High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

Autor: Pierre-Marc Delaux, Romain Guyot, Martin Crespi, Erika Sallet, Malika Laguerre, Fanchon Divol, Sébastien Carrère, Benjamin Péret, Patrick Doumas, Cecile Huneau, Matthew R. Nelson, Jemma Taylor, Alexandre Soriano, Jérôme Salse, Laurence Marquès, Veit Schubert, Fernando Geu-Flores, Davide Mancinotti, Jérôme Gouzy, Sandrine Arribat, Karine Gallardo, André Marques, Thomas Blein, Barbara Hufnagel, William Marande, Delphine Aime, Hélène Bergès, Jean Keller

Publikováno v: Nature Communications
Nature Communications, Nature Publishing Group, 2020, 11 (1), ⟨10.1038/s41467-019-14197-9⟩
Hufnagel, B, Marques, A, Soriano, A, Marquès, L, Divol, F, Doumas, P, Sallet, E, Mancinotti, D, Carrere, S, Marande, W, Arribat, S, Keller, J, Huneau, C, Blein, T, Aimé, D, Laguerre, M, Taylor, J, Schubert, V, Nelson, M, Geu-Flores, F, Crespi, M, Gallardo, K, Delaux, P-M, Salse, J, Bergès, H, Guyot, R, Gouzy, J & Péret, B 2020, ' High-quality genome sequence of white lupin provides insight into soil exploration and seed quality ', Nature Communications, vol. 11, no. 1, 492 . https://doi.org/10.1038/s41467-019-14197-9
Nature Communications, Nature Publishing Group, 2020, 11 (1), pp.492. ⟨10.1038/s41467-019-14197-9⟩
Nature Communications, Vol 11, Iss 1, Pp 1-12 (2020)
Nature Communications, 2020, 11 (1), pp.492. ⟨10.1038/s41467-019-14197-9⟩

White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploratio

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ea1b2c19c4393729a6867c2559898f4b
https://hal.archives-ouvertes.fr/hal-02460008

Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification

Autor: Anthony K. Redmond, Manu Kumar Gundappa, Fabian Grammes, Peter W. H. Holland, Fiona M. Robertson, Sigbjørn Lien, Daniel J. Macqueen, Torgeir R. Hvidsten, Simen Rød Sandve, Samuel A.M. Martin

Publikováno v: Robertson, F M, Gundappa, M K, Grammes, F, Hvidsten, T R, Redmond, A K, Lien, S, Martin, S A M, Holland, P W H, Sandve, S R & Macqueen, D J 2017, ' Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification ', Genome Biology, vol. 18, no. 1, 111 . https://doi.org/10.1186/s13059-017-1241-z
Genome Biology
Genome Biology, Vol 18, Iss 1, Pp 1-14 (2017)

Background The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification are often temporally separ

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https://www.pure.ed.ac.uk/ws/files/87865371/s13059_017_1241_z.pdf

Quantification of insect genome divergence

Autor: Peer Bork, Evgeny M. Zdobnov

Publikováno v: Trends in Genetics, Vol. 23, No 1 (2007) pp. 16-20

The recent sequencing of twelve insect genomes has enabled us to quantify their divergence using synteny conservation and sequence identity of single-copy orthologs. Protein identity correlates well with synteny and is about three times more conserve

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0d0c337d7c0caf0a1f150fb01030f781
https://doi.org/10.1016/j.tig.2006.10.004

