Literature DB >> 33104790

PhycoCosm, a comparative algal genomics resource.

Igor V Grigoriev1,2,3, Richard D Hayes1, Sara Calhoun1,3, Bishoy Kamel1,3, Alice Wang1,2, Steven Ahrendt1, Sergey Dusheyko1, Roman Nikitin1, Stephen J Mondo1, Asaf Salamov1, Igor Shabalov1, Alan Kuo1.   

Abstract

Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis. PhycoCosm (https://phycocosm.jgi.doe.gov) is an algal multi-omics portal, developed by the US Department of Energy Joint Genome Institute to support analysis and distribution of algal genome sequences and other 'omics' data. PhycoCosm provides integration of genome sequence and annotation for >100 algal genomes with available multi-omics data and interactive web-based tools to enable algal research in bioenergy and the environment, encouraging community engagement and data exchange, and fostering new sequencing projects that will further these research goals.
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Year:  2021        PMID: 33104790      PMCID: PMC7779022          DOI: 10.1093/nar/gkaa898

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  44 in total

1.  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

2.  Circos: an information aesthetic for comparative genomics.

Authors:  Martin Krzywinski; Jacqueline Schein; Inanç Birol; Joseph Connors; Randy Gascoyne; Doug Horsman; Steven J Jones; Marco A Marra
Journal:  Genome Res       Date:  2009-06-18       Impact factor: 9.043

Review 3.  The number, speed, and impact of plastid endosymbioses in eukaryotic evolution.

Authors:  Patrick J Keeling
Journal:  Annu Rev Plant Biol       Date:  2013-02-28       Impact factor: 26.379

4.  Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans.

Authors:  John M Archibald; Matthew B Rogers; Michael Toop; Ken-Ichiro Ishida; Patrick J Keeling
Journal:  Proc Natl Acad Sci U S A       Date:  2003-05-30       Impact factor: 11.205

5.  The Transporter Classification Database (TCDB): recent advances.

Authors:  Milton H Saier; Vamsee S Reddy; Brian V Tsu; Muhammad Saad Ahmed; Chun Li; Gabriel Moreno-Hagelsieb
Journal:  Nucleic Acids Res       Date:  2015-11-05       Impact factor: 16.971

6.  Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity.

Authors:  Daniel Lang; Benjamin Weiche; Gerrit Timmerhaus; Sandra Richardt; Diego M Riaño-Pachón; Luiz G G Corrêa; Ralf Reski; Bernd Mueller-Roeber; Stefan A Rensing
Journal:  Genome Biol Evol       Date:  2010-07-19       Impact factor: 3.416

7.  The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.

Authors:  Patrick J Keeling; Fabien Burki; Heather M Wilcox; Bassem Allam; Eric E Allen; Linda A Amaral-Zettler; E Virginia Armbrust; John M Archibald; Arvind K Bharti; Callum J Bell; Bank Beszteri; Kay D Bidle; Connor T Cameron; Lisa Campbell; David A Caron; Rose Ann Cattolico; Jackie L Collier; Kathryn Coyne; Simon K Davy; Phillipe Deschamps; Sonya T Dyhrman; Bente Edvardsen; Ruth D Gates; Christopher J Gobler; Spencer J Greenwood; Stephanie M Guida; Jennifer L Jacobi; Kjetill S Jakobsen; Erick R James; Bethany Jenkins; Uwe John; Matthew D Johnson; Andrew R Juhl; Anja Kamp; Laura A Katz; Ronald Kiene; Alexander Kudryavtsev; Brian S Leander; Senjie Lin; Connie Lovejoy; Denis Lynn; Adrian Marchetti; George McManus; Aurora M Nedelcu; Susanne Menden-Deuer; Cristina Miceli; Thomas Mock; Marina Montresor; Mary Ann Moran; Shauna Murray; Govind Nadathur; Satoshi Nagai; Peter B Ngam; Brian Palenik; Jan Pawlowski; Giulio Petroni; Gwenael Piganeau; Matthew C Posewitz; Karin Rengefors; Giovanna Romano; Mary E Rumpho; Tatiana Rynearson; Kelly B Schilling; Declan C Schroeder; Alastair G B Simpson; Claudio H Slamovits; David R Smith; G Jason Smith; Sarah R Smith; Heidi M Sosik; Peter Stief; Edward Theriot; Scott N Twary; Pooja E Umale; Daniel Vaulot; Boris Wawrik; Glen L Wheeler; William H Wilson; Yan Xu; Adriana Zingone; Alexandra Z Worden
Journal:  PLoS Biol       Date:  2014-06-24       Impact factor: 8.029

