Among The Most Forgotten Detail Around diglyceride

For experimental validation, we selected the MoTE-1 family because the diglyceride insertion polymorphic rates of MoTE-1 for all three isolates (HM-1, HM-2, and the reference genome) were 100% (Fig.?4A, all of the MoTE-1 sequences are located in different regions). Among the TIPs involving the MoTE-1 family and detected by PTEMD-B, 60 TIPs from HM-1 and HM-2 were randomly selected for validation (Fig.?4A, the blue and red triangles represent the selected TIPs). If the predicted TIP was authentic, the difference in PCR product size between a fungal isolate with the TE insertion and a isolate without the TE insertion would be the length of MoTE-1, which is ?1.8 kb. Using M. oryzae reference genome sequences, we designed 60 primer pairs flanking the predicted insertion I-BET-762 in vivo sites (Supplementary Table S2). The results showed that 100% of MoTE-1 TIPs in HM-1 and 93% of those in HM-2 represented true insertion polymorphism (Fig.?4B and C). To assess why two of the predicted TIPs in HM-2 (Fig.?4C, black arrows regions, 2-P6 and 2-P13) were not detected by PCR, we examined the sequence coverage for these two predicted TIPs and found that both had fewer supporting reads (2 and 3 breakpoint reads supported) than the validated insertions (��4 breakpoint reads supported, PIOX1 of reference genome, HM-1 and HM-2 and their validation. (A) Distributions of the MoTE-1 TIPs in the M. oryzae reference genome, HM-1 and HM-2 genomes. Black lines: M. oryzae chromosomes (X represents sequence that ... 3.2. Comparison of PTEMD with other relative programs To assess the proportion of polymorphic TE families in genome, we de novo detected all of the repeat sequences families in M. oryzae genome using RepeatMasker, Repeatscout, Piler, and RECON; 36, 79, 42, and 44 repeat families were identified, respectively (Fig.?5A, Venn diagram of the four program detected repeat sequence families), about half of the families are redundant, meanwhile, total non-redundant repeat families are 138 (Fig.?5B, the blue and blue-red overlapped region). Using PTEMD-A, we detected 14 polymorphic TE families. Among the 14 TE families, 12 families have highly similar (97% identity over 95% length) homologue within the 138 non-redundant repeat families, the other two families are only detected by PTEMD-A (Fig.?5B). In other words, only ?10% of the repeat families in M. oryzae genome are polymorphic TE families. The two polymorphic TE families that are only detected by PTEMD-A have low copy numbers (ranging from three to seven) in M. oryzae genome, and this explained why they are missed by other repeat scanning programs. Figure?5.