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to be filled out
LINKS NEED UPDATINGProgress on the newest reannotation can be found here.
Reference Genome 2000-2023
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| 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.
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T32B3-5SrDNA-T25B21-T3J11
GFF file of all known gaps in the Arabidopsis genome assembly April
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2008
Clones Missing or Incomplete in GenBank September 2003
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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 |