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Rocha, Sara

0000-0002-9705-1511

Current S-Index

26.7

Sum of Dataset Indices for all datasets

Average Dataset Index per Dataset

0.5

Average Dataset Index per dataset

Total Datasets

49

Total datasets for this author

Average FAIR Score

36.8%

Average FAIR Score per dataset

Total Citations

1

Total citations to the author's datasets

Total Mentions

0

Total mentions of the author's datasets

S-Index Interpretation

S-Index Over Time

Cumulative Citations Over Time

Cumulative Mentions Over Time

Datasets

Supporting data for "A draft genome sequence of the elusive giant squid, Architeuthis dux"

The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusk with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea dwelling species will allow unlocking several pending evolutionary questions. We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long-reads and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from three different tissue types from three other species of squid species (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein coding genes supported by evidence and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

Authors

  • da Fonseca, Rute, R ;
  • Couto, Alvarina ;
  • Machado, André, M. ;
  • Brejova, Brona ;
  • Albertin, Caroline, B. ;
  • Silva, Filipe ;
  • Gardner, Paul ;
  • Baril, Tobias ;
  • Hayward, Alex ;
  • Campos, Alexandre ;
  • Ribeiro, Angela, M. ;
  • Barrio-Hernandez, Inigo ;
  • Hoving, Henk-Jan ;
  • Tafur-Jimenez, Ricardo ;
  • Chu, Chong ;
  • Frazão, Bárbara ;
  • Petersen, Bent ;
  • Penaloza, Fernando ;
  • Musacchia, Francesco ;
  • Alexander Jr., Graham, C. ;
  • Osório, Hugo ;
  • Winkelmann, Inger ;
  • Simakov, Oleg ;
  • Rasmussen, Simon ;
  • Rahman, M., Ziaur ;
  • Pisani, Davide ;
  • Jarvis, Erich, D ;
  • Zhang, Guojie ;
  • Vinther, Jakob ;
  • Strugnell, Jan, M. ;
  • C. Castro, L., Filipe ;
  • Fedrigo, Olivier ;
  • Patricio, Mateus ;
  • Li, Qiye ;
  • Rocha, Sara ;
  • Antunes, Agostinho ;
  • Wu, Yufeng ;
  • Ma, Bin ;
  • Sanges, Remo ;
  • Vinar, Tomas ;
  • Blagoev, Blagoy ;
  • Sicheritz-Ponten, Thomas ;
  • Nielsen, Rasmus ;
  • Gilbert, M.Thomas, P
1 Citation0 Mentions31% FAIR0.7 Dataset Index
10.5524/100676January 2020

Genomic data from Royal penguin (<em>Eudyptes chrysolophus schlegeli</em>).

The Royal penguin is a crested penguin with golden-yellow crests found primarily on Macquarie Island, however a few individuals have also been detected in the Prince Edward Island group and other subantarctic islands. The Royal penguin is often considered a separate species from the Macaroni penguin, given its unique white facial plumage and relatively restricted breeding range. Several recent genetic studies, however, have demonstrated that the Royal penguin and Macaroni penguin are probably incipient. Historically, Royal penguins were hunted for their oil (between 1870 - 1919). The International Union for Conservation of Nature (IUCN) classifies the Royal penguin as near threatened.
We sequenced the genome of an adult Royal penguin from Green Gorge, Macquarie Island, Australia (provided by Gary Miller) to a depth of approximately 320x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.18Gb, with the contig and scaffold N50 values of 23.62Kb and 1.79Mb respectively. We identified 17191 protein-coding genes.

