Dong-Ha Ahn

The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia

Kim, S., Park, M.‐H., Jung, J.‐H., Ahn, D.‐H., Sultana, T., Kim, S., Park, J.‐K., Choi, H.‐G. & Min, G.‐S. (2012). The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia. —Zoologica Scripta, 41, 281–292.

The complete mitochondrial genome of the Japanese mud shrimp Upogebia major (Crustacea, Decapoda)

We determined a full-length sequence of mitochondrial (mt) genome from Upogebia major. This is the first complete mt genome report for infraorder Thalassinidea in Decapoda, Crustacea. Our result showed that U. major generally followed a typical pancrustacean gene order but some tRNA genes showed a very unique gene arrangement such as duplication or translocation. Since none of the complete mt genome sequences in the infraorder Thalassinidea are available yet, this report will provide additional information in relation to mt genome diversity and evolution of the decapods.

First Record of Genus Sinorchestia (Crustacea: Amphipoda: Talitridae) from Korea

We present the first record of Sinorchestia sinensis (Chilton, 1925), the sandhopper, in Korea. This species was collected from the Baengnyeongdo Island of Korea. Descriptions of diagnostic characters of the species are provided on the text. A key to the species of Sinorchestia is provided.

Two complete chloroplast genome sequences of Cannabis sativa varieties

Abstract In this study, we determined the complete chloroplast (cp) genomes from two varieties of Cannabis sativa. The genome sizes were 153,848 bp (the Korean non-drug variety, Cheungsam) and 153,854 bp (the African variety, Yoruba Nigeria). The genome structures were identical with 131 individual genes [86 protein-coding genes (PCGs), eight rRNA, and 37 tRNA genes]. Further, except for the presence of an intron in the rps3 genes of two C. sativa varieties, the cp genomes of C. sativa had conservative features similar to that of all known species in the order Rosales. To verify the position of C. sativa within the order Rosales, we conducted phylogenetic analysis by using concatenated sequences of all PCGs from 17 complete cp genomes. The resulting tree strongly supported monophyly of Rosales. Further, the family Cannabaceae, represented by C. sativa, showed close relationship with the family Moraceae. The phylogenetic relationship outlined in our study is well congruent with those previously shown for the order Rosales.

The complete mitochondrial genome of the Japanese ghost shrimp Nihonotrypaea japonica (Crustacea, Decapoda, Axiidea)

We determined the complete mitochondrial (mt) genome sequence of the Japanese ghost shrimp Nihonotrypaea japonica (Ortmann 1891) (Crustacea, Decapoda, Axiidea). The N. japonica mt genome is first represented in infraorder Axiidea, which, together with infraorder Gebiidea, belonged to infraorder Thalassinidea until recently. The genome sequence of N. japonica is 15,274 bp in size, and the gene arrangement and transcriptional polarity are partially different from that of the Japanese mud shrimp, Upogebia major, which belongs to the infraorder Gebiidea. We present the mt genome of N. japonica, which could provide useful molecular information to construct a stable classification for infraorder Thalassinidea and to better understand the phylogenetic relationship of Thalassinidea with other decapod groups.

Isolation and characterization of microsatellite loci in the Korean crayfish, Cambaroides similis and application to natural population analysis

Abstract The Korean freshwater crayfish, Cambaroides similis, has recently suffered from range reduction and habitat degradation caused by environmental changes and water pollution. For the conservation and restoration of this species, it is necessary to understand the current population structures of Korean C. similis using estimation of their genetic variation. In this study, eight microsatellite loci were developed and characterized from 49 individuals collected from four locations: one population from Mt. Bukhan (BH) and three populations from Mt. Gwanak (GA) in Seoul, Korea. As a result, the number of alleles per locus ranged from 2 to 12. The observed heterozygosities and expected heterozygosities ranged from 0.000 to 0.833 and from 0.125 to 0.943, respectively, and the former values were significantly lower than the latter ones expected under the Hardy-Weinberg equilibrium. No significant linkage disequilibrium was revealed between any of the locus pairs after Bonferroni correction. From the pairwise Fst results over all samples, higher differentiation between GA-BH population pairs (mean 0.1789) was observed than between GA population pairs (mean 0.0454). This was also supported by Mantels test showing that the genetic distances of these crayfish populations were significantly correlated with geographic distances. This result may show the regional differentiation caused by restricted gene flow between northern (BH) and southern (GA) populations within Seoul. These microsatellite markers have the potential for use in analyses of the genetic diversity and population structure of C. similis species, with implications for its conservation and management plans.

