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Background  In contrast to DNA-mediated transposable elements (TEs), retrotransposons, particularly non-long terminal repeat retrotransposons (non-LTRs), are generally considered to have a much lower propensity towards horizontal transfer. Detailed studies on site-specific non-LTR families have demonstrated strict vertical transmission. More studies are needed with non-site-specific non-LTR families to determine whether strict vertical transmission is a phenomenon related to site specificity or a more general characteristic of all non-LTRs.  Juan  is a Jockey clade non-LTR retrotransposon first discovered in mosquitoes that is widely distributed in the mosquito family  Culicidae . Being a non-site specific non-LTR,  Juan  offers an opportunity to further investigate the hypothesis that non-LTRs are genomic elements that are primarily vertically transmitted.    Results  Systematic analysis of the ~1.3 Gbp  Aedes aegypti  ( Ae. aegypti ) genome sequence suggests that  Juan-A  is the only  Juan -type non-LTR in  Aedes aegypti .  Juan-A  is highly reiterated and comprises approximately 3% of the genome. Using minimum cutoffs of 90% length and 70% nucleotide (nt) identity, 663 copies were found by BLAST using the published  Juan-A  sequence as the query. All 663 copies are at least 95% identical to  Juan-A , while 378 of these copies are 99% identical to  Juan-A , indicating that the  Juan-A  family has been transposing recently in evolutionary history. Using the 0.34 Kb 5' UTR as the query, over 2000 copies were identified that may contain internal promoters, leading to questions on the genomic impact of  Juan-A .  Juan  sequences were obtained by PCR, library screening, and database searches for 18 mosquito species of six genera including  Aedes ,  Ochlerotatus ,  Psorophora ,  Culex ,  Deinocerites , and  Wyeomyia . Comparison of host and  Juan  phylogenies shows overall congruence with few exceptions.    Conclusion   Juan-A  is a major genomic component in  Ae. aegypti  and it has been retrotransposing recently in evolutionary history. There are also indications that  Juan  has been recently active in a wide range of mosquito species. Furthermore, our research demonstrates that a Jockey clade non-LTR without target site-specificity has been sustained by vertical transmission in the mosquito family. These results strengthen the argument that non-LTRs tend to be genomic elements capable of persistence by vertical descent over a long evolutionary time.

The Juan non-LTR retrotransposon in mosquitoes: genomic impact, vertical transmission and indications of recent and widespread activity