Genome Assembly
Last modified on April 5, 2010
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The Arabidopsis thaliana genome was sequenced in 2000 by the Arabidopsis Genome Initiative (AGI) (Nature 14 Dec. 2000). The genome has five chromosomes and a total size of approximately 135-megabases. The current TIGR golden path length is 119,146,348 bp. The table below shows the approximate total length and the length of the golden path for each chromosome.
Golden path length | Approximate chromosome length | |
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Chromosome 1 | 30,427,671 bp | 34,964,571 bp |
Chromosome 2 | 19,698,289 bp | 22,037,565 bp |
Chromosome 3 | 23,459,830 bp | 25,499,034 bp |
Chromosome 4 | 18,585,056 bp | 20,862,711 bp |
Chromosome 5 | 26,975,502 bp | 31,270,811 bp |
Total | 119,146,348 bp | 134,634,692 bp |
Chromosome sequence data and AGI tiling paths are available from the TAIR FTP site.
TAIR8_Assembly_updates.xls and TAIR9_Assembly_updates.xls contains a list of all assembly updates made for the TAIR8 and TAIR9 genome releases.
For a summary of remaining gaps and and unsequenced clones go to Current Genome Status. For a description of the groups that participated in the sequencing effort go to AGI groups.
- Current Genome Status
- Known Gaps
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Centromeres and other gaps between clones in red.
Clones containing gaps in purple.
* Indicates sequence is not yet deposited in GenBank. -
Chromosome 1:
T18N24-F8L2-F2C1-F12G6-T23P23-T28N5-F11K13
T24F19-CEN1-F13P3
F9A12-F25O15-F9D18-T5F23
F27F5-T2P3-F2G19 F12A4-F1504-F14D7 T32E22-F103-T32E20 F16N3-T2E6-T6B12 F10A5-T4012-T23E18 -
Chromosome 2:
NOR2-F23H14-F10A8 T12J2-CEN2-T6C20-T14C8
T4E5-F10C8-T18E17 -
Chromosome 3:
TEL3N-T4P13 K3G3-MJL12-MTE24 MUO10-T13B17-MWE13 F8N14-T803-F1M23 T15D2-CEN3-T25F15-F23H6-T28G19-5SrDNA-F1C23-T18B3-T26P13-T14A11-
T4P3-F21A14-5SrDNA-F4M19 F7M19-T6L19- -F7K15 -
Chromosome 4:
NOR4-T15P10 F21I2-5SrDNA-F14G16
T2N12-CEN4-F13J5
T13J8-F26K10-F20O9-T5F17-F16A16
F19B15-F17A13-T16L4
F6I18-F6E21-F8F16
F4D11-T16I18-F26P21 -
Chromosome 5:
F21E1-T19N18*-T32M21
F23C8-T26N4-5SrDNA-F23B23
F28N5-CEN5-T8H11
T32B3-5SrDNA-T25B21-T3J11 - GFF file of all known gaps in the Arabidopsis genome assembly April 2008
- Clones Missing or Incomplete in GenBank September 2003
- Clones in GenBank HTG section (sequencing in progress) or missing from GenBank. Includes chromosome, status, accession number, group and comments.
- Table of Gaps and Incomplete Clones September 2003
- Includes comments from TAIR, TIGR and AGI groups on status and priority for sequencing.
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- AGI Groups
- Cold Spring Harbor Sequencing Consortium (CSHSC)
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Members: CSHL, ABI, WashU Contacts: Dick McCombie, Rob Martienssen (CSHL); Rick Wilson (WashU) Regions
sequenced:13.1 Mb including the top of chromosome 4 and 3 Mb around the centromere of chromosome 5. - European Scientists Sequencing Arabidopsis (ESSA)
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Members: John Innes Centre, MIPS, network of 18 labs Contacts: Mike Bevan (JIC); Klaus Mayer (MIPS) Regions
sequenced:Chromosomes 4 (14.5 Mb) and 5 (6Mb) - Genoscope-EU Consortium
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Members: EMBL, Genoscope, Lion, U. van Amsterdam, Valle Contacts: Marcel Salanoubat, Francis Quetier Regions
sequenced:Chromosome 3 bottom arm (9.2 Mb) - Kazusa DNA Research Institute
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Members: Kazusa Contacts: Satoshi Tabata, Kiyotaka Okada Regions
sequenced:Chromosomes 3 (9.8 Mb) and 5 (17.8 Mb) - SPP Consortium
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Members: PGEC, Stanford, UPenn (ATGC) Contacts: Sakis Theologis (PGEC); Ron Davis (Stanford); Joe Ecker (ATGC) Regions
sequenced:Chromosome 1 (20.2 Mb) - The J. Craig Venter Center (JCVI) formerly TIGR
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Members: JCVI Contacts: Christopher Town Regions
sequenced:Chromosome 2 (19.6 Mb), parts of 1 and 3