Authors

  • Pan, Hailin ;
  • Cole, Theresa ;
  • Couto, Alvarina ;
  • Bi, Xupeng ;
  • Machado, André, M. ;
  • Brejova, Brona ;
  • Fang, Miaoquan ;
  • Albertin, Caroline, B. ;
  • Zhou, Chengran ;
  • Silva, Filipe ;
  • Yang, Zhengtao ;
  • Gardner, Paul ;
  • Ksepka, Daniel, T ;
  • Baril, Tobias ;
  • Hart, Tom ;
  • Bouzat, Juan, L ;
  • Hayward, Alex ;
  • Argilla, Lisa, S ;
  • Campos, Alexandre ;
  • Bertelsen, Mads, F ;
  • Ribeiro, Angela, M. ;
  • Barrio-Hernandez, Inigo ;
  • Boersma, P, Dee ;
  • Bost, Charles-André ;
  • Hoving, Henk-Jan ;
  • Cherel, Yves ;
  • Tafur-Jimenez, Ricardo ;
  • Chu, Chong ;
  • Dann, Peter ;
  • Fiddaman, Steven, R ;
  • Frazão, Bárbara ;
  • Howard, Pauline ;
  • Petersen, Bent ;
  • Labuschagne, Kim ;
  • Penaloza, Fernando ;
  • Mattern, Thomas ;
  • Musacchia, Francesco ;
  • Alexander Jr., Graham, C. ;
  • Miller, Gary ;
  • Osório, Hugo ;
  • Parker, Patricia ;
  • Phillips, Richard, A ;
  • Winkelmann, Inger ;
  • Quillfeldt, Petra ;
  • Simakov, Oleg ;
  • Rasmussen, Simon ;
  • Ryan, Peter, G ;
  • Rahman, M., Ziaur ;
  • Taylor, Helen ;
  • Pisani, Davide ;
  • Thompson, David, R ;
  • Jarvis, Erich, D ;
  • Young, Melanie, J ;
  • Ellegaard, Martin, R ;
  • Zhang, Guojie ;
  • Gilbert, M.Thomas, P ;
  • Vinther, Jakob ;
  • Sinding, Mikkel-Holger, S ;
  • Strugnell, Jan, M. ;
  • C. Castro, L., Filipe ;
  • Pacheco, George ;
  • Fedrigo, Olivier ;
  • Shepherd, Lara, D ;
  • D Tennyson, Alan, J ;
  • Patricio, Mateus ;
  • Grosser, Stefanie ;
  • Li, Qiye ;
  • Kay, Emily ;
  • Rocha, Sara ;
  • Antunes, Agostinho ;
  • Nupen, Lisa, J ;
  • Ellenberg, Ursula ;
  • Wu, Yufeng ;
  • Houston, David, M ;
  • Ma, Bin ;
  • Reeve, Andrew, Hart ;
  • Sanges, Remo ;
  • Johnson, Kathryn ;
  • Vinar, Tomas ;
  • Blagoev, Blagoy ;
  • Masello, Juan, F ;
  • Sicheritz-Ponten, Thomas ;
  • Stracke, Thomas ;
  • McKinlay, Bruce ;
  • Nielsen, Rasmus ;
  • García Borboroglu, Pablo ;
  • Gilbert, M.Thomas, P ;
  • Zhang, De, Xing ;
  • Zhang, Guojie
0 Citations0 Mentions31% FAIR0.3 Dataset Index
10.5524/102164January 2019

Genomic data from African penguin (<em>Spheniscus demersus</em>).

The African penguin (also known as jackass penguin and black-footed penguin) is endemic to southern African coasts. The pink gland above the eyes helps to adjust to changing temperatures: when it's hotter, more blood is sent to these glands to be cooled by the surrounding air. It is a charismatic species and is popular with tourists. The African penguin has declined rapidly and the International Union for Conservation of Nature (IUCN) classifies it as endangered.
We sequenced the genome of an adult African penguin from Luderitz, Namibia (provided by Kim Labuschagne) to a depth of approximately 115x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.23Gb, with the contig and scaffold N50 values of 99.03Kb and 14.67Mb respectively. We identified 16134 protein-coding genes.

Authors

  • Pan, Hailin ;
  • Cole, Theresa ;
  • Couto, Alvarina ;
  • Bi, Xupeng ;
  • Machado, André, M. ;
  • Brejova, Brona ;
  • Fang, Miaoquan ;
  • Albertin, Caroline, B. ;
  • Zhou, Chengran ;
  • Silva, Filipe ;
  • Yang, Zhengtao ;
  • Gardner, Paul ;
  • Ksepka, Daniel, T ;
  • Baril, Tobias ;
  • Hart, Tom ;
  • Bouzat, Juan, L ;
  • Hayward, Alex ;
  • Argilla, Lisa, S ;
  • Campos, Alexandre ;
  • Bertelsen, Mads, F ;
  • Ribeiro, Angela, M. ;
  • Barrio-Hernandez, Inigo ;
  • Boersma, P, Dee ;
  • Bost, Charles-André ;
  • Hoving, Henk-Jan ;
  • Cherel, Yves ;
  • Tafur-Jimenez, Ricardo ;
  • Chu, Chong ;
  • Dann, Peter ;
  • Fiddaman, Steven, R ;
  • Frazão, Bárbara ;
  • Howard, Pauline ;
  • Petersen, Bent ;
  • Labuschagne, Kim ;
  • Penaloza, Fernando ;
  • Mattern, Thomas ;
  • Musacchia, Francesco ;
  • Alexander Jr., Graham, C. ;
  • Miller, Gary ;
  • Osório, Hugo ;
  • Parker, Patricia ;
  • Phillips, Richard, A ;
  • Winkelmann, Inger ;
  • Quillfeldt, Petra ;
  • Simakov, Oleg ;
  • Rasmussen, Simon ;
  • Ryan, Peter, G ;
  • Rahman, M., Ziaur ;
  • Taylor, Helen ;
  • Pisani, Davide ;
  • Thompson, David, R ;
  • Jarvis, Erich, D ;
  • Young, Melanie, J ;
  • Ellegaard, Martin, R ;
  • Zhang, Guojie ;
  • Gilbert, M.Thomas, P ;
  • Vinther, Jakob ;
  • Sinding, Mikkel-Holger, S ;
  • Strugnell, Jan, M. ;
  • C. Castro, L., Filipe ;
  • Pacheco, George ;
  • Fedrigo, Olivier ;
  • Shepherd, Lara, D ;
  • D Tennyson, Alan, J ;
  • Patricio, Mateus ;
  • Grosser, Stefanie ;
  • Li, Qiye ;
  • Kay, Emily ;
  • Rocha, Sara ;
  • Antunes, Agostinho ;
  • Nupen, Lisa, J ;
  • Ellenberg, Ursula ;
  • Wu, Yufeng ;
  • Houston, David, M ;
  • Ma, Bin ;
  • Reeve, Andrew, Hart ;
  • Sanges, Remo ;
  • Johnson, Kathryn ;
  • Vinar, Tomas ;
  • Blagoev, Blagoy ;
  • Masello, Juan, F ;
  • Sicheritz-Ponten, Thomas ;
  • Stracke, Thomas ;
  • McKinlay, Bruce ;
  • Nielsen, Rasmus ;
  • García Borboroglu, Pablo ;
  • Gilbert, M.Thomas, P ;
  • Zhang, De, Xing ;
  • Zhang, Guojie
0 Citations0 Mentions31% FAIR0.3 Dataset Index
10.5524/102174January 2019