8.  Multiomics resolution of molecular events during a day in the life of Chlamydomonas.

Authors:  Daniela Strenkert; Stefan Schmollinger; Sean D Gallaher; Patrice A Salomé; Samuel O Purvine; Carrie D Nicora; Tabea Mettler-Altmann; Eric Soubeyrand; Andreas P M Weber; Mary S Lipton; Gilles J Basset; Sabeeha S Merchant
Journal:  Proc Natl Acad Sci U S A       Date:  2019-01-18       Impact factor: 11.205

9.  Insights into the evolution of vitamin B12 auxotrophy from sequenced algal genomes.

Authors:  Katherine E Helliwell; Glen L Wheeler; Kyriacos C Leptos; Raymond E Goldstein; Alison G Smith
Journal:  Mol Biol Evol       Date:  2011-05-06       Impact factor: 16.240

10.  HECTAR: a method to predict subcellular targeting in heterokonts.

Authors:  Bernhard Gschloessl; Yann Guermeur; J Mark Cock
Journal:  BMC Bioinformatics       Date:  2008-09-23       Impact factor: 3.169

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  12 in total

1.  Salinity tolerance mechanisms of an Arctic Pelagophyte using comparative transcriptomic and gene expression analysis.

Authors:  Nastasia J Freyria; Alan Kuo; Mansi Chovatia; Jenifer Johnson; Anna Lipzen; Kerrie W Barry; Igor V Grigoriev; Connie Lovejoy
Journal:  Commun Biol       Date:  2022-05-25

2.  Resolving the Microalgal Gene Landscape at the Strain Level: a Novel Hybrid Transcriptome of Emiliania huxleyi CCMP3266.

Authors:  Martin Sperfeld; Dayana Yahalomi; Einat Segev
Journal:  Appl Environ Microbiol       Date:  2021-11-10       Impact factor: 5.005

3.  The 2021 Nucleic Acids Research database issue and the online molecular biology database collection.

Authors:  Daniel J Rigden; Xosé M Fernández
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

4.  A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology.

Authors:  Sara Calhoun; Tisza Ann Szeremy Bell; Lukas R Dahlin; Yuliya Kunde; Kurt LaButti; Katherine B Louie; Andrea Kuftin; Daniel Treen; David Dilworth; Sirma Mihaltcheva; Christopher Daum; Benjamin P Bowen; Trent R Northen; Michael T Guarnieri; Shawn R Starkenburg; Igor V Grigoriev
Journal:  Commun Biol       Date:  2021-03-12

5.  The APAF1_C/WD40 repeat domain-encoding gene from the sea lettuce Ulva mutabilis sheds light on the evolution of NB-ARC domain-containing proteins in green plants.

Authors:  Michiel Kwantes; Thomas Wichard
Journal:  Planta       Date:  2022-03-02       Impact factor: 4.116

6.  ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS.

Authors:  Ana B Romero-Losada; Christina Arvanitidou; Pedro de Los Reyes; Mercedes García-González; Francisco J Romero-Campero
Journal:  BMC Bioinformatics       Date:  2022-03-31       Impact factor: 3.169

7.  Unstable Relationship Between Braarudosphaera bigelowii (= Chrysochromulina parkeae) and Its Nitrogen-Fixing Endosymbiont.

Authors:  Shigekatsu Suzuki; Masanobu Kawachi; Chinatsu Tsukakoshi; Atsushi Nakamura; Kyoko Hagino; Isao Inouye; Ken-Ichiro Ishida
Journal:  Front Plant Sci       Date:  2021-12-03       Impact factor: 5.753

8.  Copper Metabolism in Naegleria gruberi and Its Deadly Relative Naegleria fowleri.

Authors:  Kateřina Ženíšková; Maria Grechnikova; Robert Sutak
Journal:  Front Cell Dev Biol       Date:  2022-04-11

9.  Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom.

Authors:  Aaron Oliver; Sheila Podell; Agnieszka Pinowska; Jesse C Traller; Sarah R Smith; Ryan McClure; Alex Beliaev; Pavlo Bohutskyi; Eric A Hill; Ariel Rabines; Hong Zheng; Lisa Zeigler Allen; Alan Kuo; Igor V Grigoriev; Andrew E Allen; David Hazlebeck; Eric E Allen
Journal:  Sci Rep       Date:  2021-08-02       Impact factor: 4.379

10.  Cation and Anion Channelrhodopsins: Sequence Motifs and Taxonomic Distribution.

Authors:  Elena G Govorunova; Oleg A Sineshchekov; Hai Li; Yumei Wang; Leonid S Brown; Alyssa Palmateer; Michael Melkonian; Shifeng Cheng; Eric Carpenter; Jordan Patterson; Gane K-S Wong; John L Spudich
Journal:  mBio       Date:  2021-07-20       Impact factor: 7.867

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