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Complete mitochondrial genome and phylogenetic analysis of Callorhinus ursinus: an endangered species from South Korea.

ABSTRACT: We present the complete mitochondrial genome and a phylogenetic analysis of Callorhinus ursinus, the northern fur seal, determined using Illumina next-generation sequencing (NGS) technology. The total length of the mitogenome was 17,154 bp, which consisted of 13 protein-coding genes, two ribosomal RNA genes, 22 tRNA genes, and one control region. The base composition of the entire mitogenome was 33.5% (A), 26.3% (C), 13.9% (G), and 26.3% (T) with an A + T bias of 59.8%. The control region contained two types of tandem repeats. A neighbour-joining (NJ) tree was constructed and comprised two clades with C. ursinus forming a monophyletic group. Data produced in this study will aid exploration of the genetic diversity of endangered C. ursinus and contribute to molecular identification of this species.

SUBMITTER: Lee SM

PROVIDER: S-EPMC7800871 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Callorhinus ursinus

Project description:Callorhinus ursinus overview

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Project description:Northern fur seal (Callorhinus ursinus) genome sequencing and assembly

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The complete mitochondrial genome and phylogenetic position of the Endangered red-spotted grouper Epinephelus akaara (Perciformes, Serranidae) collected in South Korea.

Project description:We determined complete nucleotide sequences of the mitochondrial genome of two individuals of the Red-spotted grouper, Epinephelus akaara (Perciformes, Serranidae), caught in South Korea. The mitochondrial genome had 16,795 base pairs (bp) and 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region. The two mt genomes were highly homologous (99.71% similarity). The two mt genomes of E. akaara analyzed in this study were found in Clade I with those of E. awoara, E. fasciatomaculosus, E. sexfasciatus, E. diacanthus, E. sticus, and E. morio. Here, we reported the complete mt genome sequence of E. akaara, suggesting that this may use in phylogenetic studies of Epinephelus.

| S-EPMC7800882 | biostudies-literature

Complete mitochondrial genome of the Endangered species Ellobium chinense (Pulmonata, Ellobiidae) from Korea.

Project description:The complete mitochondrial genome of Ellobium chinense (Ellobioidea, Ellobiidae), an Endangered species in South Korea, is reported here for the first time. The mitogenome of E. chinense is 13,979 base pairs in total length and includes 13 PCGs, small and large rRNAs, and 21 tRNAs. Twelve genes are encoded on the light-strand and 24 genes on the heavy-strand. Compared to four other ellobiid species, the PCGs of E. chinense have a conserved gene order except for the positions of ND4L and ND4. These data provide useful molecular information for phylogenetic studies concerning ellobiids and related species.

| S-EPMC7800294 | biostudies-literature

The mitochondrial genome of Milvus migrans (Aves, Accipitriformes, Accipitridae), an endangered species from South Korea.

Project description:The complete mitochondrial genome sequence of black kite, Milvus migrans, one of the most common diurnal raptor, was characterized using next generation sequencing. The whole genome size was 18,016?bp and consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, a putative control region (CR), and a second control region (pseudo-CR). A frameshift mutation was found in the ND3 gene. Phylogenetic analysis illustrated monophyly of the subfamily Melieraxinae with high statistical support. The genetic resource obtained here will help to resolve taxonomic issues related to subspecies of M. migrans and will act as a starting point for conservation genetics.

| S-EPMC7799986 | biostudies-literature

The complete mitochondrial genome of an endangered triton snail Charonia lampas (Littorinimorpha: Charoniidae) from South Korea.

Project description:The complete mitochondrial genome of an endangered triton snail Charonia lampas (Littorinimorpha: Charoniidae) from South Korea was determined with the size of 15,330 bp, which contained 13 protein-coding genes, 22 tRNAs, and two rRNAs. The overall features of the mitochondrial genome are similar to those of typical gastropod mitochondrial genomes, except for the absence of a control region (CR): a conserved gene order, a high A + T content (67.45% for C. lampas), preference for AT-rich codons, etc. It is the second mitochondrial genome reported from this species after Cho et al. (2017), and there is ca. 98% sequence similarity between those of the species. According to the maximum-likelihood tree, C. lampas placed within the monophyletic Tonnoidea, forming a monoclade with Cypraeoidea and Stromboidea within Littorinimorpha. Interestingly, we confirmed that Vermetoidea is placed at the basal position of the monophyletic Littorinimorpha.

