Table II.
Plant retrotransposons and their matching plant ESTs
| Query Retrotransposon
|
Homologous ESTs
|
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Elementa | Source species | Type | Total ESTs | Matching species | EST source tissueb
|
||||||
| A | B | C | D | E | F | G | |||||
| SIRE-1 | Soybean | Copia | 2 | Soybean | – | – | – | – | 1 | 1 | – |
| Tgmr | Soybean | Copia | 0 | – | – | – | – | – | – | – | – |
| diaspora | Soybean | Gypsy | 3 | Soybean | – | – | 1 | 2 | – | – | – |
| Athila | Arabidopsis | Gypsy | 1 | Arabidopsis | 1 | – | – | – | – | – | – |
| AtRE1 | Arabidopsis | Copia | 0 | – | – | – | – | – | – | – | – |
| AtRE2 | Arabidopsis | Copia | 0 | – | – | – | – | – | – | – | – |
| Ta1 | Arabidopsis | Copia | 0 | – | – | – | – | – | – | – | – |
| Tat1 | Arabidopsis | Gypsy | 0 | – | – | – | – | – | – | – | – |
| Evelknievel | Arabidopsis arenosa | Copia | 0 | – | – | – | – | – | – | – | – |
| RetroLyc | L. peruvianum | Copia | 6 | Cultivated tomato (Lycopersicum esculentum) | – | – | – | – | 3 | 2 | 1 |
| Bs1 | Maize | ? | 1c | Maize | – | – | 1 | – | – | – | – |
| Hopscotch | Maize | Copia | 0 | – | – | – | – | – | – | – | – |
| Opie-2 | Maize | Copia | 21 | Maize | 2 | – | 9 | 3 | 5 | 2 | – |
| PREM-2 | Maize | Copia | 17 | Maize | – | – | 8 | 1 | 7 | 1 | – |
| Stonor | Maize | Copia | 3 | Maize | 1 | – | 2 | – | – | – | – |
| CentA | Maize | Gypsy | 2 | Rice | – | 1 | – | – | – | – | 1 |
| Cinful1 | Maize | Gypsy | 23 | Maize | 3 | – | 7 | 3 | 10 | – | – |
| Cinful2 | Maize | ? | 22 | Maize | 4 | – | 4 | 2 | 12 | – | – |
| Grande1 | Zea diploperennis | Gypsy | 2 | Maize | 2 | – | – | – | – | – | – |
| Reina | Maize | Gypsy | 0 | – | – | – | – | – | – | – | – |
| Tekay | Maize | Gypsy | 2 | Maize | 2 | – | – | – | – | – | – |
| Zeon-1 | Maize | Gypsy | 10 | Maize | 4 | – | 5 | 1 | – | – | – |
| RIRE1 | Oryza australiensis | Copia | 2 | Barley | 1 | – | – | – | – | – | – |
| Bread wheat (Triticum aestivum) | – | – | – | 1 | – | – | – | ||||
| RIRE2 | Rice | Gypsy | 6 | Rice | – | – | – | 1 | 2 | – | 3 |
| RIRE3 | Rice | Gypsy | 8 | Rice | – | – | 7 | – | – | – | – |
| Gossypium arboreum | – | – | 1 | – | – | – | – | ||||
| RIRE7 | Rice | Gypsy | 7 | Rice | – | – | – | – | 1 | – | 1 |
| Maize | – | – | 1 | 1 | 2 | – | – | ||||
| Sorghum | – | – | – | – | – | 1 | – | ||||
| RIRE8 | Rice | Gypsy | 5 | Rice | – | – | 4 | – | – | – | 1 |
| Wis2-1 | Bread wheat | Copia | 19 | Bread wheat | – | – | 1 | 4 | 2 | 2 | – |
| Triticum monococum | – | 1 | – | – | – | – | – | ||||
| Barley | 5 | – | 3 | – | – | – | – | ||||
| Rye | – | – | – | – | – | 1 | – | ||||
| RetroSor1 | Sorghum | Gypsy | 4 | Sorghum | – | – | – | – | 3 | 1 | – |
| Levithan | Sorghum | LTR | 1 | Sorghum | – | – | – | – | 1 | – | – |
| BARE-1 | Barley | Copia | 23 | Barley | 7 | – | 6 | – | – | – | – |
| Bread wheat | – | – | 1 | 5 | 1 | 2 | – | ||||
| Rye | – | – | – | – | – | 1 | – | ||||
| Bagy-1 | Barley | Gypsy | 6 | Barley | 2 | – | 1 | – | – | – | – |
| Bread wheat | – | – | 1 | 1 | – | – | – | ||||
| Rice | – | – | 1 | – | – | – | – | ||||
| Bagy-2 | Barley | Gypsy | 7 | Barley | 4 | – | 1 | – | – | – | – |
| Bread wheat | – | – | – | – | 2 | – | – | ||||
| Cereba | Barley | Gypsy | 5 | Bread wheat | – | – | – | – | 2 | – | – |
| Maize | – | – | 1 | 1 | – | – | – | ||||
| Sorghum | – | – | – | – | – | 1 | – | ||||
| Nikita | Barley | LTR | 1 | Bread wheat | – | – | – | – | 1 | – | – |
| Sabrina | Barley | ? | 29 | Barley | 22 | – | 3 | – | – | – | – |
| Bread wheat | – | – | – | 2 | 1 | – | – | ||||
| Rye | – | – | – | – | – | 1 | – | ||||
| Sukkula | Barley | ? | 34 | Barley | 12 | – | 9 | – | 1 | – | – |
| Bread wheat | 1 | 1 | 2 | 4 | – | 3 | – | ||||
| IFG7 | Pinus radiata | Gypsy | 4 | Pinus taeda | – | 2 | 2 | – | – | – | – |
Published retrotransposon elements were used as query sequences in searches of plant EST accessions in the EST database. The matching ESTs for each retrotransposon are listed according to their source. The databases are not necessarily nonredundant.
The retrotransposon accession nos. are: SIRE-1 (U96295), Tgmr (U96748), diaspora (AF095730), Athila (X81801), AtRE1 (AB021265), AtRE2 (AB021266), Evelknievel (AF039376), Ta1 (X53976), Tat1 (AF056632), RetroLyc (AF228701), Bs1 (X16080), Hopscotch (U12626), Opie-2 (AF090446), PREM-2 (U41000), Stonor (AF082130, AF082134, and AF082133), CentA (AF078917), Cinful1 (AF049110), Cinful2 (AF049111), Grande1 (X97604), Reina (U69258), Tekay (AF050455), Zeon-1 (U11059), RIRE1 (D85597), RIRE2 (AB030283), RIRE3 (AB014738), RIRE7 (AB014740), Wis2-1 (X63184), RetroSor (AF098806), Levithan (U07816), BARE-1 (Z17327), Bagy-1 (Y14573), Bagy-2 (AF254799), Cereba (AF078801), Nikita (AF254799), Sabrina (AF254799), Sukkula (Z17327, Y14573, AFO29897, AF254799), and IFG7 (AJ004945).
Letters represent the tissue from which the EST was obtained: A, Leaf; B, shoot and root; C, flower and other reproductive organs; D, embryo and seed; E, seedling; F, stress-induced plants; and G, cultured cells.
Bs1 has been shown to contain a transduced gene corresponding to a plasma membrane H+-ATPase. For this reason, Bs1 gave homologies with many cDNAs that are transcripts from these genes. Those matches have been removed from the Table.