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Progress on the newest reannotation can be found here.
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 siteDownloads.
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 in the 2000 Chromosome Assembly
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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. |
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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.
Clone or Gap | TAIR Comment | TIGR Comment | Other Comment |
|---|---|---|---|
Chromosome 1 | |||
Clone F8L2 | CEN1: 3 asm; 3 grps. Will most likely close but mainly Athila etc. Priority 3. | ||
Clone F12G6 | GenBank PLN, centromeric, 3 unordered (SSP) | Submitted by Ecker | |
Clone T28N5 | GenBank PLN, centromeric, 11 unordered (SSP) | Submitted by Ecker | |
Clone F25O15 | CEN1: 2 asm; 1 grp. This BAC should close soon. Priority 3. | ||
Clone F9D18 | GenBank PLN, centromeric, contains gap of approx. 34 kb (SSP) | Theologis group has updated GenBank record | |
Clone T2P3 | Euchr 1: ~20 asm; 10 grps. Contains >99% identical repeats. We have made many different libraries for this BAC in attempts to get more uniform coverage. Two ~30 kb and ~ 35 kb assemblies that overlap the neighboring BACs have been annotated to assess their gene content. Transposon-based sequencing of linking clones continues. We expect to be able to reduce the number of assemblies and annotate then even if full closure is not possible. Priority 1. | ||
Chromosome 2 | |||
Clone T6C20 | CEN2: This BAC lies within the 180 bp repeats; thus full closure was not attempted in 1998-1999 when chromosome 2 was completed. We have revisited this BAC, including making a large insert library, but find that this does not help. This BAC will not be closed. Priority 4. | ||
Clone F10C8 | GenBank PLN, contains gap of approx. 20 kb consisting of 747 bp pure tandem repeats | ||
Chromosome 3 | |||
Clone T25F15 | CEN3: This BAC lies in one of two small island contigs within CEN3 and contains 180 bp repeats. It is in 2 asm, 1 grp with one apparent sequencing gap. Nested deletions of a spanning clone have been made that should in theory close this BAC and are in the sequencing queue. Priority 3. | ||
Clone T28G19 | CEN3: 22 asms; 10 grps even when edited to 6+ and assembled at 100%. This BAC lies in one of two small island contigs within CEN3. Most likely the status of this BAC cannot be improved by further effort. Priority 4. | ||
Clone T18B3 | CEN3: 8 asms; 4 grps. We can make progress with this BAC and will do so. Priority 3. | ||
Clone F21A14 | CEN3: 26 asms; 3 grps after editing and assembly at 100%. This BAC cannot be closed. Priority 4. | ||
Chromosome 4 | |||
Clone F26K10 | HTG (Sanger) | ||
Clone T5F17 | HTG (Sanger) | ||
Clone F17A13 | HTG (Sanger) | ||
Clone F6E21 | HTG (Sanger) | ||
Clone T16I18 | HTG (Sanger) | ||
Chromosome 5 | |||
Clone T19N18 | No GenBank record (Sanger?) TIGR has annotated sequence for this clone. | ||
Clone T26N4 | HTG, 15 undordered pieces | CSHL finishing (includes T22F2). Contains 5S rRNA repeats. | |
Clone T25B21 | HTG, 3 undordered pieces | CSHL finishing, contains 5S rRNA repeats. | |
Unanchored Clones | |||
F26J21 | 65 asms; 32 gps (but most sequences fall into 5 asms, 2 grps). Appears to contain many genes. We plan to close and resolve as much as possible. Awaiting more sequence. Priority 2. | ||
T13I7 | 21 asms; 9 grps. We plan to close and resolve as much as possible. Awaiting large insert library and more sequence. Priority 2. | ||
T4N13 | 52 asms; 37 grps. We plan to close and resolve as much as possible. Awaiting large insert library and more sequence. Priority 2. | ||
T17J15 | 26 asms; 14 grps. We plan to close and resolve as much as possible. Awaiting large insert library and more sequence. Priority 2. |
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) |
Genoscope-EU Consortium
| 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
| Members: | Kazusa |
| Contacts: | Satoshi Tabata, Kiyotaka Okada |
| Regions sequenced: | Chromosomes 3 (9.8 Mb) and 5 (17.8 Mb) |
SPP Consortium
| 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 |