Transposable element insertions in ca. 5.7 Mb of orthologous genomic sequences from the coelacanth species Latimeria chalumnae and L. menadoensis.

TE  =  Transposable Element; LINE  =  Long Interspersed Nuclear Element; SINE  =  Short Interspersed Nuclear Element; LTR  =  Long Terminal Repeat; CR1  =  Chicken Repeat 1; L1  =  LINE 1; L2  =  LINE 2; ERV  =  Endogenous Retrovirus; MITE  =  Miniature Inverted-repeat Transposable Element.

*The ERV insertion observed in L. menadoensis does not strictly correspond to an insertion polymorphism, the solo LTR observed at the orthologous site in L. chalumnae probably being the result of a recombination between the two LTRs framing the element (see main text).

**A composite insertion is observed in L. menadoensis, constituted by a Coeg-SINE flanked by two LF-SINEs in direct orientation. Only a “solo” LF-SINE is observed in L. chalumnae, suggesting deletion through homologous recombination between both LF-SINEs.

These “insertions” mostly comprise insertions sensu stricto but also a few deletions that occurred at the orthologous site in the other species.

Transposable element insertions in ca. 5.7 Mb of orthologous genomic sequences from the coelacanth species Latimeria chalumnae and L. menadoensis.