Table 1 Number of Copia retrotransposons in fungal genomes
From: Filamentous ascomycete genomes provide insights into Copia retrotransposon diversity in fungi
Class/Order | species | Sequences obtained with LTR Harvest | Sequences (>3Kb) obtained using RepeatMasker | ||||||
|---|---|---|---|---|---|---|---|---|---|
GalEa | FunCo1 | other Copia | GalEa/Copia | GalEa | FunCo1 | other Copia | GalEa/Copia | ||
Dothideomycetes | |||||||||
Pleosporales | Pyrenophora teres pp | 0 | 0 | 0 | ne | 1 | ne | ne | ne |
Pleosporales | Pyrenophora tritici-repentis pp | 76 | 75 | 50 | 0.38 | 85 | 89 | 59 | 0.36 |
Incertae sedis | Cenococcum geophilum sb | 1246 | 184 | 192 | 0.77 | 2368 | 279 | 401 | 0.78 |
Eurotiomycetes | |||||||||
Eurotiales | Neosartorya fischeri p | 1 | 2 | 9 | 0.08 | 1 | 2 | 11 | 0.07 |
Eurotiales | Talaromyces aculeatus s | 12 | 4 | 3 | 0.63 | 19 | 4 | 3 | 0.73 |
Eurotiales | Talaromyces marneffei p | 19 | 29 | 3 | 0.37 | 16 | 31 | 5 | 0.31 |
Eurotiales | Talaromyces stipitatus s | 40 | 30 | 14 | 0.48 | 51 | 35 | 27 | 0.45 |
Leotiomycetes | |||||||||
Erysiphales | Erysiphe pisi pp | 13 | 5 | 34 | 0.25 | 23 | 7 | 53 | 0.28 |
Helotiales | Botryotinia fuckeliana pp | 3 | 2 | 0 | ne | 6 | 1 | 0 | ne |
Helotiales | Chalara longipes s | 4 | 0 | 8 | 0.33 | 11 | 0 | 21 | 0.34 |
Helotiales | Meliniomyces bicolor sb | 156 | 8 | 21 | 0.84 | 603 | 75 | 31 | 0.85 |
Helotiales | Meliniomyces variabilis sb | 3 | 11 | 10 | 0.13 | 5 | 25 | 31 | 0.08 |
Helotiales | Sclerotinia sclerotiorum pp | 1 | 10 | 8 | 0.05 | 1 | 12 | 8 | 0.05 |
Incertae sedis | Oidiodendron maius sb | 11 | 14 | 39 | 0.17 | 17 | 17 | 57 | 0.19 |
Sordariomycetes | |||||||||
Glomerellales | Colletotrichum fiorinae pp | 0 | 0 | 1 | ne | 0 | 0 | 1 | ne |
Glomerellales | Colletotrichum graminicola pp | 19 | 0 | 35 | 0.35 | 151 | 0 | 53 | 0.74 |
Glomerellales | Colletotrichum higginsianum pp | 0 | 0 | 0 | ne | 1 | ne | ne | ne |
Glomerellales | Verticillium albo-atrum pp | 0 | 3 | 0 | ne | 1 | 3 | 0 | ne |
Glomerellales | Verticillium dahliae pp | 1 | 24 | 0 | 0.04 | 1 | 26 | 0 | 0.03 |
Hypocreales | Beauveria bassiana ip | 1 | 0 | 1 | ne | 2 | 0 | 1 | ne |
Hypocreales | Cordyceps militaris ip | 13 | 0 | 3 | 0.81 | 46 | 0 | 7 | 0.84 |
Hypocreales | Metarhizium robertsii ip | 0 | 0 | 3 | ne | 2 | 0 | 3 | ne |
Magnaporthales | Gaeumannomyces graminis pp | 0 | 5 | 2 | ne | 0 | 46 | 4 | ne |
Magnaporthales | Magnaporthe oryzae pp | 0 | 0 | 30 | 0.00 | 2 | 0 | 69 | 0.03 |
Magnaporthales | Magnaporthe poae pp | 0 | 0 | 2 | ne | 0 | 0 | 1 | ne |
Ophiostomatales | Ophiostoma piceae s | 0 | 0 | 0 | ne | 1 | ne | ne | ne |
Sordariales | Chaetomium globosum s | 5 | 7 | 6 | 0.28 | 7 | 9 | 6 | 0.32 |
Xylariales | Daldinia eschschotzii EC12sb | 0 | 0 | 0 | ne | 2 | ne | ne | ne |
Xylariales | Hypoxylon sp. CO27-5sb | 1 | 0 | 0 | ne | 4 | ne | ne | ne |
Xylariales | Hypoxylon sp. EC38sb | 0 | 0 | 1 | ne | 1 | 0 | 1 | ne |