An Amphipod Map: The fully sequenced mitochondrial genome of a freshwater shrimp

The mitochondria is the powerhouse of the cell. It is one of the primary organelles responsible for generating chemical energy within the cell; and in phylogenetic studies, its DNA is especially useful for assessing genetic diversity.

Mitochondrial DNA, or mtDNA, has a relatively high mutation rate giving it more genetic variation over a shorter period of time. Unlike nuclear DNA, it also doesn’t recombine making its mutations linear and traceable. These characteristics mean that if one observes the differences among the mtDNA of organisms between populations, one can compare how they differ and how closely related they are. This also means that you can visualize these relations in an evolutionary tree.

To do this, one would typically need to sequence at least part of the mitochondrial genome, or mitogenome of an organism, although sequencing the entire mitogenome provides more comprehensive insights.

From the Fishery Research Laboratory in Kyushu University, SEAFDEC/AQD Associate Scientist Dr. Joana Joy de la Cruz-Huervana and her co-authors sought to sequence the complete mitogenome of Gammarus nipponensis, a freshwater shrimp endemic in Japan. Given its restricted habitat and direct-developing life cycle, they considered G. nipponensis as an ideal model organism for studying the impacts of habitat fragmentation and evolutionary diversification on the genes of amphipods. Here’s what they found.

The fully sequenced circular mitogenome was 16,429 base pairs (bp) long and comprised of the typical metazoan components: 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes, along with two control regions (CR1 and CR2).

One interesting discovery in the sequencing of this mitogenome was the presence of 98 tandem repeats of TATTTTA within the second control region (CR2), spanning 686 bp. This is notable because,  among gammarid species, tandem repeats have been previously reported only in G. duebeni, but relatively few at six repeats totaling 84 to 97 bp long.

Based on the sequenced mitogenome, the researchers were able to construct an evolutionary tree. Phylogenetic analysis placed G. nipponensis within the superfamily Gammaroidea, revealing a close relationship with G. pisinnus, another East Asian species. This adds to the growing body of evidence that supports regional clustering and diversification among amphipod lineages.

The complete mitogenome of G. nipponensis opens new avenues for refining phylogenetic classifications within the genus Gammarus and provides a tool for exploring population structure, evolutionary history, and species identification.

Future studies could use this mitogenome as a reference to examine intraspecific genetic diversity. Comparative mitogenomics with other amphipods may also reveal broader evolutionary trends and mechanisms of genome organization.

If you wish to learn more of this study and see both the mitochondrial genome map and phylogenetic tree, you can view the article entitled “The complete mitochondrial genome of freshwater gammarid Gammarus nipponensis (Crustacea: Amphipoda: Gammaridae)” published in the Mitochondrial DNA Part B. You may request for a copy of the article here: https://repository.seafdec.org/handle/20.500.12066/7462.