skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Genomics and functional genomics in Chlamydomonas reinhardtii

Abstract

The availability of the Chlamydomonas reinhardtii nuclear genome sequence continues to enable researchers to address biological questions relevant to algae, land plants and animals in unprecedented ways. As we continue to characterize and understand biological processes in C. reinhardtii and translate that knowledge to other systems, we are faced with the realization that many genes encode proteins without a defined function. The field of functional genomics aims to close this gap between genome sequence and protein function. Transcriptomes, proteomes and phenomes can each provide layers of gene-specific functional data while supplying a global snapshot of cellular behavior under different conditions. Herein we present a brief history of functional genomics, the present status of the C. reinhardtii genome, how genome-wide experiments can aid in supplying protein function inferences, and provide an outlook for functional genomics in C. reinhardtii.

Authors:
 [1];  [1]
  1. Brookhaven National Lab. (BNL), Upton, NY (United States). Dept. of Biology
Publication Date:
Research Org.:
Brookhaven National Lab. (BNL), Upton, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1351725
Report Number(s):
BNL-113704-2017-JA
Journal ID: ISSN 1862-5576
Grant/Contract Number:  
SC0012704
Resource Type:
Accepted Manuscript
Journal Name:
Microbiology Monographs
Additional Journal Information:
Journal Volume: 30; Journal ID: ISSN 1862-5576
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Blaby, Ian K., and Blaby-Haas, Crysten E. Genomics and functional genomics in Chlamydomonas reinhardtii. United States: N. p., 2017. Web. doi:10.1007/978-3-319-66365-4_1.
Blaby, Ian K., & Blaby-Haas, Crysten E. Genomics and functional genomics in Chlamydomonas reinhardtii. United States. doi:10.1007/978-3-319-66365-4_1.
Blaby, Ian K., and Blaby-Haas, Crysten E. Tue . "Genomics and functional genomics in Chlamydomonas reinhardtii". United States. doi:10.1007/978-3-319-66365-4_1. https://www.osti.gov/servlets/purl/1351725.
@article{osti_1351725,
title = {Genomics and functional genomics in Chlamydomonas reinhardtii},
author = {Blaby, Ian K. and Blaby-Haas, Crysten E.},
abstractNote = {The availability of the Chlamydomonas reinhardtii nuclear genome sequence continues to enable researchers to address biological questions relevant to algae, land plants and animals in unprecedented ways. As we continue to characterize and understand biological processes in C. reinhardtii and translate that knowledge to other systems, we are faced with the realization that many genes encode proteins without a defined function. The field of functional genomics aims to close this gap between genome sequence and protein function. Transcriptomes, proteomes and phenomes can each provide layers of gene-specific functional data while supplying a global snapshot of cellular behavior under different conditions. Herein we present a brief history of functional genomics, the present status of the C. reinhardtii genome, how genome-wide experiments can aid in supplying protein function inferences, and provide an outlook for functional genomics in C. reinhardtii.},
doi = {10.1007/978-3-319-66365-4_1},
journal = {Microbiology Monographs},
number = ,
volume = 30,
place = {United States},
year = {2017},
month = {3}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies
journal, August 2015

  • Gallaher, Sean D.; Fitz-Gibbon, Sorel T.; Glaesener, Anne G.
  • The Plant Cell, Vol. 27, Issue 9
  • DOI: 10.1105/tpc.15.00508

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii
journal, January 2009


Three Acyltransferases and Nitrogen-responsive Regulator Are Implicated in Nitrogen Starvation-induced Triacylglycerol Accumulation in Chlamydomonas
journal, March 2012

  • Boyle, Nanette R.; Page, Mark Dudley; Liu, Bensheng
  • Journal of Biological Chemistry, Vol. 287, Issue 19
  • DOI: 10.1074/jbc.M111.334052

Integrating ‘omic’ information: a bridge between genomics and systems biology
journal, October 2003


MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
journal, December 2011


Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana
journal, August 2003

  • Alonso, J. M.; Stepanova, Anna N.; Leisse, Thomas J.
  • Science, Vol. 301, Issue 5633, p. 653-657
  • DOI: 10.1126/science.1086391

The chloroplast proteome: a survey from the Chlamydomonas reinhardtii perspective with a focus on distinctive features
journal, April 2011


Synexpression groups in eukaryotes
journal, December 1999

  • Niehrs, Christof; Pollet, Nicolas
  • Nature, Vol. 402, Issue 6761
  • DOI: 10.1038/990025

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection
journal, February 2006

  • Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki
  • Molecular Systems Biology, Vol. 2, Article No. 2006.0008
  • DOI: 10.1038/msb4100050

Machine learning for Big Data analytics in plants
journal, December 2014


Dynamics of post-translational modifications and protein stability in the stroma of Chlamydomonas reinhardtii chloroplasts
journal, April 2011

  • Bienvenut, Willy V.; Espagne, Christelle; Martinez, Aude
  • PROTEOMICS, Vol. 11, Issue 9
  • DOI: 10.1002/pmic.201000634

Improving Gene-finding in Chlamydomonas reinhardtii:GreenGenie2
journal, January 2009


The Proteome of Copper, Iron, Zinc, and Manganese Micronutrient Deficiency in Chlamydomonas reinhardtii
journal, October 2012

  • Hsieh, Scott I.; Castruita, Madeli; Malasarn, Davin
  • Molecular & Cellular Proteomics, Vol. 12, Issue 1
  • DOI: 10.1074/mcp.M112.021840

PlantGDB: a resource for comparative plant genomics
journal, December 2007

  • Duvick, J.; Fu, A.; Muppirala, U.
  • Nucleic Acids Research, Vol. 36, Issue Database
  • DOI: 10.1093/nar/gkm1041

AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae
journal, January 2014


Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

  • Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
  • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
  • DOI: 10.1093/nar/25.17.3389

Proteomic analysis of a eukaryotic cilium
journal, July 2005

  • Pazour, Gregory J.; Agrin, Nathan; Leszyk, John
  • The Journal of Cell Biology, Vol. 170, Issue 1
  • DOI: 10.1083/jcb.200504008

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
journal, June 2014

  • Seaver, Samuel M. D.; Gerdes, Svetlana; Frelin, Océane
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 26
  • DOI: 10.1073/pnas.1401329111

Retracted: The Chlamydomonas reinhardtii Organellar Genomes Respond Transcriptionally and Post-Transcriptionally to Abiotic Stimuli
journal, October 2002

  • Lilly, Jason W.; Maul, Jude E.; Stern, David B.
  • The Plant Cell, Vol. 14, Issue 11
  • DOI: 10.1105/tpc.005595

The nuclear proteome of the green alga Chlamydomonas reinhardtii
journal, December 2011

  • Winck, Flavia V.; Riaño-Pachón, Diego M.; Sommer, Frederik
  • PROTEOMICS, Vol. 12, Issue 1
  • DOI: 10.1002/pmic.201000782

The Sequence Read Archive
journal, November 2010

  • Leinonen, R.; Sugawara, H.; Shumway, M.
  • Nucleic Acids Research, Vol. 39, Issue Database
  • DOI: 10.1093/nar/gkq1019

PlnTFDB: updated content and new features of the plant transcription factor database
journal, October 2009

  • Pérez-Rodríguez, Paulino; Riaño-Pachón, Diego Mauricio; Corrêa, Luiz Gustavo Guedes
  • Nucleic Acids Research, Vol. 38, Issue suppl_1
  • DOI: 10.1093/nar/gkp805

Functional Genomics: It's All How You Read It
journal, October 1997


Chlamydomonas proteomics
journal, June 2009

  • Rolland, Norbert; Atteia, Ariane; Decottignies, Paulette
  • Current Opinion in Microbiology, Vol. 12, Issue 3
  • DOI: 10.1016/j.mib.2009.04.001

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
journal, July 1995


Phytozome: a comparative platform for green plant genomics
journal, November 2011

  • Goodstein, David M.; Shu, Shengqiang; Howson, Russell
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr944

Zinc Deficiency Impacts CO 2 Assimilation and Disrupts Copper Homeostasis in Chlamydomonas reinhardtii
journal, February 2013

  • Malasarn, Davin; Kropat, Janette; Hsieh, Scott I.
  • Journal of Biological Chemistry, Vol. 288, Issue 15
  • DOI: 10.1074/jbc.M113.455105

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
journal, January 2002


Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data: Mercator: sequence functional annotation server
journal, December 2013

  • Lohse, Marc; Nagel, Axel; Herter, Thomas
  • Plant, Cell & Environment, Vol. 37, Issue 5
  • DOI: 10.1111/pce.12231

Proteomic Analysis of a Fraction with Intact Eyespots of Chlamydomonas reinhardtii and Assignment of Protein Methylation
journal, December 2015

  • Eitzinger, Nicole; Wagner, Volker; Weisheit, Wolfram
  • Frontiers in Plant Science, Vol. 6
  • DOI: 10.3389/fpls.2015.01085

The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis
journal, February 2015