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Complete mitochondrial genome of Callipogon relictus Semenov (Coleoptera: Cerambycidae): a natural monument and endangered species in Korea.

Project description:In the present study, we report the first complete mitochondrial DNA genome of the genus Callipogon based on C. relictus, a natural monument and endangered species in South Korea. The mitogenome is 15,742 base pairs with 13 protein coding genes (PCGs), two rRNAs, 22 tRNAs, and a 1033?bp long AT-rich region. The overall base composition was 67.3% AT and 32.7 GC. Among 13 PCGs, seven genes (Nad2, Atp8, Atp6, Nad4L, Nad6, Cob, Nad1) harbour the typical stop codon TAA or TAG, whereas remaining five genes terminate with T. Interestingly, Cox3 employs AGA as the termination codon.

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Longitudinal study of northern fur seal (Callorhinus ursinus) hematology.

Project description:Although the causes have not been specified yet, wild populations of northern fur seals (Callorhinus ursinus) have been decreasing, which is why conservation techniques such as captive breeding and health maintenance should be established. Hematological parameters can be used to maintain the health status of northern fur seals kept in captivity for artificial reproduction and public education. Year-round fluctuations of blood parameters have not been examined for northern fur seals due to the difficulties in obtaining serial blood samples from wild animals during the oceanic migration period from late autumn to spring. In this study, blood samples were collected from four captive northern fur seals and analyzed monthly for more than three years to clarify the seasonal fluctuation patterns in 14 hematological parameters. Many hematological parameters seemed to be seasonal patterns: summer-autumn and winter-spring; leukocyte-related parameters were higher in summer and autumn than in winter and spring; erythrocyte-related parameters were lower in summer and autumn than in winter and spring. Significant seasonal differences in nine of the 14 parameters were observed using a generalized linear mixed model (GLMM) analysis. These results have improved our understanding of the seasonal patterns of hematological characteristics in the northern fur seal and can contribute to the health care of protected or captive northern fur seals.

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Characteristic of complete mitochondrial genome and phylogenetic status of a muskrat, Ondatra zibethicus (Rodentia: Cricetidae) in South Korea.

Project description:The complete mitochondrial genome of Muskrat, Ondatra zibethicus (Rodentia: Cricetidae) in Korea was sequenced for the first time using the next-generation sequencing method to understand its evolutionary relationship and to be helpful to establish a management plan. This mitogenome was 16,350 base pairs in length, containing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. Its overall A, C, G, and T contents were 32.0%, 26.9%, 12.6%, and 28.5%, respectively. A + T content (63.7%) was higher than G + C content (36.3%). We made the phylogenetic tree of muskrat and other 12 species of order Rodentia distributed in Korea.

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A comparison of gene organisations and phylogenetic relationships of all 22 squamate species listed in South Korea using complete mitochondrial DNA.

Project description:Studies using complete mitochondrial genome data have the potential to increase our understanding on gene organisations and evolutionary species relationships. In this study, we compared complete mitochondrial genomes between all 22 squamate species listed in South Korea. In addition, we constructed Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic trees using 13 mitochondrial protein-coding genes. The mitochondrial genes for all six species in the suborder Sauria followed the same organisation as the sequenced Testudines (turtle) outgroup. In contrast, 16 snake species in the suborder Serpentes contained some gene organisational variations. For example, all snake species contained a second control region (CR2), while three species in the family Viperidae had a translocated tRNA-Pro gene region. In addition, the snake species, Elapheschrenckii, carried a tRNA-Pro pseudogene. We were also able to identify a translocation of a tRNA-Asn gene within the five tRNA (WANCY gene region) gene clusters for two true sea snake species in the subfamily Hydrophiinae. Our BI phylogenetic tree was also well fitted against currently known Korean squamate phylogenetic trees, where each family and genus unit forms monophyletic clades and the suborder Sauria is paraphyletic to the suborder Serpentes. Our results may form the basis for future northeast Asian squamate phylogenetic studies.

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