Reference Genome 2024
Reference Genome 2000-2023
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 | |
|---|---|---|
| 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.
Known Gaps
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.
AGI Groups
Cold Spring Harbor Sequencing Consortium (CSHSC)
| 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)
| 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) |
| Members: | EMBL, Genoscope, Lion, U. van Amsterdam, Valle |
| Contacts: | Marcel Salanoubat, Francis Quetier |
| Regions sequenced: | Chromosome 3 bottom arm (9.2 Mb) |
| Members: | Kazusa |
| Contacts: | Satoshi Tabata, Kiyotaka Okada |
| Regions sequenced: | Chromosomes 3 (9.8 Mb) and 5 (17.8 Mb) |
| 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
| Members: | JCVI |
| Contacts: | Christopher Town |
| Regions sequenced: | Chromosome 2 (19.6 Mb), parts of 1 and 3 |