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Table 3 Amino acid divergences of proteins and RT-Int fragments of CHD-containing Gypsy LTR retrotransposons from Tcn1, Pyggy and Pyret clades

From: Evolutionary genomics revealed interkingdom distribution of Tcn1-like chromodomain-containing Gypsy LTR retrotransposons among fungi and plants

Genes or LTR retrotransposons Length Amino acid identity (%) Evolutionary rate (10-9)b
inorganic phosphate transporter (Pho88)a    
Physcomitrella patens (XM_001783642)/Schizosaccharomyces pombe (NM_001019478) 154 aa 26.8 0.420
P. patens (XM_001783642)/Coprinus cinereus (XM_001836748) 151 aa 23.1 0.445
P. patens/Phanerochaete chrysosporium (JGI: scaffold_7 [325337..326089]) 151 aa 25.0 0.428
P. patens/Cryptococcus neoformans (XM_569621) 152 aa 20.1 0.521
C. cinereus/Ph. chrysosporium 151 aa 64.9 ND
C. cinereus/C. neoformans 151 aa 51.3 0.472
Ph. chrysosporium/C. neoformans 151 aa 58.6 ND
uric acid-xanthine permease (uapA)a    
P. patens (XM_001784081)/Ashbya gossypii (NM_212305) 466 aa 40.7 0.266
P. patens/C. cinereus (XM_001839036) 456 aa 38.4 0.288
P. patens/Ph. chrysosporium (JGI: scaffold_22 [347275..348820]) 391 aa 43.6 0.263
P. patens/C. neoformans (AF542528) 472 aa 36.9 0.318
C. cinereus/Ph. chrysosporium 391 aa 67.9 ND
C. cinereus/C. neoformans 456 aa 39.6 0.560
Ph. chrysosporium/C. neoformans 391 aa 43.2 ND
Tcn1    
Tcn1 C. neoformans/Ccchromovir-1 C. cinereus 684 aa 53.6 0.441
Tcn1 C. neoformans/PcMetavir6 Ph. chrysosporium 684 aa 52.2 ND
Tcn1 C. neoformans/BatDenTy3-1 B. dendrobatidis 677 aa 49.1 0.381
PcMetavir6 Ph. chrysosporium/Ccchromovir-1 C. cinereus 688 aa 72.4 ND
PcMetavir6 Ph. chrysosporium/BatDenTy3-1 Batrachochytrium dendrobatidis 677 aa 47.0 0.412
BatDenTy3-1 B. dendrobatidis/Ccchromovir-1 C. cinereus 677 aa 46.5 0.411
Tcn1 C. neoformans/PpatensLTR1 P. patens 675 aa 52.0 0.216 (HT)
Tcn1 C. neoformans/SM-Tcn1 Selaginella moellendorffii 682 aa 50.3 0.235 (HT)
PcMetavir6 Ph. chrysosporium/PpatensLTR1 P. patens 675 aa 51.8 0.217 (HT)
PcMetavir6 Ph. chrysosporium/SM-Tcn1 S. moellendorffii 682 aa 49.5 0.230 (HT)
PpatensLTR1 P. patens/SM-Tcn1 S. moellendorffii 675 aa 58.6 0.429
Pyggy    
PyrTriTy3-2 Pyrenophora tritici-repentis/NecHaemTy3-4Nectria haematococca 706 aa 77.0 0.259 (HT)
PyrTriTy3-2 P. tritici-repentis/ChaGloTy3-8 Chaetomium globosum 706 aa 48.5 0.706
PyrTriTy3-2P. tritici-repentis/grh Magnaporthe grisea 701 aa 49.2 0.703
PyrTriTy3-2 P. tritici-repentis/Dane4Aspergillus nidulans 695 aa 55.5 0.531
AltBraTy3-2Alternaria brassicicola/NecHaemTy3-4N. haematococca 709 aa 47.7 0.880
AltBraTy3-2A. brassicicola/Dane4 A. nidulans 695 aa 49.2 0.649
grh M. grisea/Dane4 A. nidulans 695 aa 48.5 0.670
Pyret    
skippy Fusarium oxysporum/PyrTriTy3-1 P. tritici-repentis 648 aa 40.4 0.772
skippy F. oxysporum/AFLAV Aaspergillus flavus 673 aa 41.4 0.766
AFLAV A. flavus/PyrTriTy3-1 P. tritici-repentis 648 aa 44.3 0.656
  1. a The corresponding accession numbers in GenBank are provided in the brackets;
  2. b ND - not determined: information concerning time divergence between species groups is unavailable; HT - putative horizontal transmission