Table 2.
Genomic Resources for Chlamydomonas and Volvox
| Resource | Description | Reference(s) | URL |
|---|---|---|---|
| General Resources | |||
| Chlamy.org | General landing page for all information about Chlamydomonas | http://www.chlamy.org | |
| Chlamy Collection | Strain and plasmid stock center and general information about Chlamydomonas | http://www.chlamycollection.org | |
| Sequences | |||
| Phytozome | Latest assembly and annotations of the Chlamydomonas and Volvox genomes and comparison tools. | http://www.phytozome.net | |
| JGI Genome Browser for Chlamydomonas | Version 4 of the Chlamydomonas genome including use annotations. All future assemblies will be deposited on Phytozome | http://genome.jgi-psf.org/Chlre4/Chlre4.home.html | |
| Chlamydomonas reinhardtii minus mating type locus | GenBank Accession GU814015 | Ferris, Olson et al. 2010 | http://www.ncbi.nlm.nih.gov/nuccore/GU814015 |
| Chlamydomonas reinhardtii plus mating type locus | GenBank Accession GU814014 | Ferris, Olson et al. 2010 | http://www.ncbi.nlm.nih.gov/nuccore/GU814014 |
| Chlamydomonas reinhardtii chloroplast genome | GenBank Accession GU814014 | Maul et al. 2002 | http://www.chlamy.org/chloro/default.html |
| Chlamydomonas reinhardtii mitochondrial genome | GenBank Accession FJ423446 | Ma et al. 1992 | http://www.ncbi.nlm.nih.gov/nuccore/NC_001638 |
| Chlamydomonas incerta EST database | GenBank Accessions GI106792973-GI106798104 | Popescu et al. 1996 | http://megasun.bch.umontreal.ca/pepdb/pep.html |
| JGI Genome Browser for Volvox | Version 1 of the Volvox carteri genome including user annotations. All future versions of the genome will be deposited on Phytozome | http://genome.jgi.doe.gov/Volca1/Volca1.info.html | |
| Volvox carteri Female mating type locus | GenBank Accession GU784915 | Ferris, Olson et al. 2010 | http://www.ncbi.nlm.nih.gov/nuccore/GU784915 |
| Volvox carteri Male mating type locus | GenBank Accession GU784916 | Ferris, Olson et al. 2010 | http://www.ncbi.nlm.nih.gov/nuccore/GU784916 |
| Volvox carteri chloroplast genome | GenBank Accession GU084820.1 | Smith and Lee 2009 | http://www.ncbi.nlm.nih.gov/nuccore/GU084820.1 |
| Volvox carteri mitochondrial genome | GenBank Accession EU760701 | Smith and Lee 2009 | http://www.ncbi.nlm.nih.gov/nuccore/EU760701 |
| Libraries | |||
| Chlamydomonas reinhardtii genomic BAC library | http://www.genome.clemson.edu | ||
| Volvox carteri Female genomic BAC libraries | http://www.genome.arizona.edu/ | ||
| Volvox cateri Male genomic BAC libraries | Ferris, Olson et al. 2010 | http://www.genome.clemson.edu/ | |
| Chlamydomonas EST database | Asamizu et al. 2004 | http://est.kazusa.or.jp/en/plant/chlamy/EST/ | |
| Chlamydomonas 454 read database | 2 Gb of 454 sequencing of Chlamydomonas cDNAs from various growth conditions | http://genomes.mcdb.ucla.edu/Cre454/ | |
| Functional Annotation and Expression Tools | |||
| Algal Functional Annotation Tool | Comprehensive algal genomics, annotation and expression tool | Lopez et al. 2011 | http://pathways.mcdb.ucla.edu/algal/index.html |
| GreenGenie2 | Gene predictions for version 4 of the Chlamydomonas genome | Kwan et al 2009 | http://stormo.wustl.edu/GreenGenie2/ |
| ChlamyCyc | Chlamydomonas centric, integrated annotation tool that integrates with other related plant databases | http://chlamyto.mpimp-golm.mpg.de/chlamycyc/index.jsp | |
| Plant Genome Database | Plant genome annotation comparison tool that includes Chlamydomonas reinhardtii | http://www.plantgdb.org/search/misc/ | |
| PLAZA | Tools for comparative plant genomics | Van Bel et al. 2012 | http://bioinformatics.psb.ugent.be/plaza/ |
| Proteomic Databases | |||
| Chlamydomonas flagellar proteome | http://labs.umassmed.edu/chlamyfp/protector_login.php | ||
| Plant Transcription Factor Databases | |||
| Plant Transcription Factor Database | Includes both Chlamydomonas reinhardtii and Volvox carteri. Version 2.0 | Zhang et al. 2010 | http://planttfdb.cbi.edu.cn/ |
| Plant Transcription Factor Database | Includes Chlamydomonas reinhardtii. Version 3.0 | Pérez-Rodríguez et al. 200 | http://plntfdb.bio.uni-potsdam.de/v3.0/ |
| Microarrays | |||
| Chlamydomonas reinhardtii microarray | Agilent Chlamydomonas reinhardtii microarray, number 024664 | Toepel et al. 2011 | https://earray.chem.agilent.com/earray/ |
| Chlamydomonas reinhardtii UNIGENE cDNA array | cDNA array based on the first Chlamydomonas UNIGENE set superseded by the Agilent arrays | Jain et al. 2007 | |
| Chlamydomonas reinhardtii oligo array | Oligonucleotide array based on the first Chlamydomonas EST set superseded by the Agilent arrays | Eberhard et al. 2006 | |
| Chlamydomonas sRNA Database | |||
| SiLoDb sRNA Locus Database | Database of sRNA locations in the Chlamydomonas genome | http://silodb.cmp.uea.ac.uk/ | |