Evolution of genes and genomes on the Drosophila phylogeny

Autor: Adam M. Phillippy, Edward Grandbois, Pen MacDonald, Iain MacCallum, Laura K. Reed, Wojciech Makalowski, Tracey Honan, Tania Tassinari Rieger, Melissa J. Hubisz, Josep M. Comeron, Douglas Smith, Jennifer Godfrey, Sebastian Strempel, Amr Abdouelleil, Brenton Gravely, Harindra Arachi, Albert J. Vilella, Marc Azer, Sarah A. Teichmann, Roger A. Hoskins, Corbin D. Jones, Keenan Ross, Derek Wilson, Stuart J. Newfeld, John Stalker, Thomas D. Watts, Dennis C. Friedrich, Therese A. Markow, Michael U. Mollenhauer, Tina Goode, Geneva Young, Terry Shea, Krista Lance, Karin A. Remington, Kevin A. Edwards, Lynne Aftuck, Cecil Rise, Sheridon Channer, Matthew D. Rasmussen, Nicole Stange-Thomann, Annie Lui, Robert A. Reenan, Todd Sparrow, Dave Begun, Tamrat Negash, Laura K. Sirot, Adrianne Brand, Adam Brown, Daisuke Yamamoto, Pema Phunkhang, Justin Abreu, Russell Schwartz, Ana Llopart, Abderrahim Farina, Kebede Maru, Chung-I Wu, Allen Alexander, Scott Anderson, So Jeong Lee, Jason Blye, Gary H. Karpen, Wilfried Haerty, Daniel A. Barbash, Peter Rogov, Barry O'Neill, Rachel Mittelman, Jakob Skou Pedersen, Leanne Hughes, Robert K. Bradley, Graziano Pesole, Wyatt W. Anderson, Anthony J. Greenberg, Alejandro Sánchez-Gracia, Julio Rozas, Stephen W. Schaeffer, Yama Thoulutsang, Roger K. Butlin, David H. Ardell, Stuart DeGray, Chris P. Ponting, Deborah E. Stage, Corrado Caggese, Montserrat Aguadé, Casey M. Bergman, Diallo Ferguson, Peili Zhang, Jeffrey R. Powell, Hajime Sato, Xiaohong Liu, Marta Sabariego Puig, Michael Parisi, Passang Dorje, Yoshihiko Tomimura, Adal Abebe, Carlo G. Artieri, Brian Hurhula, Filip Rege, Peter D. Keightley, Andrew Barry, Pablo Alvarez, Tsamla Tsamla, Marvin Wasserman, Santosh Jagadeeshan, Daniel L. Halligan, Chelsea D. Foley, Kim D. Delehaunty, Manfred Grabherr, Sourav Chatterji, Angela N. Brooks, James C. Costello, Mieke Citroen, James A. Yorke, Hsiao Pei Yang, Charles Chapple, Jian Lu, Carlos A. Machado, Norbu Dhargay, Tsering Wangchuk, Anat Caspi, Patrick Cahill, Tashi Bayul, Lisa Levesque, Otero L. Oyono, Atanas Mihalev, Dawa Thoulutsang, Dawn N. Abt, Sujaa Raghuraman, Manyuan Long, Maria Mendez-Lago, Charles Matthews, Kimberly Dooley, Alex Wong, Melanie A. Huntley, William R. Jeck, Ira Topping, Ben Kanga, José P. Abad, Ana Cristina Lauer Garcia, Brikti Abera, Kunsang Gyaltsen, Jonathan Butler, Alicia Franke, Michael C. Schatz, Cheewhye Chin, Charles F. Aquadro, Justin Johnson, Bryant F. McAllister, Georgia Giannoukos, M. Erii Husby, Rod A. Wing, Shangtao Liu, Jean L. Chang, Jennifer Daub, Eiko Kataoka, Leopold Parts, Rakela Lubonja, Margaret Priest, Yoshiko N. Tobari, Teena Mehta, Evgeny M. Zdobnov, Yeshi Lokyitsang, Richard Elong, Matthew J. Parisi, Louis Meneus, Eric S. Lander, Alan Filipski, Gary Gearin, Nabil Hafez, Nicholas Sisneros, David B. Jaffe, Ian Holmes, Marina Sirota, Leonid Boguslavskiy, Lisa Chuda, LaDeana W. Hillier, Meizhong Luo, Phil Batterham, Michael Kleber, Richard K. Wilson, Yama Cheshatsang, Qing Yu, Rebecca Reyes, Matthew W. Hahn, Andreas Heger, Mar Marzo, Patrick Minx, Kerstin Lindblad-Toh, Vera L. S. Valente, Adam Wilson, William C. Jordan, Mohamed A. F. Noor, Chiao-Feng Lin, Asha Kamat, Heather Ebling, Mihai Pop, Frances Letendre, Mariana F. Wolfner, Don Gilbert, Ngawang Sherpa, Riza M. Daza, Oana Mihai, Gabriel C. Wu, Aaron M. Berlin, Ewen F. Kirkness, Monika