Whole-Genome Shotgun Assembly and Analysis of the Genome ofFugu rubripes

Autor: Gustavo Glusman, Daniel S. Rokhsar, Chris Detter, Greg Elgar, Paramvir S. Dehal, Susan Lucas, Sarah Smith, Melody S. Clark, Dmitry Pruss, Sean V. Tavtigian, Jarrod Chapman, Trevor Hawkins, Byrappa Venkatesh, Paul Predki, Y. H. Tan, Elia Stupka, Isaac Ho, Shawn Hoon, Justin Powell, Holly Baden, Tania Oh, Jared C. Roach, Marie Wong, Sam Rash, Leroy Hood, Nik Putnam, Arian F.A. Smit, Cheryl Evans, Paul G. Richardson, Jer Ming Chia, Alice Tay, Norman A. Doggett, Frans Verhoef, Maarten D. Sollewijn Gelpke, Mary Barnstead, Yvonne J. K. Edwards, Samuel Aparicio, Andrey Zharkikh, Alan Christoffels, Sydney Brenner, Lee Rowen

Publikováno v: Science. 297:1301-1310

The compact genome ofFugu rubripeshas been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0fae0c72175b478b4838b570593f9e92
https://doi.org/10.1126/science.1072104

Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis

Autor: Bruno W. S. Sobral, Mark Gijzen, Alon Savidor, Brett M. Tyler, Sam Rash, Francine Govers, Rays H. Y. Jiang, Paul Morris, Mi-Kyung Lee, Kurt Lamour, Anne E. Dorrance, Sucheta Tripathy, C. M. B. Damasceno, Donald J. Maclean, Richard W. Jones, Matteo Garbelotto, Sophien Kamoun, Yasuko Sakihama, Daniel S. Rokhsar, Trudy Torto-Alalibo, Stuart G. Gordon, MoÌnica Medina, Jocelyn K. C. Rose, Daolong Dou, Astrid Terry, Harold J. G. Meijer, Hong-Bin Zhang, Brian M. Smith, Zhanyou Xu, Igor V. Grigoriev, Konstantinos Krampis, Eric K. Nordberg, Niklaus J. Grünwald, Jim Beynon, Vipaporn Phuntumart, Laura Baxter, Felipe D. Arredondo, Chantel F. Scheuring, Andrea Aerts, Jarrod Chapman, Wayne Huang, W. Hayes McDonald, Paramvir S. Dehal, Joe Win, Inna Dubchak, Manuel D. Ospina-Giraldo, Douda Bensasson, Asaf Salamov, Nicholas H. Putnam, Allan W. Dickerman, Kelly Ivors, Jeffrey L. Boore, Xuemin Zhang

Publikováno v: Tyler, Brett M.; Tripathy, Sucheta; Zhang, Xuemin; Dehal, Paramvir; Jiang, Rays H. Y.; Aerts, Andrea; et al.(2006). Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis. Science. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/6r52t4vq
Science 313 (2006) 5791
Science, 313(5791), 1261-1266

Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum . Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::af8eb34cee4bbc9bbcf4ce4ad38bca56
https://pubmed.ncbi.nlm.nih.gov/16946041

The sequence and analysis of duplication-rich human chromosome 16

Autor: Kimberly L. Mcmurray, James Retterer, Nancy C. Brown, Dea Fotopulos, Michael R. Altherr, Judith G. Tesmer, Jane Grimwood, Joel Martin, Jonathan L. Longmire, Elizabeth Saunders, P. Scott White, Malinda Stalvey, Elbert Branscomb, Norman A. Doggett, Nina Thayer, C.E. Hildebrand, Mary Bao Tran-Gyamfi, Yunian Lou, Trevor Hawkins, Lucía Ramírez, Shyam Prabhakar, Ming Tsai, D. Scott, Hope Tice, Linda Meincke, Jean F. Challacombe, Gary Xie, Maria Gomez, Eidelyn Gonzales, Jeremy Schmutz, Kevin Wu, Marie-Claude Krawczyk, Heather Kimball, Graham A. Mark, David C. Torney, John C. Detter, Laurie Gordon, Albert L. Williams, Susan Lucas, Len A. Pennacchio, Linda S. Thompson, Robert K. Moyzis, Kristen Kadner, Arthur Kobayashi, Larry L. Deaven, Richard D. Nandkeshwar, E.W. Campbell, Patricia L. Wills, Andrea Aerts, Joan Yang, Darryl O. Ricke, Mark Dickson, Astrid Terry, Steve Lowry, Paul Gilna, Paul G. Richardson, Thom Ludeman, Olivier Couronne, Timothy Shough, Chitra Manohar, David Bruce, Jamie Jett, Evan E. Eichler, Pieter J. deJong, Mark Mundt, Judith M. Buckingham, Robert D. Sutherland, Roxanne Tapia, Heather Blumer, Wayne Huang, Leslie Chasteen, A. Christine Munk, Sanjay Israni, Deborah L. Grady, Igor V. Grigoriev, Stacey Black, Judith D. Cohn, David F. Callen, Han C. Chi, William J. Bruno, Cliff Han, Mirian Denys, Mira Dimitrijevic-Bussod, Martin Pollard, Connie S. Campbell, Richard M. Myers, Yee Man Chan, Sam Pitluck, Sam Rash, Joseph J. Fawcett, Mari Christensen, Lauren Haydu, Frederick Lopez, Lynn M. Clark, Julio Escobar, B. Parson-Quintana, Raymond L. Stallings, Tina Leyba, Dave Flowers, Eva Bajorek, Jenna Morgan, Mary L. Campbell, Anna Ustaszewska, Donna L. Robinson, Nu Vo, Edward M. Rubin, Lynne Goodwin, Paul Predki, Uffe Hellsten, Daniel S. Rokhsar, Phillip B. Jewett, Matthew Groza, Tijana Glavina, Chenier Caoile, Alex Rodriguez, Xinwei She, David Goodstein, Jung-Rung Wu, Levy E. Ulanovsky, Asaf Salamov, Nancy Hammon, Olga Chertkov

