The mitochondrial genome of Faughnia haani (Stomatopoda): novel organization of the control region and phylogenetic position of the superfamily Parasquilloidea.

BACKGROUND: Stomatopod crustaceans are aggressive marine predators featuring complex compound eyes and powerful raptorial appendages used for "smashing" or "spearing" prey and/or competitors. Among them, parasquilloids (superfamily Parasquilloidea) possess eyes with 2-3 midband rows of hexagonal ommatidia and spearing appendages. Here, we assembled and analyzed the complete mitochondrial genome of the parasquilloid Faughnia haani and explored family- and superfamily-level phylogenetic relationships within the Stomatopoda based on mitochondrial protein coding genes (PCGs). RESULTS: The mitochondrial genome of F. haani is 16,089 bp in length and encodes 13 protein coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region that is relatively well organized, containing 2 GA-blocks, 4 poly-T stretches, various [TA(A)]n-blocks, and 2 hairpin structures. This organized control region is likely a synapomorphic characteristic in the Stomatopoda. Comparison of the control region among superfamilies shows that parasquilloid species are more similar to gonodactyloids than to squilloids and lysiosquilloids given the presence of various  poly-T stretches between the hairpin structures and [TA(A)]n-blocks. Synteny is identical to that reported for other stomatopods and corresponds to the Pancrustacea ground pattern. A maximum-likelihood phylogenetic tree based on PCGs revealed that Parasquilloidea is sister to Lysiosquilloidea and Gonodactyloidea and not to Squilloidea, contradicting previous phylogenetic studies. CONCLUSIONS: The novel phylogenetic position of Parasquilloidea revealed by our study indicates that 'spearing' raptorial appendages are plesiomorphic and that the 'smashing' type is either derived (as reported in previous studies) or apomorphic. Our results raise the possibility that the spearing raptorial claw may have independently evolved twice. The superfamily Parasquilloidea exhibits a closer relationship with other stomatopod superfamilies with a different raptorial claw type and with dissimilar numbers of midband rows of hexagonal ommatidia. Additional studies focusing on the assembly of mitochondrial genomes from species belonging to different genera, families, and superfamilies within the order Stomatopoda are warranted to reach a robust conclusion regarding the evolutionary history of this iconic clade based on mitochondrial PCGs.

Complete mitochondrial genome of the European common barnacle Perforatus perforatus Bruguière, 1789 (balanomorpha: balanidae).

This study is the first to sequence the complete mitochondrial genome (mitogenome) of Perforatus perforatus Bruguière, 1789 (Balanomorpha: Balanidae). The 15,536-bp long P. perforatus mitogenome contained a typical set of animal mitochondrial genes, along with one control region. The P. perforatus mitogenome had an inverted gene block (trnP-ND4L-ND4-trnH-ND5-trnF) between trnS(gct) and trnT. This inverted gene block had been detected six species in three subfamilies of the Balanidae family (Balaninae, Acastinae and Megabalaninae), but our results show that it is also present in Concavinae, in which P. perforatus is included. The phylogenetic tree based on the concatenated sequences of the 13 protein-coding genes and two rRNA genes showed that P. perforatus is closely associated with Acasta sulcate and Balanus trigonus within Balanidae.

Population genetic analysis reveals secondary contact between Eriocheir sinensis and E. japonica in South Korea.

BACKGROUND: The Chinese mitten crab (Eriocheir sinensis) and the Japanese mitten crab (E. japonica) of the family Varunidae, which are also critical fishery species in their native habitats, including China, Japan, and South Korea, exhibit a rare migration life history for the decapod life cycle. Eriocheir sinensis and E. japonica in South Korea may have originated from speciation or secondary contact in South Korea after speciation of these two species; however, the genetic relationship between these South Korean populations remains unclear, and need to be clarified. OBJECTIVE: This study examined the population genetic properties of E. sinensis and E. japonica in South Korea to reveal the origin of their co-existence. METHODS: Mitochondrial DNA cytochrome c oxidase I sequences of 120 E. sinensis and E. japonica from 6 sampling sites in South Korea were sequenced. Their genetic diversity and haplotype data were compared to previously reported data from the Chinese mainland, Taiwan, Japan, and Russia. RESULTS: The haplotype network, analysis of molecular variance, FST values, Mantel test, and Bayesian skyline plot results of South Korean E. sinensis and E. japonica demonstrated that E. sinensis and E. japonica were isolated from their central populations, Chinese and Japanese populations, by the distance due to the temperature, salinity, ocean current flow, or a geohistorical event. In addition, genetic analysis indicated that the South Korean populations of the two species were marginal populations, exhibiting low genetic diversity, significant negative neutrality values, and radial haplotype networks. The current results also suggest that the Geum River is an overlapping habitat for the natural populations of E. sinensis and E. japonica in South Korea. Further research is required to examine the geohistorical and evolutionary event between E. sinensis and E. japonica in South Korea. CONCLUSIONS: The co-existence of E. sinensis and E. japonica in South Korea may have originated from secondary contact after their speciation.

Cryptic diversity and population genetic structure of the mantis shrimp Oratosquilla oratoria in South Korea.