Genomic data from King penguin (<em>Aptenodytes patagonicus</em>).

The King penguin is the second largest species of penguin. They have a circumpolar range, breeding on the subantarctic islands at the northern reaches of Antarctica, South Georgia, and other temperate islands. They were heavily hunted for oil on Macquarie Island. King penguins appear to have suffered a major population declines, and 70% are expected to disappear in the next eighty years, however they are still considered as Least Concern by the International Union for Conservation of Nature (IUCN).
We sequenced the genome of an adult King penguin from Fortuna Bay, South Georgia (provided by Tom Hart) to a depth of approximately 120x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.24Gb, with the contig and scaffold N50 values of 114.03Kb and 2.77Mb respectively. We identified 15195 protein-coding genes.

Authors

  • Pan, Hailin ;
  • Cole, Theresa ;
  • Couto, Alvarina ;
  • Bi, Xupeng ;
  • Machado, André, M. ;
  • Brejova, Brona ;
  • Fang, Miaoquan ;
  • Albertin, Caroline, B. ;
  • Zhou, Chengran ;
  • Silva, Filipe ;
  • Yang, Zhengtao ;
  • Gardner, Paul ;
  • Ksepka, Daniel, T ;
  • Baril, Tobias ;
  • Hart, Tom ;
  • Bouzat, Juan, L ;
  • Hayward, Alex ;
  • Argilla, Lisa, S ;
  • Campos, Alexandre ;
  • Bertelsen, Mads, F ;
  • Ribeiro, Angela, M. ;
  • Barrio-Hernandez, Inigo ;
  • Boersma, P, Dee ;
  • Bost, Charles-André ;
  • Hoving, Henk-Jan ;
  • Cherel, Yves ;
  • Tafur-Jimenez, Ricardo ;
  • Chu, Chong ;
  • Dann, Peter ;
  • Fiddaman, Steven, R ;
  • Frazão, Bárbara ;
  • Howard, Pauline ;
  • Petersen, Bent ;
  • Labuschagne, Kim ;
  • Penaloza, Fernando ;
  • Mattern, Thomas ;
  • Musacchia, Francesco ;
  • Alexander Jr., Graham, C. ;
  • Miller, Gary ;
  • Osório, Hugo ;
  • Parker, Patricia ;
  • Phillips, Richard, A ;
  • Winkelmann, Inger ;
  • Quillfeldt, Petra ;
  • Simakov, Oleg ;
  • Rasmussen, Simon ;
  • Ryan, Peter, G ;
  • Rahman, M., Ziaur ;
  • Taylor, Helen ;
  • Pisani, Davide ;
  • Thompson, David, R ;
  • Jarvis, Erich, D ;
  • Young, Melanie, J ;
  • Ellegaard, Martin, R ;
  • Zhang, Guojie ;
  • Gilbert, M.Thomas, P ;
  • Vinther, Jakob ;
  • Sinding, Mikkel-Holger, S ;
  • Strugnell, Jan, M. ;
  • C. Castro, L., Filipe ;
  • Pacheco, George ;
  • Fedrigo, Olivier ;
  • Shepherd, Lara, D ;
  • D Tennyson, Alan, J ;
  • Patricio, Mateus ;
  • Grosser, Stefanie ;
  • Li, Qiye ;
  • Kay, Emily ;
  • Rocha, Sara ;
  • Antunes, Agostinho ;
  • Nupen, Lisa, J ;
  • Ellenberg, Ursula ;
  • Wu, Yufeng ;
  • Houston, David, M ;
  • Ma, Bin ;
  • Reeve, Andrew, Hart ;
  • Sanges, Remo ;
  • Johnson, Kathryn ;
  • Vinar, Tomas ;
  • Blagoev, Blagoy ;
  • Masello, Juan, F ;
  • Sicheritz-Ponten, Thomas ;
  • Stracke, Thomas ;
  • McKinlay, Bruce ;
  • Nielsen, Rasmus ;
  • García Borboroglu, Pablo ;
  • Gilbert, M.Thomas, P ;
  • Zhang, De, Xing ;
  • Zhang, Guojie
0 Citations0 Mentions31% FAIR0.3 Dataset Index
10.5524/102182January 2019

Genomic data from Gentoo penguin (<em>Pygoscelis papua</em>).

