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Start Over Author "Chow, William" Publisher uppsala universitet, evolutionsbiologi
11 results on '"Chow, William"'

1. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author

Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., Komoroske, Lisa M., Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., and Komoroske, Lisa M.

Abstract

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.

Published
2023
Full Text
View/download PDF

2. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author

Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., Komoroske, Lisa M., Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., and Komoroske, Lisa M.

Abstract

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.

Published
2023
Full Text
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3. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author

Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., Komoroske, Lisa M., Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., and Komoroske, Lisa M.

Abstract

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.

Published
2023
Full Text
View/download PDF

4. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author

Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., Komoroske, Lisa M., Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., and Komoroske, Lisa M.

Abstract

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.

Published
2023
Full Text
View/download PDF

5. 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, Francoise, 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, Waldenstroem, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., Short, Kirsty R., 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, Francoise, 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, Waldenstroem, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Background The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Results Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan. Conclusion Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.

Published
2023
Full Text
View/download PDF

6. 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, Francoise, 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, Waldenstroem, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., Short, Kirsty R., 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, Francoise, 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, Waldenstroem, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Background The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Results Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan. Conclusion Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.

Published
2023
Full Text
View/download PDF

7. 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, Francoise, 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, Waldenstroem, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., Short, Kirsty R., 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, Francoise, 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, Waldenstroem, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Background The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Results Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan. Conclusion Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.

Published
2023
Full Text
View/download PDF

8. 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, Francoise, 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, Waldenstroem, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., Short, Kirsty R., 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, Francoise, 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, Waldenstroem, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Background The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Results Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan. Conclusion Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.

Published
2023
Full Text
View/download PDF

9. 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, Francoise, 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, Waldenstroem, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., Short, Kirsty R., 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, Francoise, 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, Waldenstroem, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Background The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Results Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan. Conclusion Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.

Published
2023
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10. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author

Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., Komoroske, Lisa M., Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., and Komoroske, Lisa M.

Abstract

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.

Published
2023
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11. Third Report on Chicken Genes and Chromosomes 2015

Author

Schmid, Michael, Smith, Jacqueline, Burt, David W., Aken, Bronwen L., Antin, Parker B., Archibald, Alan L., Ashwell, Chris, Blackshear, Perry J., Boschiero, Clarissa, Brown, C. Titus, Burgess, Shane C., Cheng, Hans H., Chow, William, Coble, Derrick J., Cooksey, Amanda, Crooijmans, Richard P. M. A., Damas, Joana, Davis, Richard V. N., de Koning, Dirk-Jan, Delany, Mary E., Derrien, Thomas, Desta, Takele T., Dunn, Ian C., Dunn, Matthew, Ellegren, Hans, Eoery, Lel, Erb, Ionas, Farre, Marta, Fasold, Mario, Fleming, Damarius, Flicek, Paul, Fowler, Katie E., Fresard, Laure, Froman, David P., Garceau, Valerie, Gardner, Paul P., Gheyas, Almas A., Griffin, Darren K., Groenen, Martien A. M., Haaf, Thomas, Hanotte, Olivier, Hart, Alan, Haesler, Julien, Hedges, S. Blair, Hertel, Jana, Howe, Kerstin, Hubbard, Allen, Hume, David A., Kaiser, Pete, Kedra, Darek, Kemp, Stephen J., Klopp, Christophe, Kniel, Kalmia E., Kuo, Richard, Lagarrigue, Sandrine, Lamont, Susan J., Larkin, Denis M., Lawal, Raman A., Markland, Sarah M., McCarthy, Fiona, McCormack, Heather A., McPherson, Marla C., Motegi, Akira, Muljo, Stefan A., Muensterberg, Andrea, Nag, Rishi, Nanda, Indrajit, Neuberger, Michael, Nitsche, Anne, Notredame, Cedric, Noyes, Harry, O'Connor, Rebecca, O'Hare, Elizabeth A., Oler, Andrew J., Ommeh, Sheila C., Pais, Helio, Persia, Michael, Pitel, Frederique, Preeyanon, Likit, Barja, Pablo Prieto, Pritchett, Elizabeth M., Rhoads, Douglas D., Robinson, Charmaine M., Romanov, Michael N., Rothschild, Max, Roux, Pierre-Francois, Schmidt, Carl J., Schneider, Alisa-Sophia, Schwartz, Matthew G., Searle, Steve M., Skinner, Michael A., Smith, Craig A., Stadler, Peter F., Steeves, Tammy E., Steinlein, Claus, Sun, Liang, Takata, Minoru, Ulitsky, Igor, Wang, Qing, Wang, Ying, Warren, Wesley C., Wood, Jonathan M. D., Wragg, David, Zhou, Huaijun, Schmid, Michael, Smith, Jacqueline, Burt, David W., Aken, Bronwen L., Antin, Parker B., Archibald, Alan L., Ashwell, Chris, Blackshear, Perry J., Boschiero, Clarissa, Brown, C. Titus, Burgess, Shane C., Cheng, Hans H., Chow, William, Coble, Derrick J., Cooksey, Amanda, Crooijmans, Richard P. M. A., Damas, Joana, Davis, Richard V. N., de Koning, Dirk-Jan, Delany, Mary E., Derrien, Thomas, Desta, Takele T., Dunn, Ian C., Dunn, Matthew, Ellegren, Hans, Eoery, Lel, Erb, Ionas, Farre, Marta, Fasold, Mario, Fleming, Damarius, Flicek, Paul, Fowler, Katie E., Fresard, Laure, Froman, David P., Garceau, Valerie, Gardner, Paul P., Gheyas, Almas A., Griffin, Darren K., Groenen, Martien A. M., Haaf, Thomas, Hanotte, Olivier, Hart, Alan, Haesler, Julien, Hedges, S. Blair, Hertel, Jana, Howe, Kerstin, Hubbard, Allen, Hume, David A., Kaiser, Pete, Kedra, Darek, Kemp, Stephen J., Klopp, Christophe, Kniel, Kalmia E., Kuo, Richard, Lagarrigue, Sandrine, Lamont, Susan J., Larkin, Denis M., Lawal, Raman A., Markland, Sarah M., McCarthy, Fiona, McCormack, Heather A., McPherson, Marla C., Motegi, Akira, Muljo, Stefan A., Muensterberg, Andrea, Nag, Rishi, Nanda, Indrajit, Neuberger, Michael, Nitsche, Anne, Notredame, Cedric, Noyes, Harry, O'Connor, Rebecca, O'Hare, Elizabeth A., Oler, Andrew J., Ommeh, Sheila C., Pais, Helio, Persia, Michael, Pitel, Frederique, Preeyanon, Likit, Barja, Pablo Prieto, Pritchett, Elizabeth M., Rhoads, Douglas D., Robinson, Charmaine M., Romanov, Michael N., Rothschild, Max, Roux, Pierre-Francois, Schmidt, Carl J., Schneider, Alisa-Sophia, Schwartz, Matthew G., Searle, Steve M., Skinner, Michael A., Smith, Craig A., Stadler, Peter F., Steeves, Tammy E., Steinlein, Claus, Sun, Liang, Takata, Minoru, Ulitsky, Igor, Wang, Qing, Wang, Ying, Warren, Wesley C., Wood, Jonathan M. D., Wragg, David, and Zhou, Huaijun

Published
2015
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