Skip to main content

Table 2 Full-length endogenous betaretroviruses identified in the Illumina sequenced transcriptome of P. alecto and the Sanger sequenced genomes of P. vampyrus and M. lucifugus

From: Identification of diverse full-length endogenous betaretroviruses in megabats and microbats

        Extra LTR   
   Genome gag b pro c pol env ORFsd Lengthe PBSf Additional notes
   Sizea(nt)      ≥ 300 nt (nt)   
P. vampyrus           
  PvERV-βA 7,705 Defective Defective Defective Defective 0 407* Unknown 100 nt NSR overlapping 5' LTR and beginning of gag gene
  PvERV-βB 9,257 Defective Intact Intact Defective 1 1265 Lys 3 102 nt NSR within gag gene
  PvERV-βC 7,126 Defective Defective Defective Intact 0 366* Lys 3 Short env gene may indicate in-frame deletion
  PvERV-βD 7,928 Defective Defective Defective Defective 1 398 Lys 1,2 NSRs overlapping 5' LTR and pro-pol junction
  PvERV-βE 7,879 Intact Defective Intact Intact 1 371* Lys 3 A single stop mutation in pro prevents this ERV being intact
  PvERV-βF 7,804 Intact Defective Defective Defective 1 370 Lys 3 41 nt NSR at extreme 5' end of the 5′ LTR
  PvERV-βG 7,631 Defective Intact Defective Defective 0 387* Lys 3 Appears to contain a deletion that overlaps PPT and 3'LTR
  PvERV-βH 7,843 Defective Intact Defective Defective 1 361 Lys 3  
  PvERV-βI 7,809 Defective Defective Defective Defective 0 371* Lys 3  
  PvERV-βJ 8,773 Defective Intact Intact Intact 2 427* Lys 1,2  
  PvERV-βK 8,611 Defective Defective Intact Intact 1 425* Lys 1,2 3' LTR appears truncated
P. alecto           
  PaERV-βA >8,103§ Defective Defective Defective Defective 2 Unknown Unknown Contains artifact ORF (denoted as ORF* in Figure 1)
M. lucifugus           
  MlERV-βA 9,866 Defective Intact Defective Defective 0 422* Lys 1,2 Large foreign insertion in 5' LTR
  MlERV-βB 8,121 Unknown Defective Intact Defective 0 480 Lys 3 669 nt NSR within gag gene
  MlERV-βC 8,102 Intact Intact Intact Intact 0 479* Lys 3 Completely intact
  MlERV-βD 9,007 Defective Defective Defective Intact 0 479* Lys 3 Contains short foreign insertions in pro and pol genes
  MlERV-βE 7,890 Defective Defective Defective Defective 1 440 Lys  
  MlERV-βF 8,235 Intact Intact Defective Defective 1 470 Lys 3 Small ~45nt deletion overlapping pol and env genes
  1. a The genome size is given for the proviral version of the βERVs. § The genome size of PaERV-βA is uncertain as the known sequence begins 25nt upstream of the gag gene and does not include the (unique 5') region.
  2. b The core retroviral genes gag, pro, pol, and env that contain frameshift or premature stop mutations are described as ‘defective’, those that contain neither of these are described as ‘intact’ in bold font.
  3. c The pro open reading frame (ORF) of each βERV was found to encode a betaretroviral dUTPase protein domain.
  4. d The number of ORFs that do not code for the core genes and are 300 nucleotides or greater in length.
  5. e The length of the long terminal repeats (LTRs). * For those βERVs whose 5′ and 3′ LTR lengths differ, the value of the 5′ LTR is given.
  6. f The specific lysine (Lys) tRNA complementary to the primer binding site (PBS) for each βERV is given. The specific identity of the PBS of MlERV-βE is uncertain. NSR: non-sequenced region.