Files for visualisation in IGV (Integrative Genomics Viewer, http://software.broadinstitute.org/software/igv/)
| Organism | Chlamydomonas reinhardtii |
|---|---|
| NCBI-Taxonomy-ID | 3055 |
| Strain | CC-503 MT + |
| Genome type | nuclear |
| Assembly-version | v5.0 |
| Annotation-version | v5.5 |
| References | Merchant et al. (2007), Phytozome v12.1 |
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2018-04-26_Creinhardtii_CC-503_v5.0.fa
Nucleotide FASTA format of the genomic assembly v5.0 (downloaded from Phytozome on 2018-04-26, in .zip or .gz format)
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2018-04-26_Creinhardtii_CC-503_v5.0.fa.fai
FASTA index file of the genomic assembly v5.0 (created using igvtools)
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2019-03-07_Creinhardtii_CC-503_v5.5.gene.gff3
Summary of annotation details based on annotation data v5.5 (downloaded from Phytozome on 2018-04-26 and improved for visualisation in IGV by A Holzer)
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2019-03-21_Creinhardtii_CC-503_v5.5.genome
IGV readable reference genome (created using itv on 2019-03-21; requires all other files in this subdirectory)
| Organism | Chlamydomonas reinhardtii |
|---|---|
| NCBI-Taxonomy-ID | 3055 |
| Strain | CC-503 MT + |
| Genome type | nuclear |
| Assembly-version | v5.0 |
| Annotation-version | v5.6 |
| References | Merchant et al. (2007), Phytozome v12.1 |
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2018-12-14_Creinhardtii_CC-503_v5.0.fasta
Nucleotide FASTA format of the genomic assembly v5.0 (downloaded from Phytozome on 2018-12-14, in .zip or .gz format)
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2018-12-14_Creinhardtii_CC-503_v5.0.fasta.fai
FASTA index file of the genomic assembly v5.0 (created using igvtools)
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2019-03-07_Creinhardtii_CC-503_v5.6.gene.gff3
Summary of annotation details based on annotation data v5.5 (downloaded from Phytozome on 2018-12-14 and improved for visualisation in igv by A Holzer)
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2019-03-21_Creinhardtii_CC-503_v5.6.genome
IGV readable reference genome (created using itv on 2019-03-21; requires all other files in this subdirectory)
| Organism | Chlamydomonas reinhardtii |
|---|---|
| NCBI-Taxonomy-ID | 3055 |
| Strain | CC-503 MT + |
| Genome type | chloroplast and mitochondria |
| Assembly-version | v4.0 |
| Annotation-version | v4.4 |
| References | Gallagher et al. (2017) |
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2019-03-04_Cre.CP.MT.genomes.fasta
Nucleotide FASTA format of the genomic assembly v4.0 (downloaded from here on 2019-03-04)
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2019-03-04_Cre.CP.MT.genomes.fasta.fai
FASTA index file of the genomic assembly v5.0 (created using igvtools)
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2019-03-04_Cre.CP.MT.annotations.gff3
Summary of annotation details based on annotation data v5.5 (downloaded from here on 2019-03-04)
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2019-03-21_Creinhardtii_CC-503_Cp+Mt_v4.4.genome
IGV readable reference genome (created using itv on 2019-03-21; requires all other files in this subdirectory)
| Organism | Chlamydomonas reinhardtii |
|---|---|
| NCBI-Taxonomy-ID | 3055 |
| Strain | CC-503 MT + |
| Genome type | nuclear, chloroplast and mitochondria |
| Assembly-version | v5.0 (nuclear) + v4.0 (Cp + Mt) |
| Annotation-version | v5.6 (nuclear) + v4.4 (Cp + Mt) |
| References | Merchant et al. (2007), Phytozome v12.1, Gallagher et al. (2017) |
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2019-03-08_Creinhardtii_CC-503_v5.0+Cre.CP.MT.genomes_v4.4
Nucleotide FASTA format of the nuclear v5.0 and chloroplast + mitochondrial genomic assembly v4.0 (downloaded from Phytozome (2018-12-14) and here (2019-03-04); merged into one FASTA file; in .zip or .gz format)
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2019-03-08_Creinhardtii_CC-503_v5.0+Cre.CP.MT.genomes_v4.4.fasta.fai
FASTA index file of the nuclear v5.0 and chloroplast + mitochondrial genomic assembly v4.0 (created using igvtools)
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2019-03-08_Creinhardtii_CC-503_v5.6.gene+Cre.CP.MT.annotations_v4.4.gff3
Summary of annotation details based on annotation of the nuclear (v5.6) and chloroplast + mitochondrial (v4.4) data (downloaded from Phytozome (2018-12-14), and here (2019-03-04); merged and improved for visualisation by A Holzer)
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2019-03-21_Creinhardtii_CC-503_v5.6_Cp+Mt_v4.4.genome
IGV readable reference genome (created using itv on 2019-03-21; requires all other files in this subdirectory)
When using this data please cite as follows:
Andre Holzer. (2019). The Chlamydomonas reference genomes for visualisation in IGV (Version v1.0) [Data set]. Zenodo.
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Merchant SS, Prochnuk SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernández E, Fukuzawa H, González-Ballester D, González-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riaño-Pachón DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martínez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR, The Chlamydomonas genome reveals the evolution of key animal and plant functions., Science (New York, N.Y.). 2007 Oct 12; 318 5848 245-50
https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Creinhardtii
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Sean D. Gallaher, Sorel T. Fitz-Gibbon, Daniela Strenkert, Samuel O. Purine, Matteo Pellegrini, and Sabeeha S. Merchant, High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyse expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates., The Plant Journal. 2017 Nov 24; 93 545-565