The Gentoo penguin is easily recognized by the wide white stripe extending across the top of its head, and its bright orange-red bill. It has a long tail. Gentoos are the third-largest species of penguin after the Emperor penguin and the King penguin. Gentoos are well adapted to extremely cold and harsh climates. Breeding colonies are located on ice-free surfaces. Gentoos breed on many sub-Antarctic islands, with main colonies are on the Falkland Islands, South Georgia and the South Sandwich Islands, and Kerguelen Islands. Gentoo penguins exhibit population genetic structure, and different populations are occasionally considered to represent several subspecies. They are considered as Least Concern by the International Union for Conservation of Nature (IUCN).
We sequenced the genome of an adult Gentoo penguin from West Antarctic Peninsula, Antarctica (provided by Tom Hart) to a depth of approximately 105x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.26Gb, with the contig and scaffold N50 values of 91.59Kb and 2.65Mb respectively. We identified 16698 protein-coding genes.

Authors

  • Pan, Hailin ;
  • Cole, Theresa ;
  • Couto, Alvarina ;
  • Bi, Xupeng ;
  • Machado, André, M. ;
  • Brejova, Brona ;
  • Fang, Miaoquan ;
  • Albertin, Caroline, B. ;
  • Zhou, Chengran ;
  • Silva, Filipe ;
  • Yang, Zhengtao ;
  • Gardner, Paul ;
  • Ksepka, Daniel, T ;
  • Baril, Tobias ;
  • Hart, Tom ;
  • Bouzat, Juan, L ;
  • Hayward, Alex ;
  • Argilla, Lisa, S ;
  • Campos, Alexandre ;
  • Bertelsen, Mads, F ;
  • Ribeiro, Angela, M. ;
  • Barrio-Hernandez, Inigo ;
  • Boersma, P, Dee ;
  • Bost, Charles-André ;
  • Hoving, Henk-Jan ;
  • Cherel, Yves ;
  • Tafur-Jimenez, Ricardo ;
  • Chu, Chong ;
  • Dann, Peter ;
  • Fiddaman, Steven, R ;
  • Frazão, Bárbara ;
  • Howard, Pauline ;
  • Petersen, Bent ;
  • Labuschagne, Kim ;
  • Penaloza, Fernando ;
  • Mattern, Thomas ;
  • Musacchia, Francesco ;
  • Alexander Jr., Graham, C. ;
  • Miller, Gary ;
  • Osório, Hugo ;
  • Parker, Patricia ;
  • Phillips, Richard, A ;
  • Winkelmann, Inger ;
  • Quillfeldt, Petra ;
  • Simakov, Oleg ;
  • Rasmussen, Simon ;
  • Ryan, Peter, G ;
  • Rahman, M., Ziaur ;
  • Taylor, Helen ;
  • Pisani, Davide ;
  • Thompson, David, R ;
  • Jarvis, Erich, D ;
  • Young, Melanie, J ;
  • Ellegaard, Martin, R ;
  • Zhang, Guojie ;
  • Gilbert, M.Thomas, P ;
  • Vinther, Jakob ;
  • Sinding, Mikkel-Holger, S ;
  • Strugnell, Jan, M. ;
  • C. Castro, L., Filipe ;
  • Pacheco, George ;
  • Fedrigo, Olivier ;
  • Shepherd, Lara, D ;
  • D Tennyson, Alan, J ;
  • Patricio, Mateus ;
  • Grosser, Stefanie ;
  • Li, Qiye ;
  • Kay, Emily ;
  • Rocha, Sara ;
  • Antunes, Agostinho ;
  • Nupen, Lisa, J ;
  • Ellenberg, Ursula ;
  • Wu, Yufeng ;
  • Houston, David, M ;
  • Ma, Bin ;
  • Reeve, Andrew, Hart ;
  • Sanges, Remo ;
  • Johnson, Kathryn ;
  • Vinar, Tomas ;
  • Blagoev, Blagoy ;
  • Masello, Juan, F ;
  • Sicheritz-Ponten, Thomas ;
  • Stracke, Thomas ;
  • McKinlay, Bruce ;
  • Nielsen, Rasmus ;
  • García Borboroglu, Pablo ;
  • Gilbert, M.Thomas, P ;
  • Zhang, De, Xing ;
  • Zhang, Guojie
0 Citations0 Mentions31% FAIR0.8 Dataset Index
10.5524/102180January 2019

Genomic data from Chinstrap penguin (<em>Pygoscelis antarctica</em>).

The Chinstrap penguin inhabits a variety of islands and shores in the Southern Pacific and the Antarctic Oceans. It has a narrow black band under its head. They breed in Antarctica, Argentina, Bouvet Island, Chile, the Falkland Islands, the French Southern Territories, and South Georgia and the South Sandwich Islands. Populations of Chinstrap penguin are considered to be decreasing overall, however in many sites the populations are increasing or stable. They are considered as Least Concern by the International Union for Conservation of Nature (IUCN).
We sequenced the genome of an adult Chinstrap penguin from Thule Island, South Sandwich Islands (provided by Tom Hart) to a depth of approximately 125x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.24Gb, with the contig and scaffold N50 values of 115.56Kb and 5.89Mb respectively. We identified 15488 protein-coding genes.

