PMC:3091637 / 59072-61536
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3091637","sourcedb":"PMC","sourceid":"3091637","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3091637","text":"Vermetid mt genomes also shared an interesting gene order change with two other members of the superfamily Littorinimorpha, Littorina saxatilis and Oncomelania hupensis, associated with the position of the two leucine tRNA genes, trnLUUR and trnLCUN (Figure 5). Within the mt genome of Haliotis, Octopus, and Katharina, these two leucine tRNAs are sandwiched between rrnL and nad1 in the following arrangement: rrnL-trnLCUN-trnLUUR-nad1. This gene order is retained in all caenogastropod mt genomes sampled to date, except for Littorina, Oncomelania, Dendropoma maximum, D. gregarium, and Vermetus erectus, where the relative position of these two genes has switched, such that trnLUUR is located directly upstream from trnLCUN. (Note: this gene order is incorrectly annotated in [48] (pg 40), and this gene order change is not recognized in [15](page 11) or [53](page 4), where it is stated that there are no differences in gene order between the partial genome of Littorina and complete genome of neogastropods). This difference in the order of these two tRNAs is also present in several other vermetid taxa (data not shown), but is not present in two additional members of the Littorinimorpha: Cymatium parthenopeum and Calyptraea chinensis [53]. While this shared gene rearrangement may be a synapomorphy defining a clade within the Littorinimorpha to which the Littorinidae (Littorina), Pomatiopsidae (Oncomelania) and Vermetidae belong, changes in tRNA positions involving neighbouring leucine tRNA genes should be treated with caution. Gene translocations among neighbouring genes appear to occur with increased frequency in mt genomes and thus may be more likely to arise independently [23]. Such \"position switches\" between neighbours may therefore be less reliable phylogenetic characters for addressing deeper level phylogenetic questions. In addition, simple changes in position of these two leucine tRNA genes can mask more complicated dynamics that may involve gene duplications and tRNA remolding events [28] (see Evidence for tRNA remolding and recruitment, below). Uncovering the dynamics that have occurred within this region of the genome can be essential to interpreting gene identity correctly and accurately reconstructing past gene rearrangement events. The discovery of two trnLUUR genes side by side between rrnL and nad1 of Thylacodes squamigerus further suggests that such tRNA remolding events may be at play within vermetid mt genomes.","tracks":[{"project":"2_test","denotations":[{"id":"20642828-16806344-10659386","span":{"begin":781,"end":783},"obj":"16806344"},{"id":"20642828-18302768-10659387","span":{"begin":843,"end":845},"obj":"18302768"},{"id":"20642828-19698157-10659388","span":{"begin":860,"end":862},"obj":"19698157"},{"id":"20642828-19698157-10659389","span":{"begin":1245,"end":1247},"obj":"19698157"},{"id":"20642828-9914213-10659390","span":{"begin":1695,"end":1697},"obj":"9914213"},{"id":"20642828-14673095-10659391","span":{"begin":2020,"end":2022},"obj":"14673095"}],"attributes":[{"subj":"20642828-16806344-10659386","pred":"source","obj":"2_test"},{"subj":"20642828-18302768-10659387","pred":"source","obj":"2_test"},{"subj":"20642828-19698157-10659388","pred":"source","obj":"2_test"},{"subj":"20642828-19698157-10659389","pred":"source","obj":"2_test"},{"subj":"20642828-9914213-10659390","pred":"source","obj":"2_test"},{"subj":"20642828-14673095-10659391","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#99ec93","default":true}]}]}}