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Table 2 Type, localization and characteristics of repeated elements in the RGA08 locus of M. balbisiana

From: Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana)

Name Type ID Location Length 5' LTR 3'LTR TSD Divergence time
    (bp) (bp) length TG CA length TG CA   (MY)
RE1 Copia-like element MbP032N20c_te030 129477 2855 - - - - - - - -
RE1   MbP036B13_te010 100745 2882 - - - - - - - -
Clio LARD MbP032N20c_te010 28466 4441 382 TG CA 382 TG CA ATAC/ATAC 0.294
Clio   MbP032N20c_te040 148954 4441 382 TG CA 382 TG CA GGAG/GGAG 1.189
Clio   MbP036B13_te020 120343 4441 382 TG CA 382 TG CA GGAG/-  
Clio*   MbP036B13_te030 124784 1606 - - - - - - -  
Mooz Copia-like element MbP032N20c_te050 166534 3849 115 - - 112 - - - -
Mooz   MbP032N20c_te060 225945 3346 231 - - 447 TG CA - -
Mooz   MbP036B13_te050 185390 3688 447 TG CA 447 TG CA CTTTG/CTTTC 2.183
Mooz*   MbP036B13_te040 181339 2464 447 TG CA - - - CTTTG/-  
RE5 Copia-like element MbP032N20c_te020 124026 4301 94 TG - 171 TG CA ACCAC/ACCAC -
  1. LTR features (length, presence of TG and CA at their ends) and Target Site Duplication (TSD) were determined using LTR_FINDER followed by manual annotation. For complete elements with clearly identified TSD and with LTR length exceeding the empirical limit of 300 bp, divergence time was calculated based on the Kimura-2 parameter distance between LTRs with a substitution rate of 0.9 × 10-8 mutation per site per year. Stars indicate TE fragments. MY, million years.