Authors

  • Pan, Hailin ;
  • Cole, Theresa ;
  • Couto, Alvarina ;
  • Bi, Xupeng ;
  • Machado, André, M. ;
  • Brejova, Brona ;
  • Fang, Miaoquan ;
  • Albertin, Caroline, B. ;
  • Zhou, Chengran ;
  • Silva, Filipe ;
  • Yang, Zhengtao ;
  • Gardner, Paul ;
  • Ksepka, Daniel, T ;
  • Baril, Tobias ;
  • Hart, Tom ;
  • Bouzat, Juan, L ;
  • Hayward, Alex ;
  • Argilla, Lisa, S ;
  • Campos, Alexandre ;
  • Bertelsen, Mads, F ;
  • Ribeiro, Angela, M. ;
  • Barrio-Hernandez, Inigo ;
  • Boersma, P, Dee ;
  • Bost, Charles-André ;
  • Hoving, Henk-Jan ;
  • Cherel, Yves ;
  • Tafur-Jimenez, Ricardo ;
  • Chu, Chong ;
  • Dann, Peter ;
  • Fiddaman, Steven, R ;
  • Frazão, Bárbara ;
  • Howard, Pauline ;
  • Petersen, Bent ;
  • Labuschagne, Kim ;
  • Penaloza, Fernando ;
  • Mattern, Thomas ;
  • Musacchia, Francesco ;
  • Alexander Jr., Graham, C. ;
  • Miller, Gary ;
  • Osório, Hugo ;
  • Parker, Patricia ;
  • Phillips, Richard, A ;
  • Winkelmann, Inger ;
  • Quillfeldt, Petra ;
  • Simakov, Oleg ;
  • Rasmussen, Simon ;
  • Ryan, Peter, G ;
  • Rahman, M., Ziaur ;
  • Taylor, Helen ;
  • Pisani, Davide ;
  • Thompson, David, R ;
  • Jarvis, Erich, D ;
  • Young, Melanie, J ;
  • Ellegaard, Martin, R ;
  • Zhang, Guojie ;
  • Gilbert, M.Thomas, P ;
  • Vinther, Jakob ;
  • Sinding, Mikkel-Holger, S ;
  • Strugnell, Jan, M. ;
  • C. Castro, L., Filipe ;
  • Pacheco, George ;
  • Fedrigo, Olivier ;
  • Shepherd, Lara, D ;
  • D Tennyson, Alan, J ;
  • Patricio, Mateus ;
  • Grosser, Stefanie ;
  • Li, Qiye ;
  • Kay, Emily ;
  • Rocha, Sara ;
  • Antunes, Agostinho ;
  • Nupen, Lisa, J ;
  • Ellenberg, Ursula ;
  • Wu, Yufeng ;
  • Houston, David, M ;
  • Ma, Bin ;
  • Reeve, Andrew, Hart ;
  • Sanges, Remo ;
  • Johnson, Kathryn ;
  • Vinar, Tomas ;
  • Blagoev, Blagoy ;
  • Masello, Juan, F ;
  • Sicheritz-Ponten, Thomas ;
  • Stracke, Thomas ;
  • McKinlay, Bruce ;
  • Nielsen, Rasmus ;
  • García Borboroglu, Pablo ;
  • Gilbert, M.Thomas, P ;
  • Zhang, De, Xing ;
  • Zhang, Guojie
0 Citations0 Mentions31% FAIR0.3 Dataset Index
10.5524/102181January 2019

Genomic data from Galápagos penguin (<em>Spheniscus mendiculus</em>).

The Galápagos penguin is endemic to the Galápagos Islands, and is the only penguin with breeding colonies north of the equator. The cool waters of the Humboldt and Cromwell Currents allow the species to survive in the tropics, and they have evolved unique adaptations to survive in a tropical environment. The International Union for Conservation of Nature (IUCN) classifies them as endangered.
We sequenced the genome of an adult Galápagos penguin from Galápagos Islands (provided by Patricia Parker) to a depth of approximately 87x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.35Gb, with the contig and scaffold N50 values of 70.85Kb and 0.36Mb respectively. We identified 16390 protein-coding genes.