D. Huard, Robert S. Fulton, Randall H. Brown, Danni Zhong, Sharon Stavropoulos, Venky N. Iyer, Xu Mu, Christina R. Gearin, David M. Rand, Jerry A. Coyne, Dan Hultmark, Jill Falk, Christopher Patti, Montserrat Papaceit, James Meldrim, Valentine Mlenga, Muneo Matsuda, Sven Findeiß, Todd A. Schlenke, Kevin McKernan, Brian P. Walenz, Timothy B. Sackton, Leonardo Koerich, Peter An, Robert Nicol, Chuong B. Do, Dmitry Khazanovich, Carmen Segarra, Maura Costello, St Christophe Acer, Claudia Rohde, Serafim Batzoglou, Hadi Quesneville, Evan Mauceli, Andy Vo, Luciano M. Matzkin, Susan E. Celniker, Patrick M. O’Grady, William M. Gelbart, Lloyd Low, Jamal Abdulkadir, Jessica Spaulding, Brian R. Calvi, Charlotte Henson, Robert David, Jennifer L. Hall, Andrew G. Clark, Anastasia Gardiner, Susan M. Russo, Birhane Hagos, Kerri Topham, Amy Denise Reily, Eli Venter, Jerome Naylor, Sandra W. Clifton, Valer Gotea, Samuel R. Gross, Manolis Kellis, Claude Bonnet, Christopher Strader, Tashi Lokyitsang, Nyima Norbu, Jennifer Baldwin, Stephen M. Mount, Robert L. Strausberg, Shailendra Yadav, Kristipati Ravi Ram, Steven L. Salzberg, Erik Gustafson, David A. Garfield, Eva Freyhult, Arthur L. Delcher, Enrico Blanco, Granger G. Sutton, Jason M. Tsolas, Charles Robin, Angie S. Hinrichs, Christopher D. Smith, Jane Wilkinson, Brendan McKernan, Fritz Pierre, William McCusker, Brian Oliver, Barry E. Garvin, Sudhir Kumar, Peter Kisner, Kunsang Dorjee, A. Bernardo Carvalho, Anna Montmayeur, Andrew Zimmer, Diana Shih, Wei Tao, Shiaw Pyng Yang, Sante Gnerre, Sampath Settipalli, Thu Nguyen, Paolo Barsanti, Brian P. Lazzaro, Sonja J. Prohaska, J. Craig Venter, Senait Tesfaye, Susan McDonough, Kim D. Pruitt, Alexander Stark, Sergio Castrezana, Lucinda Fulton, Richard T. Lapoint, Greg Gibson, John Spieth, Boris Adryan, Georgius De Haan, Sheila Fisher, Daniel A. Pollard, Seva Kashin, Rob J. Kulathinal, Michael B. Eisen, Nathaniel Novod, Christina Demaso, Alan Dupes, Amanda M. Larracuente, Toby Bloom, Alfredo Villasante, Charles H. Langley, Rama S. Singh, Niall J. Lennon, Kristi L. Montooth, Daniel Barker, Wolfgang Stephan, David Sturgill, Ruiqiang Li, Andrew Hollinger, Boris Boukhgalter, Talene Thomson, Patrick Cooke, Zac Zwirko, Nadia D. Singh, Michael Weiand, Lior Pachter, Roderic Guigó, Yu Zhang, Jay D. Evans, Stephanie Bosak, Rosie Levine, Lu Shi, Kiyohito Yoshida, Carolyn S. McBride, Pouya Kheradpour, William Brockman, Alberto Civetta, Hiroshi Akashi, Marcia Lara, Susan Faro, Sam Griffiths-Jones, Michael R. Brent, Thomas H. Eickbush, Gane Ka-Shu Wong, Elizabeth P. Ryan, Erica Anderson, Roberta Kwok, Asif T. Chinwalla, Sahal Osman, Nga Nguyen, Damiano Porcelli, Missole Doricent, Saverio Vicario, Marc Rubenfield, Bárbara Negre, Gillian M. Halter, Erin E. Dooley, Elena R. Lozovsky, William Lee, Alville Collymore, Catherine Stone, Tanya Mihova, Jun Wang, Karsten Kristiansen, Imane Bourzgui, Michael F. Lin, Katie D'Aco, Filipe G. Vieira, Choe Norbu, Yu-Hui Rogers, Aaron L. Halpern, Eugene W. Myers, Sharleen Grewal, Robert T. Good, Alfredo Ruiz, Dave Kudrna, Joseph Graham, Alex Lipovsky, Leonidas Mulrain, Tsering Wangdi, Roman Arguello, Mira V. Han, Arjun Bhutkar, Rasmus Nielsen, David J. Saranga, Aleksey V. Zimin, Vasilia Magnisalis, Helen Vassiliev, Thomas C. Kaufman, Eva Markiewicz, Temple F. Smith, Jinlei Liu, Loryn Gadbois, Michael G. Ritchie, Lisa Zembek, Daniel Bessette, Pasang Bachantsang, Adam Navidi