BACKGROUND: The Japanese mantis shrimp Oratosquilla oratoria has two genetic lineages in its Chinese and Japanese populations, which are considered cryptic species. However, the Korean O. oratoria populations have only been studied morphologically, and their genetic diversity pattern remains unknown. OBJECTIVE: To examine the genetic diversity of the Korean O. oratoria populations to explore its cryptic diversity and underlying processes. METHODS: We sequenced the mitochondrial cytochrome c oxidase I gene of 107 O. oratoria individuals from 8 sampling sites in South Korea. Their genetic diversity and haplotype data were compared to previously reported data from 16 Chinese and 6 Japanese populations. RESULTS: The haplotype network, analysis of molecular variance, FST values, and Bayesian skyline plot of the Korean O. oratoria populations confirmed that they were divided into two genetic lineages corresponding to the two previously identified cryptic species, which might be correlated to ocean currents and water temperature. In addition, the population genetic analysis indicated that both lineages had high genetic diversity. Although the Geoje region belongs to the southern group, it only contained lineage N, which could be related to the specific environmental characteristics of Geoje or the hybridization of the two lineages of O. oratoria. CONCLUSION: Korean O. oratoria populations have enough cryptic diversity to be described as cryptic species and are correlated with ocean currents and water temperatures. Lineage N dominance in Geoje might be related to environmental characteristics or hybridization.

First record of the complete mitochondrial genome of the mantis shrimp, Gonodactylaceus randalli (Manning, 1978) (Stomatopoda: Gonodactylidae).

Biofouling has long been known as a major route for the invasion by non-indigenous species. The mantis shrimp, Gonodactylaceus randalli, is the first stomatopod species that has been identified in a biofouling community. In this study, we sequenced and analyzed the complete mitochondrial genome sequence of this species for the first time. Its mitochondrial genome is 15,907 bp in length and comprises 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding A + T-rich region. The overall base composition in the heavy strand is as follows: A: 37.3%, T: 31.3%, G: 11.9%, and C: 19.4%, with a G + C content of 31.3%. The phylogenetic analysis revealed that G. randalli belonged to the families Protosquillidae, Gonodactylidae, and Takuidae, in the same clade, within the superfamily Gonodactyloidea. This is the first record of the complete mitochondrial genome sequence of the genus Gonodactylaceus.

Complete mitochondrial genome of the mantis shrimp Taku spinosocarinatus (Fukuda, 1909) (Stomatopoda: Gonodactyloidea: Takuidae) in South Korea.

The superfamily Gonodactyloidea is polyphyletic because of Hemisquillidae, but to date, mitochondrial genome of that family does not exist. As valuable data that can be compared in the future with that family within this superfamily, we report the first complete mitochondrial genome sequence of Taku spinosocarinatus of the family Takuidae. The mitochondrial genome is 15,960 bp in length and consists of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding A + T rich region. The overall base composition in the heavy strand was as follows: A: 34.2%, G: 13.4%, C: 19.8%, and T: 32.6%, with a G + C content of 33.2%. Phylogenetic analysis revealed that this species was most closely related to Gonodactylus chiragra of Gonodactylidae, registered with NCBI to date. The result of this study will enable additional comparisons between families in the future.

Complete mitochondrial genome of the mantis shrimp, Chorisquilla orientalis Hwang, Ahyong, & Kim, 2018 (Stomatopoda: Protosquillidae).

In this study, we determined the mitochondrial genome of a stomatopod, Chorisquilla orientalis, collected from Korean waters. The complete mitochondrial genome comprised 15,880 bp, encoding 13 proteins, 22 transfer RNAs, 2 ribosomal RNAs genes, and a non-coding A + T rich region. The overall base composition in the heavy strand was A: 35.5%, G: 12.4%, C: 18.3%, and T: 33.7%, with a G + C content of 30.8%. Phylogenetic analysis showed that C. orientalis belonged to the families Gonodactylidae and Takuidae in the same clade, and to the superfamily Gonodactyloidea within Stomatopoda. This is the first record of the complete mitochondrial genome sequence of the family Protosquillidae.

A new species of Chorisquilla Manning, 1969 (Stomatopoda: Protosquillidae) from Korea and Japan with redescription of C. mehtae Erdmann Manning, 1998.

A new species of protosquillid mantis shrimp is described from the coastal waters of Korea and Japan. Chorisquilla orientalis n. sp. is distinguished from congeners by the combination of deep grooves and pits on the dorsal surface of abdominal somite 5, 8-14 spines on lateral margin of the telson, numerous minute dorsal spines on the telson and abdominal somite 6, and large, pyriform submedian bosses on the telson preceded by a small rounded boss. Chorisquilla orientalis is morphologically closest to C. mehtae Erdmann Manning, 1998, from Indonesia, but differs chiefly in the dorsal ornamentation of abdominal somite 6 and the telson and reaches a considerably larger size. Chorisquilla orientalis n. sp. shows developmental changes from juvenile to adult in the shape of the ocular scales and anterior margin of lateral plates of carapace, and in the number of lateral spines on telson. Also, C. mehtae Erdmann Manning, 1998, which, to date has not been adequately illustrated, is redescribed and figured. A key to the Korean gonodactyloids is presented.

Metagenomic analysis of the marine coastal invertebrates of South Korea as assessed by Ilumina MiSeq.

Metagenomic analysis was carried out for the first time on the marine coastal invertebrates of South Korea. Samples collected from coastal areas of Korea were filtered through a 63 µm mesh, then their 18S rDNA V4 regions were amplified. High-throughput sequencing of PCR amplicons using Illumina MiSeq and BLAST against the SILVA database showed that a total of 319 eukaryotic Operational Taxonomic Units were identified at the species level. Annelida, Arthropoda, Mollusca, Nematoda, and Platyhelminthes and for 92.23% of the total 103 metazoan species belonging to 101 genera, 75 families, and 10 phyla. Of these, several taxa previously unreported to exist in Korea were detected at the family level compared with the integrated database from three main Korean biodiversity DBs (MABIK, KOMBIS, and MRBR). Analysis of beta diversity of the community structure of invertebrates indicated that the composition of marine invertebrates is likely to be affected by habitat type rather than geographical distance. The present study showed that metagenomic high-throughput technology can be used to unravel species diversity and for various studies regarding marine invertebrate community structure.