Authors

  • Pan, Hailin ;
  • Cole, Theresa ;
  • Couto, Alvarina ;
  • Bi, Xupeng ;
  • Machado, André, M. ;
  • Brejova, Brona ;
  • Fang, Miaoquan ;
  • Albertin, Caroline, B. ;
  • Zhou, Chengran ;
  • Silva, Filipe ;
  • Yang, Zhengtao ;
  • Gardner, Paul ;
  • Ksepka, Daniel, T ;
  • Baril, Tobias ;
  • Hart, Tom ;
  • Bouzat, Juan, L ;
  • Hayward, Alex ;
  • Argilla, Lisa, S ;
  • Campos, Alexandre ;
  • Bertelsen, Mads, F ;
  • Ribeiro, Angela, M. ;
  • Barrio-Hernandez, Inigo ;
  • Boersma, P, Dee ;
  • Bost, Charles-André ;
  • Hoving, Henk-Jan ;
  • Cherel, Yves ;
  • Tafur-Jimenez, Ricardo ;
  • Chu, Chong ;
  • Dann, Peter ;
  • Fiddaman, Steven, R ;
  • Frazão, Bárbara ;
  • Howard, Pauline ;
  • Petersen, Bent ;
  • Labuschagne, Kim ;
  • Penaloza, Fernando ;
  • Mattern, Thomas ;
  • Musacchia, Francesco ;
  • Alexander Jr., Graham, C. ;
  • Miller, Gary ;
  • Osório, Hugo ;
  • Parker, Patricia ;
  • Phillips, Richard, A ;
  • Winkelmann, Inger ;
  • Quillfeldt, Petra ;
  • Simakov, Oleg ;
  • Rasmussen, Simon ;
  • Ryan, Peter, G ;
  • Rahman, M., Ziaur ;
  • Taylor, Helen ;
  • Pisani, Davide ;
  • Thompson, David, R ;
  • Jarvis, Erich, D ;
  • Young, Melanie, J ;
  • Ellegaard, Martin, R ;
  • Zhang, Guojie ;
  • Gilbert, M.Thomas, P ;
  • Vinther, Jakob ;
  • Sinding, Mikkel-Holger, S ;
  • Strugnell, Jan, M. ;
  • C. Castro, L., Filipe ;
  • Pacheco, George ;
  • Fedrigo, Olivier ;
  • Shepherd, Lara, D ;
  • D Tennyson, Alan, J ;
  • Patricio, Mateus ;
  • Grosser, Stefanie ;
  • Li, Qiye ;
  • Kay, Emily ;
  • Rocha, Sara ;
  • Antunes, Agostinho ;
  • Nupen, Lisa, J ;
  • Ellenberg, Ursula ;
  • Wu, Yufeng ;
  • Houston, David, M ;
  • Ma, Bin ;
  • Reeve, Andrew, Hart ;
  • Sanges, Remo ;
  • Johnson, Kathryn ;
  • Vinar, Tomas ;
  • Blagoev, Blagoy ;
  • Masello, Juan, F ;
  • Sicheritz-Ponten, Thomas ;
  • Stracke, Thomas ;
  • McKinlay, Bruce ;
  • Nielsen, Rasmus ;
  • García Borboroglu, Pablo ;
  • Gilbert, M.Thomas, P ;
  • Zhang, De, Xing ;
  • Zhang, Guojie
0 Citations0 Mentions31% FAIR0.8 Dataset Index
10.5524/102175January 2019

Genomic data from Little blue penguin (<em>Eudyptula minor minor</em>).

The New Zealand little blue penguin (also known as fairy penguin, blue penguin, little penguin and koror in Mori) is one of the smallest penguins. It is found on the coastlines of New Zealand and the Chatham Islands. They have a slate-blue plumage. Recent genetic, morphological and behavioral research has demonstrated that the New Zealand little blue penguin is a seperate species to the Australian fairy penguin, however this still remains controversial. Populations have recently declined, and they are considered as Least Concern by the International Union for Conservation of Nature (IUCN), however this assessment still classifies the Australian and New Zealand species as conspecific. The New Zealand little penguin is a Taonga, or treasured possession in Mori culture.
We sequenced the genome of an adult Little blue penguin from National Aquarium of New Zealand, New Zealand North Island (provided by Helen Taylor) to a depth of approximately 87x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.3Gb, with the contig and scaffold N50 values of 86.12Kb and 20.15Mb respectively. We identified 17802 protein-coding genes.

Authors

  • Pan, Hailin ;
  • Cole, Theresa ;
  • Couto, Alvarina ;
  • Bi, Xupeng ;
  • Machado, André, M. ;
  • Brejova, Brona ;
  • Fang, Miaoquan ;
  • Albertin, Caroline, B. ;
  • Zhou, Chengran ;
  • Silva, Filipe ;
  • Yang, Zhengtao ;
  • Gardner, Paul ;
  • Ksepka, Daniel, T ;
  • Baril, Tobias ;
  • Hart, Tom ;
  • Bouzat, Juan, L ;
  • Hayward, Alex ;
  • Argilla, Lisa, S ;
  • Campos, Alexandre ;
  • Bertelsen, Mads, F ;
  • Ribeiro, Angela, M. ;
  • Barrio-Hernandez, Inigo ;
  • Boersma, P, Dee ;
  • Bost, Charles-André ;
  • Hoving, Henk-Jan ;
  • Cherel, Yves ;
  • Tafur-Jimenez, Ricardo ;
  • Chu, Chong ;
  • Dann, Peter ;
  • Fiddaman, Steven, R ;
  • Frazão, Bárbara ;
  • Howard, Pauline ;
  • Petersen, Bent ;
  • Labuschagne, Kim ;
  • Penaloza, Fernando ;
  • Mattern, Thomas ;
  • Musacchia, Francesco ;
  • Alexander Jr., Graham, C. ;
  • Miller, Gary ;
  • Osório, Hugo ;
  • Parker, Patricia ;
  • Phillips, Richard, A ;
  • Winkelmann, Inger ;
  • Quillfeldt, Petra ;
  • Simakov, Oleg ;
  • Rasmussen, Simon ;
  • Ryan, Peter, G ;
  • Rahman, M., Ziaur ;
  • Taylor, Helen ;
  • Pisani, Davide ;
  • Thompson, David, R ;
  • Jarvis, Erich, D ;
  • Young, Melanie, J ;
  • Ellegaard, Martin, R ;
  • Zhang, Guojie ;
  • Gilbert, M.Thomas, P ;
  • Vinther, Jakob ;
  • Sinding, Mikkel-Holger, S ;
  • Strugnell, Jan, M. ;
  • C. Castro, L., Filipe ;
  • Pacheco, George ;
  • Fedrigo, Olivier ;
  • Shepherd, Lara, D ;
  • D Tennyson, Alan, J ;
  • Patricio, Mateus ;
  • Grosser, Stefanie ;
  • Li, Qiye ;
  • Kay, Emily ;
  • Rocha, Sara ;
  • Antunes, Agostinho ;
  • Nupen, Lisa, J ;
  • Ellenberg, Ursula ;
  • Wu, Yufeng ;
  • Houston, David, M ;
  • Ma, Bin ;
  • Reeve, Andrew, Hart ;
  • Sanges, Remo ;
  • Johnson, Kathryn ;
  • Vinar, Tomas ;
  • Blagoev, Blagoy ;
  • Masello, Juan, F ;
  • Sicheritz-Ponten, Thomas ;
  • Stracke, Thomas ;
  • McKinlay, Bruce ;
  • Nielsen, Rasmus ;
  • García Borboroglu, Pablo ;
  • Gilbert, M.Thomas, P ;
  • Zhang, De, Xing ;
  • Zhang, Guojie
0 Citations0 Mentions31% FAIR0.3 Dataset Index
10.5524/102178January 2019

