The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): evidence for its evolution via gene duplication

Abstract

The translocation of tRNA genes has occurred frequently among multiple independent arthropod lineages. However, the mechanisms of such gene rearrangement are still unclear. In this study we sequenced the nearly complete mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Decapoda, Brachyura, Potamidae). Its size is relatively large (app. 24 kb) for higher animal mtDNA and is due to the presence of many intergenic noncoding sequences (IGNs), one of which is a large repeat region (>7.0 kb). Excluding the repeat region and the putative control region (514 bp), the total size of IGNs (1953 bp) is still the largest reported in arthropods. In comparison to the proposed ancestral arrangement for the insect-crustacean clade, G. dehaani displays changes in the positional order for three tRNA genes (trnQ, trnL(uur) and trnH). At the putative former and current locations for trnQ and trnH, there are IGNs with high similarities to corresponding sequences in the ancestral arrangement. This suggests the occurrence of partial duplication, followed by a loss of function for one copy of these two duplicated genes in G. dehaani. Furthermore, three trnLs (one trnL(uur) and two trnL(cun)s) are found in G. dehaani; their sequences are highly similar to each other (70.8-82.5%) and similar to the trnL(cun) of other arthropods. This suggests that duplication of trnL(cun) occurred at least twice, and the current trnL(uur) of G. dehaani arose by a subsequent anticodon alternation. These observations provide direct evidence for the "duplication-random loss" model for mtDNA gene rearrangement. Comparisons with other available Brachyuran data(http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/6657.html) suggest that two of the three tRNA translocations are unique in G. dehaani. For G. dehaani, where duplications have occurred but deletion of extra sequences is incomplete, the IGNs found at the ancestral or trans-locations are likely to be footprints of relatively recent mitochondrial genome evolution.