  • Park, Jeong-Jin; Wang, Hongxia; Gargouri, Mahmoud
  • The Plant Journal, Vol. 81, Issue 4
  • DOI: 10.1111/tpj.12747

Nitrogen-Sparing Mechanisms in Chlamydomonas Affect the Transcriptome, the Proteome, and Photosynthetic Metabolism
journal, April 2014

  • Schmollinger, Stefan; Mühlhaus, Timo; Boyle, Nanette R.
  • The Plant Cell, Vol. 26, Issue 4
  • DOI: 10.1105/tpc.113.122523

Generation of an oligonucleotide array for analysis of gene expression in Chlamydomonas reinhardtii
journal, December 2005


Profiling Chlamydomonas Metabolism under Dark, Anoxic H 2 -Producing Conditions Using a Combined Proteomic, Transcriptomic, and Metabolomic Approach
journal, October 2014

  • Subramanian, Venkataramanan; Dubini, Alexandra; Astling, David P.
  • Journal of Proteome Research, Vol. 13, Issue 12
  • DOI: 10.1021/pr500342j

How Well is Enzyme Function Conserved as a Function of Pairwise Sequence Identity?
journal, October 2003


The challenges of integrating multi-omic data sets
journal, October 2010

  • Palsson, Bernhard; Zengler, Karsten
  • Nature Chemical Biology, Vol. 6, Issue 11
  • DOI: 10.1038/nchembio.462

Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III
journal, December 1992


Characterizing the Anaerobic Response of Chlamydomonas reinhardtii by Quantitative Proteomics
journal, February 2010

  • Terashima, Mia; Specht, Michael; Naumann, Bianca
  • Molecular & Cellular Proteomics, Vol. 9, Issue 7
  • DOI: 10.1074/mcp.M900421-MCP200

The Chlamydomonas genome project: a decade on
journal, October 2014


ChlamyNET: a Chlamydomonas gene co-expression network reveals global properties of the transcriptome and the early setup of key co-expression patterns in the green lineage
journal, March 2016

  • Romero-Campero, Francisco J.; Perez-Hurtado, Ignacio; Lucas-Reina, Eva
  • BMC Genomics, Vol. 17, Issue 1
  • DOI: 10.1186/s12864-016-2564-y

C HLAMYDOMONAS AS A M ODEL O RGANISM
journal, June 2001


Proteomic Analysis of Isolated Chlamydomonas Centrioles Reveals Orthologs of Ciliary-Disease Genes
journal, June 2005


The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions
journal, October 2007

  • Merchant, S. S.; Prochnik, S. E.; Vallon, O.
  • Science, Vol. 318, Issue 5848, p. 245-250
  • DOI: 10.1126/science.1143609

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
journal, September 2005


Proteomic Analysis of the Eyespot of Chlamydomonas reinhardtii Provides Novel Insights into Its Components and Tactic Movements
journal, June 2006

  • Schmidt, Melanie; Geßner, Gunther; Luff, Matthias
  • The Plant Cell, Vol. 18, Issue 8
  • DOI: 10.1105/tpc.106.041749

The Human Genome Browser at UCSC
journal, May 2002

  • Kent, W. J.; Sugnet, C. W.; Furey, T. S.
  • Genome Research, Vol. 12, Issue 6
  • DOI: 10.1101/gr.229102

mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
journal, March 2004


PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors
journal, October 2013

  • Jin, Jinpu; Zhang, He; Kong, Lei
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1016

Historical perspective on Chlamydomonas as a model for basic research: 1950–1970
journal, March 2015


Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways inChlamydomonas reinhardtii
journal, December 2006


Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii
journal, September 2015

  • Flowers, Jonathan M.; Hazzouri, Khaled M.; Pham, Gina M.
  • The Plant Cell, Vol. 27, Issue 9
  • DOI: 10.1105/tpc.15.00492

Use and misuse of the gene ontology annotations
journal, May 2008

  • Yon Rhee, Seung; Wood, Valerie; Dolinski, Kara
  • Nature Reviews Genetics, Vol. 9, Issue 7
  • DOI: 10.1038/nrg2363

Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii
journal, January 2010


Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
journal, January 2008


Phosphoprotein SAK1 is a regulator of acclimation to singlet oxygen in Chlamydomonas reinhardtii
journal, May 2014


pico-PLAZA, a genome database of microbial photosynthetic eukaryotes: Genomics update
journal, July 2013

  • Vandepoele, Klaas; Van Bel, Michiel; Richard, Guilhem
  • Environmental Microbiology, Vol. 15, Issue 8
  • DOI: 10.1111/1462-2920.12174

