Complete mitochondrial genome of saw-jawed monocle bream Scolopsis ciliata and its phylogenetic relationship in genus Scolopsis

The complete mitochondrial genome of the saw-jawed monocle bream, Scolopsis ciliata was deter�mined by the next generation sequencing (NGS) technique. The circular mitogenome of S. ciliata (16,733 bp) encoded the canonical 37 genes including 13 proteins, 22 tRNA genes, 2 rRNAs (12S rRNA and 16S rRNA), and two non-coding regions; the origin of light strand replication (OL) and the putative control region (D-Loop). The gene arrangement of the S. ciliata mitogenome was identical to its rela�tive, Scolopsis vosmeri. Phylogenetic analysis based on the full mitochondrial genome sequences showed that S. ciliata is most closely related to S. vosmeri with 83% nucleotide sequence identity. The mitogenome information of S. ciliata would be the useful information to understand the evolutional relationship of fishes in genus Scolopsi

Environmental DNA (eDNA) metabarcoding: Diversity study around the Pondok Dadap fish landing station, Malang, Indonesia

Molecular identification of species is now fast growing and currently widely applied method in the diversity estimation of aquatic biota; even though morphological identification is still carried out. The molecular approach is beneficial complementing on regular surveys e.g. use of nets, traps, fishing rods, and even with poisons. In this study, the eDNA metabarcoding was applied to water samples around the Pondok Dadap fish landing station, Indonesia to determine the diversity of fish around the waters and also to identify marine fish landed in this area. Molecular identification was carried out on fish samples obtained from the fish market improved GenBank database on COI and ITS. While, seawater samples were carried out by using the next-generation sequencing (NGS) platform to obtain the eDNA metabarcoding data for the first time. Molecular identification obtained 34 species (68 sequences of COI and ITS regions) belonging to 28 genera, 18 families, 4 orders, while the eDNA metabarcoding approach identified 53 marine fish species by using the MiFish pipeline representing 38 genera, 27 families, and 7 orders. From the present study, we can able to estimated fish diversity by eDNA metabarcoding, and this finding will be helpful for baseline data preparation for future effective management of resources in this area

Complete mitochondrial genome of green shrimp, Chlorotocus crassicornis (Crustacea: Decapoda: Pandalidae) in Korean water

The complete mitochondrial genome of green shrimp, Chlorotocus crassicornis (Costa, 1871) was generated by the combination of next-generation sequencing platform and long PCR technique. The mitochondrial genome of C. crassicornis was 16,500 bp, in which 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a putative control region was encoded. Based on the 13 protein-coding genes region, the phylogenetic tree was clearly demonstrated that C. crassicornis is closest to Pandalopsis japonica and Pandalus borealis with 77% identity. This mitogenome information will be helpful for the further studies of deep-sea fisheries resources management strategies in Korea including C. crassicornis species

Complete mitochondrial genome of Staghorn damselfish, Amblyglyphidodon curacao (Perciformes, Pomacentridae)

The complete mitochondrial genome of the Staghorn damselfish, Amblyglyphidodon curacao was determined by next-generation sequencing (NGS) platform. The circular mitochondrial genome of A. curacao (16,612 bp) encoded the 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions (origin of light strand replication (OL) and the control region (D-Loop)). All the tRNAs have typical clover-leaf structures except for tRNA-Ser. Phylogenetic analysis based on the currently reported mitochondrial genomes in Pomacentridae showed that A. curacao was most closely related to Amphiprion frenatus. The complete mitogenome sequence of A. curacao would provide essential genetic information of Pomacentrinae related to them for their scientific management in the coral-reef ecosystem in Indonesian waters

Sequence and phylogenetic analysis of the complete mitochondrial genome for the grey stingfish Minous monodactylus (Scorpaeniformes: Synanceiidae)

The mitochondrial genome sequence of Minous monodactylus (16,459 bp) was determined by the MiSeq platform for the first time in the genus Minous. It encoded the 37 genes (13 protein-coding genes, 22 tRNAs, and two ribosomal RNAs) and two conserved noncoding regions; control region (D-loop) and the origin of light strand (OL). Twenty-eight genes were encoded on the heavy (H) strand, while eight tRNAs and ND6 genes were on the light (L) strand. According to the phylogenetic analysis with other complete mitogenomes from order Scorpaeniformes, M. monodactylus was clustered with Synanceia verrucosa as family Synanceiidae with 81% sequence identity

The complete mitochondrial genome of spearnose grenadier, Coelorinchus multispinulosus, Katayama, 1942 (Gadiformes: Macrouridae)