The complete mitochondrial genome of the red-banded lobster Metanephrops thomsoni (Crustacea, Astacidea, Nephropidae): a novel gene order

Abstract The complete mitochondrial genome (mitogenome) of the red-banded lobster, Metanephrops thomsoni (Decapoda, Astacidea, Nephropidae), is 19,835 bp in length and contains 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 24 transfer RNAs (including additional copies of trnW and trnL1), and 2 control regions (CR). The mitogenome of M. thomsoni has 10 long intergenic sequences (71–237 bp) with a high AT content (70.0%). The two CRs show 59.6% similarity and have an identical sequence region with a length of 295 bp. The mitogenome of M. thomsoni shows a novel gene arrangement compared with the pancrustacean ground pattern and is identical to that of M. sibogae, except for the two additional tRNAs (trnW and trnL1). Phylogenetic tree from maximum likelihood analysis using the concatenated sequences of 13 PCGs depicted M. thomsoni as one of the members of the superfamily Nephropoidea within Astacidea.

Complete mitochondrial genome of the hydrothermal vent ghost shrimp Paraglypturus tonganus (Crustacea, Axiidea, Callianassidae)

Abstract Ghost shrimps are burrowing decapods that serve as bioturbators and habitat providers in seafloor environments. The hydrothermal vent ghost shrimp, Paraglypturus tonganus, was collected from a hydrothermal vent in the Tonga Arc. This species has a mitochondrial genome (mitogenome) of 15,924 bp in length with an AT content of 66.1%. The mitogenome was identical to the typical gene arrangement and transcriptional polarity of the infraorder Axiidea. Paraglypturus tonganus showed 65.3–70.1% nucleotide similarity with the known mitogenomes of other axiid shrimps. These results are useful for understanding the phylogenetic relationships among the members of Axiidea within the decapods.

Freshwater Invertebrates of Jindo Island in Korea

We surveyed the freshwater invertebrates of Jindo Island twice on July and September 2016, as part of a joint faunal survey conducted to commemorate the 30th anniversary of the Korean Society of Systematic Zoology. Aquatic insects were not included in this study. We found 38 freshwater species from seven phyla: Porifera, Platyhelminthes, Nematomorpha, Mollusca, Annelida, Arthropoda, and Bryozoa. Twenty-one of the 38 species (55.3%) represented the first record of their respective species on Jindo Island. Among these species, a freshwater shrimp-parasitic isopod, Tachaea n. sp., was identified as a new species.

The complete mitochondrial genome of the Violet-spotted reef lobster Enoplometopus debelius (Crustacea, Astacidea, Enoplometopidae)

Abstract The violet-spotted reef lobster Enoplometopus debelius Holthuis, 1983 (Decapoda, Astacidea, Enoplometopidae) is found in the tropical reef areas of the Indo-Pacific region, and is a highly prized and very popular species in the aquarium trade industry. The complete mitochondrial genome of E. debelius has 15,641 base pairs consisting of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region of 746 bp. The base composition of E. debelius is 36.4% A, 35.3% T, 18.1% C, 10.3% G, and the species has an AT content of 71.7%. The E. debelius mitogenome was found to have a gene arrangement and transcriptional polarity identical to that of the Homarus americanus mitogenome, a representative of the arthropod ground pattern. Here, we present the complete mitogenome sequence of E. debelius, which is the first in the superfamily Enoplometopoidea. These data will provide a useful molecular resource for the phylogenetic study of the infraorder Astacidea/order Decapoda.