A phenotypic screening platform to identify small molecule modulators of Chlamydomonas reinhardtii growth, motility and photosynthesis
journal, January 2012


Beyond Complementation. Map-Based Cloning in Chlamydomonas reinhardtii
journal, January 2005

  • Rymarquis, Linda A.; Handley, Jocelyn M.; Thomas, Mabel
  • Plant Physiology, Vol. 137, Issue 2
  • DOI: 10.1104/pp.104.054221

Genetic tools and techniques for Chlamydomonas reinhardtii
journal, May 2015


PredAlgo: A New Subcellular Localization Prediction Tool Dedicated to Green Algae
journal, July 2012

  • Tardif, Marianne; Atteia, Ariane; Specht, Michael
  • Molecular Biology and Evolution, Vol. 29, Issue 12
  • DOI: 10.1093/molbev/mss178

Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

Tying Down Loose Ends in the Chlamydomonas Genome: Functional Significance of Abundant Upstream Open Reading Frames
journal, December 2015


Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri
journal, July 2010


Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes
journal, February 2005

  • Stolc, V.; Samanta, M. P.; Tongprasit, W.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 10
  • DOI: 10.1073/pnas.0408358102

Systems and Trans -System Level Analysis Identifies Conserved Iron Deficiency Responses in the Plant Lineage
journal, October 2012

  • Urzica, Eugen I.; Casero, David; Yamasaki, Hiroaki
  • The Plant Cell, Vol. 24, Issue 10
  • DOI: 10.1105/tpc.112.102491

RNA-Seq: revelation of the messengers
journal, April 2013


Proteomic Analysis of Isolated Ciliary Transition Zones Reveals the Presence of ESCRT Proteins
journal, February 2015


The Phosphoproteome of a Chlamydomonas reinhardtii Eyespot Fraction Includes Key Proteins of the Light Signaling Pathway
journal, December 2007

  • Wagner, Volker; Ullmann, Katharina; Mollwo, Anne
  • Plant Physiology, Vol. 146, Issue 2
  • DOI: 10.1104/pp.107.109645

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
journal, October 2003


Systems Biology Approach in Chlamydomonas Reveals Connections between Copper Nutrition and Multiple Metabolic Steps
journal, April 2011

  • Castruita, Madeli; Casero, David; Karpowicz, Steven J.
  • The Plant Cell, Vol. 23, Issue 4
  • DOI: 10.1105/tpc.111.084400

What's in a genome?
journal, July 1992

  • Bork, Peer; Ouzounis, Christos; Sander, Chris
  • Nature, Vol. 358, Issue 6384
  • DOI: 10.1038/358287a0

RNA Interference Silencing of a Major Lipid Droplet Protein Affects Lipid Droplet Size in Chlamydomonas reinhardtii
journal, November 2009

  • Moellering, Eric R.; Benning, Christoph
  • Eukaryotic Cell, Vol. 9, Issue 1
  • DOI: 10.1128/EC.00203-09

Using native and syntenically mapped cDNA alignments to improve de novo gene finding
journal, January 2008


Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment
journal, February 2015

  • Kleessen, Sabrina; Irgang, Susann; Klie, Sebastian
  • The Plant Journal, Vol. 81, Issue 5
  • DOI: 10.1111/tpj.12763

Insights into the Survival of Chlamydomonas reinhardtii during Sulfur Starvation Based on Microarray Analysis of Gene Expression
journal, October 2004


An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii
journal, January 2016

  • Li, Xiaobo; Zhang, Ru; Patena, Weronika
  • The Plant Cell, Vol. 28, Issue 2
  • DOI: 10.1105/tpc.15.00465

Systematic genome-wide screens of gene function
journal, January 2004

  • Carpenter, Anne E.; Sabatini, David M.
  • Nature Reviews Genetics, Vol. 5, Issue 1
  • DOI: 10.1038/nrg1248

The model organism as a system: integrating 'omics' data sets
journal, March 2006

  • Joyce, Andrew R.; Palsson, Bernhard Ø.
  • Nature Reviews Molecular Cell Biology, Vol. 7, Issue 3
  • DOI: 10.1038/nrm1857

Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics
journal, August 2012


Molecular techniques to interrogate and edit the Chlamydomonas nuclear genome
journal, March 2015

  • Jinkerson, Robert E.; Jonikas, Martin C.
  • The Plant Journal, Vol. 82, Issue 3
  • DOI: 10.1111/tpj.12801

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
journal, December 2009


A Biological Atlas of Functional Maps
journal, February 2001