Publikováno v: Clark, A G, Eisen, M B, Smith, D R, Bergman, C M, Oliver, B, Markow, T A, Kaufman, T C, Kellis, M, Gelbart, W, Iyer, V N, Pollard, D A, Sackton, T B, Larracuente, A M, Singh, N D, Abad, J P, Abt, D N, Adryan, B, Aguade, M, Akashi, H, Anderson, W W, Aquadro, C F, Ardell, D H, Arguello, R, Artieri, C G, Barbash, D A, Barker, D, Barsanti, P, Batterham, P, Batzoglou, S, Begun, D, Bhutkar, A, Blanco, E, Bosak, S A, Bradley, R K, Brand, A D, Brent, M R, Brooks, A N, Brown, R H, Butlin, R K, Caggese, C, Calvi, B R, Bernardo de Carvalho, A, Caspi, A, Castrezana, S, Celniker, S E, Chang, J L, Chapple, C, Chatterji, S, Kristiansen, K, Pedersen, J S & Drosophila 12 Genomes Consortium 2007, ' Evolution of genes and genomes on the Drosophila phylogeny ', Nature, vol. 450, no. 7167, pp. 203-18 . https://doi.org/10.1038/nature06341
Nature
Nature, Nature Publishing Group, 2007, 450 (7167), pp.203-18. ⟨10.1038/nature06341⟩
Clark, A G, Eisen, M B, Smith, D R, Bergman, C M, Oliver, B, Markow, T A, Kaufman, T C, Kellis, M, Gelbart, W, Iyer, V N, Pollard, D A, Sackton, T B, Larracuente, A M, Singh, N D, Abad, J P, Abt, D N, Adryan, B, Aguade, M, Akashi, H, Anderson, W W, Aquadro, C F, Ardell, D H, Arguello, R, Artieri, C G, Barbash, D A, Barker, D, Barsanti, P, Batterham, P, Batzoglou, S, Begun, D, Bhutkar, A, Blanco, E, Bosak, S A, Bradley, R K, Brand, A D, Brent, M R, Brooks, A N, Brown, R H, Butlin, R K, Caggese, C, Calvi, B R, Bernardo de Carvalho, A, Caspi, A, Castrezana, S, Celniker, S E, Chang, J L, Chapple, C, Chatterji, S, Chinwalla, A, Civetta, A, Clifton, S W, Comeron, J M, Costello, J C, Coyne, J A, Daub, J, David, R G, Delcher, A L, Delehaunty, K, Do, C B, Ebling, H, Edwards, K, Eickbush, T, Evans, J D, Filipski, A, Findeiss, S, Freyhult, E, Fulton, L, Fulton, R, Garcia, A C L, Gardiner, A, Garfield, D A, Garvin, B E, Gibson, G, Gilbert, D, Gnerre, S, Godfrey, J, Good, R, Gotea, V, Gravely, B, Greenberg, A J, Griffiths-Jones, S, Gross, S, Guigo, R, Gustafson, E A, Haerty, W, Hahn, M W, Halligan, D L, Halpern, A L, Halter, G M, Han, M V, Heger, A, Hillier, L, Hinrichs, A S, Holmes, I, Hoskins, R A, Hubisz, M J, Hultmark, D, Huntley, M A, Jaffe, D B, Jagadeeshan, S, Jeck, W R, Johnson, J, Jones, C D, Jordan, W C, Karpen, G H, Kataoka, E, Keightley, P D, Kheradpour, P, Kirkness, E F, Koerich, L B, Kristiansen, K, Kudrna, D, Kulathinal, R J, Kumar, S, Kwok, R, Lander, E, Langley, C H, Lapoint, R, Lazzaro, B P, Lee, S-J, Levesque, L, Li, R, Lin, C-F, Lin, M F, Lindblad-Toh, K, Llopart, A, Long, M, Low, L, Lozovsky, E, Lu, J, Luo, M, Machado, C A, Makalowski, W, Marzo, M, Matsuda, M, Matzkin, L, McAllister, B, McBride, C S, McKernan, B, McKernan, K, Mendez-Lago, M, Minx, P, Mollenhauer, M U, Montooth, K, Mount, S M, Mu, X, Myers, E, Negre, B, Newfeld, S, Nielsen, R, Noor, M A F, O'Grady, P, Pachter, L, Papaceit, M, Parisi, M J, Parisi, M, Parts, L, Pedersen, J S, Pesole, G, Phillippy, A M, Ponting, C P, Pop, M, Porcelli, D, Powell, J R, Prohaska, S, Pruitt, K, Puig, M, Quesneville, H, Ram, K R, Rand, D, Rasmussen, M D, Reed, L K, Reenan, R, Reily, A, Remington, K A, Rieger, T T, Ritchie, M G, Robin, C, Rogers, Y-H, Rohde, C, Rozas, J, Rubenfield, M J, Ruiz, A, Russo, S, Salzberg, S