Characteristics of LTR Retrotransposons from Hemiascomycetous Yeasts
| Species | Element | ORF1 size (AA) | ORF2 size (AA) | Frameshift | LTR | |||
| name | size (bp) | copy number | size (bp) | terminal inverted repeats | ||||
| Ty1-like elements | ||||||||
| S. cerevisiae | Ty1-br | 5917 | 32 | 435 | 1321 | CUUAGGC | 332 | TG…CA |
| S. cerevisiae | Ty2-b | 5959 | 13 | 431 | 1359 | CUUAGGC | 332 | TGT…ACA |
| K. marxianus | Tkm1 | 5994 | 10–15 | 421 | 1339 | CUUAGGC | 385 | TGTTG…CAACA |
| S. exiguus | Tse1 | 5691 | 15–20 | 383 | 1235 | CUUAGGC | 424 | TGA…TCA |
| S. kluyveri | Tsk1 | 5905 | 8 | 435 | 1320 | CUUAGGC | 322–333 | TG…CA |
| K. lactis | Tkl1.1 | 5425 | 1 | 202 | 1335 | CUUAGGC | 393–398 | TGTTG…AAACA or TGTTG…CAACA |
| K. lactis | Tkl1.2 | 1 | 391 | CUUAGGC | ?…AAACA | |||
| S. servazzii | Tss1 | 1–2 | ||||||
| Ty4-like elements | ||||||||
| S. cerevisiae | Ty4-j | 6227 | 3 | 363 | 1440 | CUUAGGC | 371 | TGTTG…CAACA |
| S. bayanus | Tsu4 | 6095 | 15–20 | 358 | 1433 | CUUAGGC | 321 | TGTTG…CAACA |
| Ty5-like elements | ||||||||
| D. hansenii | Tdh5 | 5349 | ∼20 | – | 1490 | – | 457 | TGTTGAA…TTCAACA |
| P. angusta | Tpa5 | 4883 | 10–15 | – | 1417 | – | 322 | TGTTG…CAACA |
| S. exiguus | Tse5.1 | 5286 | 8–10 | – | 1531 | – | 370 | TGTTG…CAACA |
| C. albicans | Tca5 | 5588 | 0–5 | – | 1477 | – | 685 | TGTTG…CAACA |
| S. paradoxus | Ty5 | 5376 | 10–15 | – | 1698 | – | 251 | TGTTGA…TCAACA |
| Tca2-like elements | ||||||||
| D. hansenii | Tdh2 | 5928 | 3–5 | 336 | 1340 | no, stop codon | 379 | TGTTGG…CCAATA |
| C. albicans | Tca2 | 6426 | 5–10 | 324 | 1576 | no, stop codon | 280 | TGTTGG…CCATCA |
| gypsy elements | ||||||||
| S. cerevisiae | Ty3-g | 5351 | 2 | 285 | 1262 | GCGAGUU | 340 | TGTTGTAT…ATACAACA |
| S. exiguus | Tse3 | 6487 | 10–15 | 257 | 1181 | AUUAGUA | 945–947 | TGTAAC…GTTACA |
| Y. lipolytica | Yltl | 9451 | 35 | 1097 | 1069 | ? | 714 | TGT…ACA |
| S. kluyveri | Tsk3 | 1–2 | ||||||
| D. hansenii | Tdh3 | 1–2 | ||||||
| S. servazzii | Tss3 | 1–2 | ||||||
| Y. lipolytica | Tyl3 | 1–3 | ||||||
| Z. rouxii | Tzr3 | 3–5 | ||||||
| C. tropicalis | Tct3 | 1–3 | ||||||
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↵Defective element.
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↵Incomplete sequence.
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↵The name of the elements specifically identified in this study are in bold.
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↵The copy number was determined for Ty elements; it does not include solo LTRs.
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↵The first part of gag from Tkl1.1 was deleted.
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↵This ORF has a frameshift between positions 1909 and 1931.
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↵This ORF has a frameshift at position 1490 (ggg instead of gg).
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↵The beginning of the LTR was not determined.
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↵Sizes of Ylt1 ORF1 and ORF2 are only indicative because the locus that underwent the frameshift could not be precisely determined.
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bp, base pairs; AA, amino acids; ORF, open reading frame; LTR, long terminal repeat.