Publikováno v: Nature. 432(7020)

Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annot

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8c276ed50b94aee10912d5b8017726bd
https://pubmed.ncbi.nlm.nih.gov/15616553

The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins

Autor: Stephen T. Chin-Bow, Masako Sano, Ian A. Meinertzhagen, Fumiko Yoshizaki, Sachiko Miura, Shungo Kano, Patrick Lemaire, Chitra Manohar, Diego Martinez, Antoinetta Spagnuolo, Akie Nakayama, Hisayo Nomoto, Fumiko Ohta, Paul G. Richardson, Kaoru Azumi, Kazuo Inaba, Sharon A. Doyle, Shinobu Haga, Lixy Yamada, Susan Lucas, Chris Detter, Maarten D. Sollewijn Gelpke, Yasunori Sasakura, Paramvir S. Dehal, Wayne Huang, Kyosuke Hino, Bernard M. Degnan, Trevor Hawkins, Michael Levine, Akane Sasaki, Daniel S. Rokhsar, Kenneth E. M. Hastings, Simona Necula, Miho Suzuki, Takeshi Kawashima, Tijana Glavina, Steve Mount, Miki Tokuoka, Satoko Nishizaka, Shuichi Wada, Jeffrey L. Boore, Isaac Ho, Pilar Francino, Isidore Rigoutsos, Masaru Nonaka, Rosaria DeSantis, Astrid Terry, Robert K. Campbell, Nik Putnam, Naoe Harafuji, Didier Y.R. Stainier, Tadasu Shin-I, Kohji Hotta, Naohito Takatori, Kazuhiro W. Makabe, David N. Keys, Yasuaki Mochizuki, David Goodstein, Jarrod Chapman, Anna Di Gregorio, Yuji Kohara, Mónica Medina, Byung In Lee, Brad Davidson, Yutaka Satou, Tomomi Morishita, Anthony W. De Tomaso, Olivier Tassy, Hiroko Hayashi, Kasumi Yagi, Masanobu Satake, Nori Satoh, Kaoru S. Imai, Margherita Branno, Norman A. Doggett, Eiichi Shoguchi, P. Douglas Hyatt, Cindy Zhang, Frank W. Larimer, Sam Rash, Kenji Kobayashi, Mari Kobayashi, Hidetoshi Saiga, Giorgio Matassi, Kazuko Oishi, Hong Gang Wang, Satoko Awazu

Publikováno v: Science (New York, N.Y.). 298(5601)

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1920765edb3fcce7f7419c7dff66d00c
https://pubmed.ncbi.nlm.nih.gov/12481111

Community involved fungal genome annotation at the JGI-LANL

Autor: Gary Xie, Berka, Randy M., Bernard Henrissat, Markku Saloheimo, Jon Magnuson, Alfredo de Leon, Daniel Cullen, Beth Nelson, Mikko Arvas, Ann Westerholm-Parvinen, Sandy Merino, Baker, Scott E., Monika Schmoll, Paul Harris, Mick Ward, Larrondo, Luis F., Jian Yao, Merja Penttilä, Melissa Jackson, Monica Misra, David Goodstein, Nina Thayer, Astrid Terry, Wayne Huang, Sam Rash, Paramvir Dehal, Nick Putnam, Jarrod Chapman, Barbara Robbertse, Kubicek, Christian P., Dan Rokhsar, Paul Gilna, Tom Brettin, Susan Lucas, Martinez, Diego A.

Publikováno v: VTT Technical Research Centre of Finland-PURE
Xie, G, Berka, R M, Henrissat, B, Saloheimo, M, Magnuson, J, de Leon, A, Cullen, D, Nelson, B, Arvas, M, Westerholm-Parvinen, A, Merino, S, Baker, S E, Schmoll, M, Harris, P, Ward, M, Larrondo, L F, Yao, J, Penttilä, M, Jackson, M, Misra, M, Goodstein, D, Thayer, N, Terry, A, Huang, W, Rash, S, Dehal, P, Putnam, N, Chapman, J, Robbertse, B, Kubicek, C P, Rokhsar, D, Gilna, P, Brettin, T, Lucas, S & Martinez, D A 2006, Community involved fungal genome annotation at the JGI-LANL . in I S Druzhinina, A G Kopchinskiy & C P Kubicek (eds), 8th European Conference on Fungal Genetics : Book of Abstracts ., IIo-2, Vienna University of Technology, pp. 21, 8th European Conference on Fungal Genetics, Vienna, Austria, 8/04/06 . < http://www.fgsc.net/ecfg8/symposiumIIoral.pdf >

The role of the fungal genome annotation team at LANL is to provide high quality manually curated annotation of fungal genomic sequence. The JGI-LANL and fungal research community are teaming up to publish a full analysis and annotation of Trichoderm

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::f6ccecaeb6df905c091a8c0c5043b65a
https://cris.vtt.fi/en/publications/423d1512-6d4d-4dbc-8c4f-7b35994d0dc2