L, Sanchez-Gracia, A, Saranga, D J, Sato, H, Schaeffer, S W, Schatz, M C, Schlenke, T, Schwartz, R, Segarra, C, Singh, R S, Sirot, L, Sirota, M, Sisneros, N B, Smith, C D, Smith, T F, Spieth, J, Stage, D E, Stark, A, Stephan, W, Strausberg, R L, Strempel, S, Sturgill, D, Sutton, G, Sutton, G G, Tao, W, Teichmann, S, Tobari, Y N, Tomimura, Y, Tsolas, J M, Valente, V L S, Venter, E, Venter, J C, Vicario, S, Vieira, F G, Vilella, A J, Villasante, A, Walenz, B, Wang, J, Wasserman, M, Watts, T, Wilson, D, Wilson, R K, Wing, R A, Wolfner, M F, Wong, A, Wong, G K-S, Wu, C-I, Wu, G, Yamamoto, D, Yang, H-P, Yang, S-P, Yorke, J A, Yoshida, K, Zdobnov, E, Zhang, P, Zhang, Y, Zimin, A V, Baldwin, J, Abdouelleil, A, Abdulkadir, J, Abebe, A, Abera, B, Abreu, J, Acer, S C, Aftuck, L, Alexander, A, An, P, Anderson, E, Anderson, S, Arachi, H, Azer, M, Bachantsang, P, Barry, A, Bayul, T, Berlin, A, Bessette, D, Bloom, T, Blye, J, Boguslavskiy, L, Bonnet, C, Boukhgalter, B, Bourzgui, I, Brown, A, Cahill, P, Channer, S, Cheshatsang, Y, Chuda, L, Citroen, M, Collymore, A, Cooke, P, Costello, M, D'Aco, K, Daza, R, De Haan, G, DeGray, S, DeMaso, C, Dhargay, N, Dooley, K, Dooley, E, Doricent, M, Dorje, P, Dorjee, K, Dupes, A, Elong, R, Falk, J, Farina, A, Faro, S, Ferguson, D, Fisher, S, Foley, C D, Franke, A, Friedrich, D, Gadbois, L, Gearin, G, Gearin, C R, Giannoukos, G, Goode, T, Graham, J, Grandbois, E, Grewal, S, Gyaltsen, K, Hafez, N, Hagos, B, Hall, J, Henson, C, Hollinger, A, Honan, T, Huard, M D, Hughes, L, Hurhula, B, Husby, M E, Kamat, A, Kanga, B, Kashin, S, Khazanovich, D, Kisner, P, Lance, K, Lara, M, Lee, W, Lennon, N, Letendre, F, LeVine, R, Lipovsky, A, Liu, X, Liu, J, Liu, S, Lokyitsang, T, Lokyitsang, Y, Lubonja, R, Lui, A, MacDonald, P, Magnisalis, V, Maru, K, Matthews, C, McCusker, W, McDonough, S, Mehta, T, Meldrim, J, Meneus, L, Mihai, O, Mihalev, A, Mihova, T, Mittelman, R, Mlenga, V, Montmayeur, A, Mulrain, L, Navidi, A, Naylor, J, Negash, T, Nguyen, T, Nguyen, N, Nicol, R, Norbu, C, Norbu, N, Novod, N, O'Neill, B, Osman, S, Markiewicz, E, Oyono, O L, Patti, C, Phunkhang, P, Pierre, F, Priest, M, Raghuraman, S, Rege, F, Reyes, R, Rise, C, Rogov, P, Ross, K, Ryan, E, Settipalli, S, Shea, T, Sherpa, N, Shi, L, Shih, D, Sparrow, T, Spaulding, J, Stalker, J, Stange-Thomann, N, Stavropoulos, S, Stone, C, Strader, C, Tesfaye, S, Thomson, T, Thoulutsang, Y, Thoulutsang, D, Topham, K, Topping, I, Tsamla, T, Vassiliev, H, Vo, A, Wangchuk, T, Wangdi, T, Weiand, M, Wilkinson, J, Wilson, A, Yadav, S, Young, G, Yu, Q, Zembek, L, Zhong, D, Zimmer, A, Zwirko, Z, Jaffe, D B, Alvarez, P, Brockman, W, Butler, J, Chin, C, Gnerre, S, Grabherr, M, Kleber, M, Mauceli, E & MacCallum, I 2007, ' Evolution of genes and genomes on the Drosophila phylogeny ', Nature, vol. 450, no. 7167, pp. 203-218 . https://doi.org/10.1038/nature06341
Nature, Vol. 450, No 7167 (2007) pp. 203-218
ResearcherID

Affiliations des auteurs : cf page 216 de l'article; International audience; Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust res

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::185fcef84a75fcef336e3156b9953635
https://resolver.caltech.edu/CaltechAUTHORS:20170307-113900780