Genomic data from Fairy penguin (<em>Eudyptula novaehollandiae</em>).

The Australian fairy penguin (also known as little blue penguin, blue penguin and little penguin) is one of the smallest penguins. It is found widely along the southern coastlines of Australia and the Otago coast of New Zealand. They have a slate-blue plumage. Recent genetic, morphological and behavioral research has demonstrated that the Australian fairy penguin is a separate species to the New Zealand little blue penguin, however this still remains controversial. Populations have recently declined, and they are considered as Least Concern by the International Union for Conservation of Nature (IUCN), however this assessment still classifies the Australian and New Zealand species as conspecific.
We sequenced the genome of an adult Fairy penguin from Phillip Island, Victoria, Australia (provided by Peter Dann) to a depth of approximately 137x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.28Gb, with the contig and scaffold N50 values of 119.59Kb and 27.92Mb respectively. We identified 17188 protein-coding genes.

Authors

  • Pan, Hailin ;
  • Cole, Theresa ;
  • Couto, Alvarina ;
  • Bi, Xupeng ;
  • Machado, André, M. ;
  • Brejova, Brona ;
  • Fang, Miaoquan ;
  • Albertin, Caroline, B. ;
  • Zhou, Chengran ;
  • Silva, Filipe ;
  • Yang, Zhengtao ;
  • Gardner, Paul ;
  • Ksepka, Daniel, T ;
  • Baril, Tobias ;
  • Hart, Tom ;
  • Bouzat, Juan, L ;
  • Hayward, Alex ;
  • Argilla, Lisa, S ;
  • Campos, Alexandre ;
  • Bertelsen, Mads, F ;
  • Ribeiro, Angela, M. ;
  • Barrio-Hernandez, Inigo ;
  • Boersma, P, Dee ;
  • Bost, Charles-André ;
  • Hoving, Henk-Jan ;
  • Cherel, Yves ;
  • Tafur-Jimenez, Ricardo ;
  • Chu, Chong ;
  • Dann, Peter ;
  • Fiddaman, Steven, R ;
  • Frazão, Bárbara ;
  • Howard, Pauline ;
  • Petersen, Bent ;
  • Labuschagne, Kim ;
  • Penaloza, Fernando ;
  • Mattern, Thomas ;
  • Musacchia, Francesco ;
  • Alexander Jr., Graham, C. ;
  • Miller, Gary ;
  • Osório, Hugo ;
  • Parker, Patricia ;
  • Phillips, Richard, A ;
  • Winkelmann, Inger ;
  • Quillfeldt, Petra ;
  • Simakov, Oleg ;
  • Rasmussen, Simon ;
  • Ryan, Peter, G ;
  • Rahman, M., Ziaur ;
  • Taylor, Helen ;
  • Pisani, Davide ;
  • Thompson, David, R ;
  • Jarvis, Erich, D ;
  • Young, Melanie, J ;
  • Ellegaard, Martin, R ;
  • Zhang, Guojie ;
  • Gilbert, M.Thomas, P ;
  • Vinther, Jakob ;
  • Sinding, Mikkel-Holger, S ;
  • Strugnell, Jan, M. ;
  • C. Castro, L., Filipe ;
  • Pacheco, George ;
  • Fedrigo, Olivier ;
  • Shepherd, Lara, D ;
  • D Tennyson, Alan, J ;
  • Patricio, Mateus ;
  • Grosser, Stefanie ;
  • Li, Qiye ;
  • Kay, Emily ;
  • Rocha, Sara ;
  • Antunes, Agostinho ;
  • Nupen, Lisa, J ;
  • Ellenberg, Ursula ;
  • Wu, Yufeng ;
  • Houston, David, M ;
  • Ma, Bin ;
  • Reeve, Andrew, Hart ;
  • Sanges, Remo ;
  • Johnson, Kathryn ;
  • Vinar, Tomas ;
  • Blagoev, Blagoy ;
  • Masello, Juan, F ;
  • Sicheritz-Ponten, Thomas ;
  • Stracke, Thomas ;
  • McKinlay, Bruce ;
  • Nielsen, Rasmus ;
  • García Borboroglu, Pablo ;
  • Gilbert, M.Thomas, P ;
  • Zhang, De, Xing ;
  • Zhang, Guojie
0 Citations0 Mentions31% FAIR0.3 Dataset Index
10.5524/102179January 2019

Genomic data from White-flippered penguin (<em>Eudyptula minor albosignata</em>).

