Literature DB >> 34047993

Lipid Pathway Databases with a Focus on Algae.

Naoki Sato1, Takeshi Obayashi2.   

Abstract

Pathways of lipid biosynthesis are highly complex and have been established in model organisms such as Arabidopsis thaliana and Chlamydomonas reinhardtii, whereas in other organisms, we need bioinformatic tools to map individual enzymes onto reference pathways. In this chapter, we explain representative tools that are useful in identifying algal orthologs of lipid biosynthetic enzymes and finding new enzymes that are possibly involved in the pathway of interest. All descriptions in this chapter refer to in silico (i.e., computer-based) methods rather than laboratory experiments.

Entities:  

Keywords:  Algae; Bioinformatics; Lipid pathway

Year:  2021        PMID: 34047993     DOI: 10.1007/978-1-0716-1362-7_26

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  12 in total

1.  Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.

Authors:  Motomichi Matsuzaki; Osami Misumi; Tadasu Shin-I; Shinichiro Maruyama; Manabu Takahara; Shin-Ya Miyagishima; Toshiyuki Mori; Keiji Nishida; Fumi Yagisawa; Keishin Nishida; Yamato Yoshida; Yoshiki Nishimura; Shunsuke Nakao; Tamaki Kobayashi; Yu Momoyama; Tetsuya Higashiyama; Ayumi Minoda; Masako Sano; Hisayo Nomoto; Kazuko Oishi; Hiroko Hayashi; Fumiko Ohta; Satoko Nishizaka; Shinobu Haga; Sachiko Miura; Tomomi Morishita; Yukihiro Kabeya; Kimihiro Terasawa; Yutaka Suzuki; Yasuyuki Ishii; Shuichi Asakawa; Hiroyoshi Takano; Niji Ohta; Haruko Kuroiwa; Kan Tanaka; Nobuyoshi Shimizu; Sumio Sugano; Naoki Sato; Hisayoshi Nozaki; Naotake Ogasawara; Yuji Kohara; Tsuneyoshi Kuroiwa
Journal:  Nature       Date:  2004-04-08       Impact factor: 49.962

2.  The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism.

Authors:  E Virginia Armbrust; John A Berges; Chris Bowler; Beverley R Green; Diego Martinez; Nicholas H Putnam; Shiguo Zhou; Andrew E Allen; Kirk E Apt; Michael Bechner; Mark A Brzezinski; Balbir K Chaal; Anthony Chiovitti; Aubrey K Davis; Mark S Demarest; J Chris Detter; Tijana Glavina; David Goodstein; Masood Z Hadi; Uffe Hellsten; Mark Hildebrand; Bethany D Jenkins; Jerzy Jurka; Vladimir V Kapitonov; Nils Kröger; Winnie W Y Lau; Todd W Lane; Frank W Larimer; J Casey Lippmeier; Susan Lucas; Mónica Medina; Anton Montsant; Miroslav Obornik; Micaela Schnitzler Parker; Brian Palenik; Gregory J Pazour; Paul M Richardson; Tatiana A Rynearson; Mak A Saito; David C Schwartz; Kimberlee Thamatrakoln; Klaus Valentin; Assaf Vardi; Frances P Wilkerson; Daniel S Rokhsar
Journal:  Science       Date:  2004-10-01       Impact factor: 47.728

3.  Gclust: trans-kingdom classification of proteins using automatic individual threshold setting.

Authors:  Naoki Sato
Journal:  Bioinformatics       Date:  2009-01-21       Impact factor: 6.937

4.  Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features.

Authors:  Evelyne Derelle; Conchita Ferraz; Stephane Rombauts; Pierre Rouzé; Alexandra Z Worden; Steven Robbens; Frédéric Partensky; Sven Degroeve; Sophie Echeynié; Richard Cooke; Yvan Saeys; Jan Wuyts; Kamel Jabbari; Chris Bowler; Olivier Panaud; Benoît Piégu; Steven G Ball; Jean-Philippe Ral; François-Yves Bouget; Gwenael Piganeau; Bernard De Baets; André Picard; Michel Delseny; Jacques Demaille; Yves Van de Peer; Hervé Moreau
Journal:  Proc Natl Acad Sci U S A       Date:  2006-07-25       Impact factor: 11.205

5.  The Phaeodactylum genome reveals the evolutionary history of diatom genomes.

Authors:  Chris Bowler; Andrew E Allen; Jonathan H Badger; Jane Grimwood; Kamel Jabbari; Alan Kuo; Uma Maheswari; Cindy Martens; Florian Maumus; Robert P Otillar; Edda Rayko; Asaf Salamov; Klaas Vandepoele; Bank Beszteri; Ansgar Gruber; Marc Heijde; Michael Katinka; Thomas Mock; Klaus Valentin; Fréderic Verret; John A Berges; Colin Brownlee; Jean-Paul Cadoret; Anthony Chiovitti; Chang Jae Choi; Sacha Coesel; Alessandra De Martino; J Chris Detter; Colleen Durkin; Angela Falciatore; Jérome Fournet; Miyoshi Haruta; Marie J J Huysman; Bethany D Jenkins; Katerina Jiroutova; Richard E Jorgensen; Yolaine Joubert; Aaron Kaplan; Nils Kröger; Peter G Kroth; Julie La Roche; Erica Lindquist; Markus Lommer; Véronique Martin-Jézéquel; Pascal J Lopez; Susan Lucas; Manuela Mangogna; Karen McGinnis; Linda K Medlin; Anton Montsant; Marie-Pierre Oudot-Le Secq; Carolyn Napoli; Miroslav Obornik; Micaela Schnitzler Parker; Jean-Louis Petit; Betina M Porcel; Nicole Poulsen; Matthew Robison; Leszek Rychlewski; Tatiana A Rynearson; Jeremy Schmutz; Harris Shapiro; Magali Siaut; Michele Stanley; Michael R Sussman; Alison R Taylor; Assaf Vardi; Peter von Dassow; Wim Vyverman; Anusuya Willis; Lucjan S Wyrwicz; Daniel S Rokhsar; Jean Weissenbach; E Virginia Armbrust; Beverley R Green; Yves Van de Peer; Igor V Grigoriev
Journal:  Nature       Date:  2008-10-15       Impact factor: 49.962

