Klaus-Peter, Shapiro, Beth, Johnson, Warren E, Di Palma, Federica, Marques-Bonet, Tomas, Teeling, Emma C, Warnow, Tandy, Graves, Jennifer Marshall, Ryder, Oliver A, Haussler, David, O'Brien, Stephen J, Korlach, Jonas, Lewin, Harris A, Howe, Kerstin, Myers, Eugene W, Durbin, Richard, Phillippy, Adam M, and Jarvis, Erich D

Subjects
Genome, Sex Chromosomes, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Genomics, Sequence Analysis, DNA, Birds, Genome Size, Haplotypes, Genome, Mitochondrial, Vertebrates, Animals, 14. Life underwater, Sequence Alignment, Gene Library
Abstract

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

41. Additional file 4 of Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

Author

Quinn, Nicole L, Boroevich, Keith A, Lubieniecki, Krzysztof P, Chow, William, Davidson, Evelyn A, Phillips, Ruth B, Koop, Ben F, and Davidson, William S

Subjects
animal structures, fungi, 14. Life underwater
Abstract

Additional file 4: Table S3: Putative α and β hemoglobin genes from other teleosts and Xenopus tropicalis used to generate phylogenetic trees. The table lists all predicted intact α and β hemoglobin genes indentified within Biomart [69] for teleost genomes that have been sequenced and annotated (medaka, zebrafish, tetraodon, danio) and Xenopus tropicalis, which was used as an outgroup. For each hemoglobin gene identified, the table lists the species, chromosome or scaffold, start and stop positions, strand of transcription, Ensembl gene ID and our assigned gene name used in the phylogenetic trees. (PDF 51 KB)

42. Additional file 2 of Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

Author

Quinn, Nicole L, Boroevich, Keith A, Lubieniecki, Krzysztof P, Chow, William, Davidson, Evelyn A, Phillips, Ruth B, Koop, Ben F, and Davidson, William S

Subjects
endocrine system, food and beverages, 14. Life underwater, hormones, hormone substitutes, and hormone antagonists
Abstract

Additional file 2: Table S2A-C: Identified Atlantic salmon putatively functional and pseudogenized hemoglobin genes. S2A) Identified putatively functional Atlantic salmon α hemoglobin genes with chromosome, sequence contig number and approximate location (kb), strand of transcription, most highly similar Atlantic salmon EST cluster (if any), whether the gene has a corresponding full-length EST, whether the gene matches any of the previously published Atlantic salmon hemoglobin genes at the amino acid level and whether the gene is identical to any of those identified on the other Atlantic salmon chromosome. S2B) Identified putatively functional Atlantic salmon β hemoglobin genes with chromosome, sequence contig number and approximate location (kb), strand of transcription, most highly similar Atlantic salmon EST cluster (if any), whether the gene has a corresponding full-length EST, whether the gene matches any of the previously identified Atlantic salmon hemoglobin genes at the amino acid level, whether the gene is identical to any of those identified on the other Atlantic salmon chromosome, and whether the β hemoglobin gene possesses the hallmarks of lacking the Bohr effect. S2C) Putatively identified Atlantic salmon hemoglobin pseudogenes with chromosome, sequence contig, location (kb), direction and descriptions of each exon. (PDF 46 KB)

44. Additional file of Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

Author

Quinn, Nicole L, Boroevich, Keith A, Lubieniecki, Krzysztof P, Chow, William, Davidson, Evelyn A, Phillips, Ruth B, Koop, Ben F, and Davidson, William S

Subjects
endocrine system, animal diseases, 14. Life underwater, hormones, hormone substitutes, and hormone antagonists
Abstract

Additional file of Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

45. Additional file of Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

Author

Quinn, Nicole L, Boroevich, Keith A, Lubieniecki, Krzysztof P, Chow, William, Davidson, Evelyn A, Phillips, Ruth B, Koop, Ben F, and Davidson, William S

Subjects
endocrine system, animal diseases, 14. Life underwater, hormones, hormone substitutes, and hormone antagonists
Abstract

Additional file of Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

47. An improved pig reference genome sequence to enable pig genetics and genomics research

Author

Warr, Amanda, Affara, Nabeel, Aken, Bronwen, Beiki, Hamid, Bickhart, Derek M, Billis, Konstantinos, Chow, William, Eory, Lel, Finlayson, Heather A, Flicek, Paul, Girón, Carlos G, Griffin, Darren K, Hall, Richard, Hannum, Greg, Hourlier, Thibaut, Howe, Kerstin, Hume, David A, Izuogu, Osagie, Kim, Kristi, Koren, Sergey, Liu, Haibou, Manchanda, Nancy, Martin, Fergal J, Nonneman, Dan J, O'Connor, Rebecca E, Phillippy, Adam M, Rohrer, Gary A, Rosen, Benjamin D, Rund, Laurie A, Sargent, Carole A, Schook, Lawrence B, Schroeder, Steven G, Schwartz, Ariel S, Skinner, Ben M, Talbot, Richard, Tseng, Elizabeth, Tuggle, Christopher K, Watson, Mick, Smith, Timothy PL, and Archibald, Alan L

Subjects
2. Zero hunger, pig, reference assembly, Genome, genome annotation, Swine, Research, Sus scrofa, Computational Biology, Reproducibility of Results, Molecular Sequence Annotation, Genomics, Sequence Analysis, DNA, pig genomes, Animals
Abstract

BACKGROUND: The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete, and unresolved redundancies, short-range order and orientation errors, and associated misassembled genes limited its utility. RESULTS: We present 2 annotated highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. CONCLUSIONS: These highly contiguous assemblies plus annotation of a further 11 short-read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

50. Additional file 2 of Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

Author

Quinn, Nicole L, Boroevich, Keith A, Lubieniecki, Krzysztof P, Chow, William, Davidson, Evelyn A, Phillips, Ruth B, Koop, Ben F, and Davidson, William S

Subjects
endocrine system, food and beverages, 14. Life underwater, hormones, hormone substitutes, and hormone antagonists
Abstract

Additional file 2: Table S2A-C: Identified Atlantic salmon putatively functional and pseudogenized hemoglobin genes. S2A) Identified putatively functional Atlantic salmon α hemoglobin genes with chromosome, sequence contig number and approximate location (kb), strand of transcription, most highly similar Atlantic salmon EST cluster (if any), whether the gene has a corresponding full-length EST, whether the gene matches any of the previously published Atlantic salmon hemoglobin genes at the amino acid level and whether the gene is identical to any of those identified on the other Atlantic salmon chromosome. S2B) Identified putatively functional Atlantic salmon β hemoglobin genes with chromosome, sequence contig number and approximate location (kb), strand of transcription, most highly similar Atlantic salmon EST cluster (if any), whether the gene has a corresponding full-length EST, whether the gene matches any of the previously identified Atlantic salmon hemoglobin genes at the amino acid level, whether the gene is identical to any of those identified on the other Atlantic salmon chromosome, and whether the β hemoglobin gene possesses the hallmarks of lacking the Bohr effect. S2C) Putatively identified Atlantic salmon hemoglobin pseudogenes with chromosome, sequence contig, location (kb), direction and descriptions of each exon. (PDF 46 KB)

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