Resolve ninja / aurora-element naming issue

[cbergman]

Two TEs discovered in D. melanogaster (aurora-element) and D. simulans (ninja) are closely related and the similarity between these elements has caused confusion among workers in the field. The founding sequences of this family were LTRs from a non-functional aurora-element discovered in D. melanogaster reported by Shevelyov (1993) http://www.ncbi.nlm.nih.gov/pubmed/8389978. A full length element from D. simulans was then discovered independently by Ogura et al (1996) http://www.ncbi.nlm.nih.gov/pubmed/8925473, who reported similarity to the LTRs of the aurora-element of Shevelyov (1993).

Kanamori et al (1998) then obtained the original clone from Shevelyov, sequenced the full-length insert of this defective aurora-element from D. melanogaster http://www.ncbi.nlm.nih.gov/pubmed/10333568. Kanamori et al (1998) showed that aurora-element and ninja were very similar across the length of the whole element, but that aurora-element had a number of deletions that rendered it inactive. Kanamori et al (1998) also cloned and sequenced a number of 5' LTRs from multiple strains of D. melanogaster and D. simulans and used diagnostic variants from the original aurora-element and ninja 5' LTRs to classify LTRs as being aurora-type or ninja-type. aurora-type LTRs were found in both D. melanogaster and D. simulans, and the latter were designated aurora-sim. ninja-type LTRs were only found in D. simulans, but not D. melanogaster. Further analysis showed aurora-sim elements to be defective in D. simulans, like aurora-elements in D. melanogaster. Kanamori et al (1998) concluded that all full length functional copies of this family in D. simulans were ninja elements, and all non-functional copies in D. simulans or D. melanogaster are aurora-elements. In other words, Kanamori et al (1998) suggest that ninja and aurora-element are subfamilies of the same TE family, with all active members being from the ninja subfamily and all in inactive members from the aurora-subfamily.

The close similarity and presence of both the D. simulans ninja and D. melanogaster aurora-elements in the Drosophila transposon sequence set used in the D. melanogaster R4 genome annotation caused TEs from this family to be annotated variously as aurora-elements (FBte0000112) or ninja-Dsim-like elements (FBte0001097):

• aurora-element: http://flybase.org/cgi-bin/uniq.html?([fbti-INSERTED_ELEMENT:FBte0000112]%3Efbti&[fbti-LOCATION_MIN:IS%20NOT%20NULL]%3Efbti)%3Efbti
• ninja-Dsim-like: http://flybase.org/cgi-bin/uniq.html?([fbti-INSERTED_ELEMENT:FBte0001097]%3Efbti&[fbti-LOCATION_MIN:IS%20NOT%20NULL]%3Efbti)%3Efbti

Assigning different names in the same species to elements from this family is unwarranted and has caused confusion for a number of workers in the field. Resolution of this naming conflict depends on the interpretation of the evolutionary history of this family. Several scenarios are possible, which are presented in increasing order of interpretability to the community:

1. Kanamori et al's (1998) interpretation that ninja and aurora-element are subfamilies of the same TE family, with all active members being from the ninja subfamily and all in active members from the aurora-subfamily is correct. If so, then all full length active members of this family should be named ninja and all inactive, truncated members should be named aurora-element, regardless of whether they are in found in D. simulans or D. melanogaster. This is essentially a structural classification and would lead to two TE names in both species. This solution leaves open the naming clash issues and in fact makes it worse by causing the same issue in D. simulans.
2. Species specific differences between aurora-element and ninja are acknowleged sufficiently to call these different families from the same super family. All copies in D. melanogaster should be called aurora-element and all copies in D. simulans should be called ninja. This would solve naming clashes in both species, but future annotation efforts would require post-processing of hits to the hetero-specific TE sequence.
3. aurora-element and ninja are considered the same family and given the name of the founding member of this family: aurora-element. The Dsim/ninja element would be renamed Dsim/aurora-element and all copies in both species would be named aurora-element. I support this solution since I believe it better represents the evolutionary history of the family and resolves the intra-specific and inter-specific naming issues.

Thoughts on this proposal are welcome below.