6.  The Chlamydomonas genome reveals the evolution of key animal and plant functions.

Authors:  Sabeeha S Merchant; Simon E Prochnik; Olivier Vallon; Elizabeth H Harris; Steven J Karpowicz; George B Witman; Astrid Terry; Asaf Salamov; Lillian K Fritz-Laylin; Laurence Maréchal-Drouard; Wallace F Marshall; Liang-Hu Qu; David R Nelson; Anton A Sanderfoot; Martin H Spalding; Vladimir V Kapitonov; Qinghu Ren; Patrick Ferris; Erika Lindquist; Harris Shapiro; Susan M Lucas; Jane Grimwood; Jeremy Schmutz; Pierre Cardol; Heriberto Cerutti; Guillaume Chanfreau; Chun-Long Chen; Valérie Cognat; Martin T Croft; Rachel Dent; Susan Dutcher; Emilio Fernández; Hideya Fukuzawa; David González-Ballester; Diego González-Halphen; Armin Hallmann; Marc Hanikenne; Michael Hippler; William Inwood; Kamel Jabbari; Ming Kalanon; Richard Kuras; Paul A Lefebvre; Stéphane D Lemaire; Alexey V Lobanov; Martin Lohr; Andrea Manuell; Iris Meier; Laurens Mets; Maria Mittag; Telsa Mittelmeier; James V Moroney; Jeffrey Moseley; Carolyn Napoli; Aurora M Nedelcu; Krishna Niyogi; Sergey V Novoselov; Ian T Paulsen; Greg Pazour; Saul Purton; Jean-Philippe Ral; Diego Mauricio Riaño-Pachón; Wayne Riekhof; Linda Rymarquis; Michael Schroda; David Stern; James Umen; Robert Willows; Nedra Wilson; Sara Lana Zimmer; Jens Allmer; Janneke Balk; Katerina Bisova; Chong-Jian Chen; Marek Elias; Karla Gendler; Charles Hauser; Mary Rose Lamb; Heidi Ledford; Joanne C Long; Jun Minagawa; M Dudley Page; Junmin Pan; Wirulda Pootakham; Sanja Roje; Annkatrin Rose; Eric Stahlberg; Aimee M Terauchi; Pinfen Yang; Steven Ball; Chris Bowler; Carol L Dieckmann; Vadim N Gladyshev; Pamela Green; Richard Jorgensen; Stephen Mayfield; Bernd Mueller-Roeber; Sathish Rajamani; Richard T Sayre; Peter Brokstein; Inna Dubchak; David Goodstein; Leila Hornick; Y Wayne Huang; Jinal Jhaveri; Yigong Luo; Diego Martínez; Wing Chi Abby Ngau; Bobby Otillar; Alexander Poliakov; Aaron Porter; Lukasz Szajkowski; Gregory Werner; Kemin Zhou; Igor V Grigoriev; Daniel S Rokhsar; Arthur R Grossman
Journal:  Science       Date:  2007-10-12       Impact factor: 47.728

7.  Phytozome: a comparative platform for green plant genomics.

Authors:  David M Goodstein; Shengqiang Shu; Russell Howson; Rochak Neupane; Richard D Hayes; Joni Fazo; Therese Mitros; William Dirks; Uffe Hellsten; Nicholas Putnam; Daniel S Rokhsar
Journal:  Nucleic Acids Res       Date:  2011-11-22       Impact factor: 16.971

8.  CyanoBase: a large-scale update on its 20th anniversary.

Authors:  Takatomo Fujisawa; Rei Narikawa; Shin-Ichi Maeda; Satoru Watanabe; Yu Kanesaki; Koichi Kobayashi; Jiro Nomata; Mitsumasa Hanaoka; Mai Watanabe; Shigeki Ehira; Eiji Suzuki; Koichiro Awai; Yasukazu Nakamura
Journal:  Nucleic Acids Res       Date:  2016-11-29       Impact factor: 16.971

9.  MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons.

Authors:  Ikuo Uchiyama; Motohiro Mihara; Hiroyo Nishide; Hirokazu Chiba; Masaki Kato
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

10.  ALCOdb: Gene Coexpression Database for Microalgae.

Authors:  Yuichi Aoki; Yasunobu Okamura; Hiroyuki Ohta; Kengo Kinoshita; Takeshi Obayashi
Journal:  Plant Cell Physiol       Date:  2015-12-07       Impact factor: 4.927

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