The complete mitochondrial genome of Coelorinchus multispinulosus was determined using the MiSeq platform. The mitogenome of C. multispinulosus (15,937 bp) contained 13 protein-coding genes, 22 tRNAs, two ribosomal RNAs (12S and 16S), and a control region (D-Loop). The G + C content of its mitogenome was 44.69%, which was lower than A + T contents (55.31%). Unusual start codon (GTG) was identified in three protein-coding genes including COX1, ND2, and ND3. Incomplete stop codons (TA–/T–) were shown in six genes including COX1, COX2, COX3, ND3, ND4, and ATP6. Based on the phylogenetic tree with the currently reported mitogenomes in the family Macrouridae, C. multispinulosus was most closely related to Coelorinchus kishinouyei with 85% nucleotide sequence identity

Molecular Identification and Phylogenetic Trees Reconstruction of Blue Swimming Crabs (Decapoda: Portunidae) from Pangpang Bay, Banyuwangi

Crabs are a group of Decapoda (Portunidae) that act as keystone species from Pangpang Bay as the marine benthic organism. Besides having an ecological function, crab also provides essential components for human health. The crab identification technique is usually conducted based on morphology and anatomy characteristics, in which certain body parts as the key for identification. This study used two identification methods, i.e. morphological features and a molecular approach. Although morphological identification has been carried out, the molecular techniques provide better accuracy and, at the same time, provide additional information about the characteristics of mitochondrial DNA. The purpose of this study is to identify the blue swimming crab caught by a traditional fisherman at Pangpang Bay, Banyuwangi, based on mitochondrial DNA sequence on cytochrome c oxidase subunit I, and reconstructed the phylogenetic tree including genetic distance also was analysed. The nucleotide sequences of the COI gene were analysed by Chromas, Clustalω, Reverse-Complement, and the MegaX. The phylogenetic tree and genetic distance calculations were carried out using Mega X software through the Neighbor-Joining (NJ) Algorithm with the addition of several sequences from the NCBI online database. This study confirmed that the specimen of Pangpang Bay is Portunus pelagicus (BWIPP001 and BWIPP003) and Portunus sanguinolentus (BWIPP002). The species of P. pelagicus have 99.99% similarities with the same species (KJ168060) from China, while the P. sanguinolentus is close to the same species (EU284144) with a per cent identity is 99.97%. The genetic distance, for P. pelagicus and P. sanguinolentus, were in range of 0.00-0.066 and 0.00-0.005 respectively

Characterization of the complete mitochondrial genome of Chionobathyscus dewitti (Perciformes, Channichthyidae)

The complete mitochondrial genome sequence of the Icefish, Chionobathyscus dewitti was determined by the Next Generation Sequencing (NGS) analysis. The complete mitogenome was 17,452 bp in length, which encoded the canonical 13 protein-coding genes, 22 tRNAs, two rRNAs, and two non-coding regions. As shown in the other notothenids, translocation of ND6 and an additional non–coding region were identified, which is different from the typical vertebrate mitochondrial genomes. The C. dewitti was clustered distinctly from the those in the Chinodraco and Chaenocephalus, which supported the idea that this species should be classified in the different genus, Chionobathyscus in the family Channichthyidae

Assessment of fish biodiversity in four Korean rivers using environmental DNA metabarcoding

Environmental DNA (eDNA) metabarcoding is a cost-effective novel approach to estimate biodiversity in an ecosystem. In this study, the MiFish pipeline was employed to test if the system methodology is sufficiently reliable to estimate fish biodiversity in Korean rivers. A total of 125 unique haplotypes and 73 species were identified at the species level from 16 water samples collected from a single survey in four Korean rivers (Hyeongsan, Taehwa, Seomjin, and Nakdong). Among the four rivers, the highest species richness was recorded in the Seomjin River (52 species), followed by the Taehwa (42 species) and Hyeongsan (40 species) rivers. The Nakdong River (26 species) presented the lowest species richness and number of endemic species, presumably due to its metropolitan location and anthropogenic impacts, such as dams or weirs. We were also able to detect that five exotic species (Carassius cuvieri, Cyprinus carpio, Cyprinus megalophthalmus, Lepomis macrochirus, and Micropterus salmoides) are widely distributed in all surveyed rivers, a situation that might be problematic in terms of conservation. Our findings indicate that the eDNA metabarcoding technique is one of the most cost-effective scientific tools available for the management and conservation of the freshwater fish resources available in Korea. However, the low number of 12S sequences of endemic species in the database and low resolution of the MiFish region for differentiating several taxa should be upgraded for their wide use