The White-flippered penguin is a small penguin closely related to the New Zealand little blue penguin. It is occasionally considered a unique species or sometimes a subspecies of the New Zealand little blue penguin, however genetic research indicates that the two taxa are probably incipient. The reason it is occasionally considered a separate species or subspecies is because it has white markings on its flippers. Most taxonomists consider it to be a colour morph of the New Zealand little blue penguin. It nests in headlands, caves, rock jumbles and in the sheltered areas at the bases of bays, only on Banks Peninsula and Motunau Island near Christchurch, New Zealand. The white-flippered penguin is a Taonga, or treasured possession in Mori culture. The International Union for Conservation of Nature (IUCN) considers all Eudyptula penguins as least concern.
We sequenced the genome of an adult White-flippered penguin from Christchurch Antarctic Centre, originally from Banks Peninsula, Canterbury, New Zealand South Island (provided by Pauline Howard) to a depth of approximately 100x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.3Gb, with the contig and scaffold N50 values of 93.53Kb and 20.85Mb respectively. We identified 17424 protein-coding genes.

Authors

  • Pan, Hailin ;
  • Cole, Theresa ;
  • Couto, Alvarina ;
  • Bi, Xupeng ;
  • Machado, André, M. ;
  • Brejova, Brona ;
  • Fang, Miaoquan ;
  • Albertin, Caroline, B. ;
  • Zhou, Chengran ;
  • Silva, Filipe ;
  • Yang, Zhengtao ;
  • Gardner, Paul ;
  • Ksepka, Daniel, T ;
  • Baril, Tobias ;
  • Hart, Tom ;
  • Bouzat, Juan, L ;
  • Hayward, Alex ;
  • Argilla, Lisa, S ;
  • Campos, Alexandre ;
  • Bertelsen, Mads, F ;
  • Ribeiro, Angela, M. ;
  • Barrio-Hernandez, Inigo ;
  • Boersma, P, Dee ;
  • Bost, Charles-André ;
  • Hoving, Henk-Jan ;
  • Cherel, Yves ;
  • Tafur-Jimenez, Ricardo ;
  • Chu, Chong ;
  • Dann, Peter ;
  • Fiddaman, Steven, R ;
  • Frazão, Bárbara ;
  • Howard, Pauline ;
  • Petersen, Bent ;
  • Labuschagne, Kim ;
  • Penaloza, Fernando ;
  • Mattern, Thomas ;
  • Musacchia, Francesco ;
  • Alexander Jr., Graham, C. ;
  • Miller, Gary ;
  • Osório, Hugo ;
  • Parker, Patricia ;
  • Phillips, Richard, A ;
  • Winkelmann, Inger ;
  • Quillfeldt, Petra ;
  • Simakov, Oleg ;
  • Rasmussen, Simon ;
  • Ryan, Peter, G ;
  • Rahman, M., Ziaur ;
  • Taylor, Helen ;
  • Pisani, Davide ;
  • Thompson, David, R ;
  • Jarvis, Erich, D ;
  • Young, Melanie, J ;
  • Ellegaard, Martin, R ;
  • Zhang, Guojie ;
  • Gilbert, M.Thomas, P ;
  • Vinther, Jakob ;
  • Sinding, Mikkel-Holger, S ;
  • Strugnell, Jan, M. ;
  • C. Castro, L., Filipe ;
  • Pacheco, George ;
  • Fedrigo, Olivier ;
  • Shepherd, Lara, D ;
  • D Tennyson, Alan, J ;
  • Patricio, Mateus ;
  • Grosser, Stefanie ;
  • Li, Qiye ;
  • Kay, Emily ;
  • Rocha, Sara ;
  • Antunes, Agostinho ;
  • Nupen, Lisa, J ;
  • Ellenberg, Ursula ;
  • Wu, Yufeng ;
  • Houston, David, M ;
  • Ma, Bin ;
  • Reeve, Andrew, Hart ;
  • Sanges, Remo ;
  • Johnson, Kathryn ;
  • Vinar, Tomas ;
  • Blagoev, Blagoy ;
  • Masello, Juan, F ;
  • Sicheritz-Ponten, Thomas ;
  • Stracke, Thomas ;
  • McKinlay, Bruce ;
  • Nielsen, Rasmus ;
  • García Borboroglu, Pablo ;
  • Gilbert, M.Thomas, P ;
  • Zhang, De, Xing ;
  • Zhang, Guojie
0 Citations0 Mentions31% FAIR0.3 Dataset Index
10.5524/102177January 2019