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The complete mitochondrial genome of Leptychaster arcticus, deep-sea inhabited asteroid, was examined in this study. The complete mitogenome of L. arcticus is 16,253 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. No gene rearrangements or deletions were observed in compared to other Paxillosida. The ND4L and ND3 genes have 'ATT' as its start codon, which is a feature that has been found in previous echinoderm mitochondrial studies. In the ML tree analysis based on the superorder Valvatacea, it was difficult to establish the molecular phylogenetic relationship at lower taxonomic levels, such as order and family, due to the lack of asteroid molecular data available. Therefore, we expect to contribute to the expansion of the data and determine the phylogenetic positioning in future studies.
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Monitoring studies are necessary to understand the biodiversity of marine ecosystems and are useful for identifying and managing rare or invasive species. Because monitoring has traditionally relied only on visual surveys (e.g., trapping, netting, electrofishing, and SCUBA diving) with limited time and physical resources, environmental DNA (eDNA) analysis is being applied as an efficient monitoring method. This study compared whether the eDNA metabarcoding technique can replace the traditional visual survey in an ascidian fauna study. We designed ascidian-specific primers and identified a clear gap (3.75%) by barcoding gap analysis. Then, we collected seawater samples for eDNA analysis during the summer (August-September) of 2021 at three sites (Mokpo, Yeosu, and Uljin) in South Korea. In the survey sites of this study, 25 species were observed through literature and visual survey, among which 9 species were detected by metabarcoding and 16 species were not detected. On the other hand, 10 species were detected only by metabarcoding, and one of them was identified as Pyura mirabilis, an unrecorded species in South Korea. This study succeeded in detecting cryptic or rare species with one seawater collection, which can be used to determine their unexplored habitat. Therefore, we conclude that monitoring using eDNA is more efficient than visual surveys for detecting rare or cryptic ascidian species. We also suggest that, when combined with traditional monitoring methods, it could be a tool to complement ascidian fauna studies.
Asunto(s)
ADN Ambiental , Urocordados , Animales , Ecosistema , Código de Barras del ADN Taxonómico/métodos , Urocordados/genética , Monitoreo del Ambiente/métodos , BiodiversidadRESUMEN
In this study, we use a specimen from wild-caught individual to determine the complete mitochondrial genome of the Amur soft-shelled turtle (Pelodiscus maackii). The complete mitogenome of P. maackii has 16,258 bp in length and consists of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and one control region. The arrangement of genes of P. maackii is identical with previously reported mitogenomes in the family Trionychoidea. According to our result, the ML tree for the phylogenetic reconstruction revealed that the individuals used in present study is closely related with the previously reported sequences of P. sinensis (AY962573 and MG431983) in p-distance 0.7% and 2.5%.
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Liobagrus hyeongsanensis, Korean indigenous catfish, was reported as a new species in 2015. The complete mitochondrial DNA sequence of L. hyeongsanensis was sequenced by next-generation sequencing (NGS) analysis. The mitochondrial genome was assembled with 16,529 bp in length and encoded 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and one control region (D-loop). Also, the gene structures such as gene order and content were totally identical with the congeneric species. Molecular phylogenetic analysis determined the taxonomical position of L. hyeongsanensis in species level among the genus Liobagrus.
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In this study, the complete mitochondrial genome sequence of Anneissia pinguis was examined by next-generation sequencing analysis. The complete mitogenome of A. pinguis has 15,912 bp in length and 37 genomes consist of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and 1 control region (D-loop). Both gene orders and characteristics were in accordance with other species belonging to the phylum Echinodermata. Phylogenetic analysis revealed the establishment of molecular taxonomic relationship in class Crinoidea based on complete mitogenome.
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The complete sequence of the mitochondrial genome of Balanus trigonus Darwin, 1854 was examined using next-generation sequencing analysis. The complete mitogenome of B. trigonus has 15,336 bp in length and comprises 37 genes, namely, 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. Both the gene order and characteristics are consistent with those of other species within the family Balanidae. Phylogenetic analysis based on complete mitogenomes revealed taxonomic relationships among members of the family Balanidae.
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Environmental DNA (eDNA) method used by many ecologists as effective investigation tool can detect endangered species, rare species, and invasive species. In case of invasive species, eDNA method help to monitor the target species when the species was hard to detect through the traditional survey such as the early stage of invasion, low abundance, and larva or juvenile stage. The bryozoan, Bugulina californica, was known as a marine fouling invasive species in Korea since its first reported in 1978. This species expanded nationwide, and damages to ascidian aquaculture through attached on the ship hulls and artificial facilities. To monitor the distribution and biomass of invasive bryozoan, B. californica, the qPCR analysis of environmental DNA was performed on seawater samples from 12 harbors. In this study, we designed species-specific markers which can calculate the detected DNA copies of B. californica, and the presence and monitoring of this species can be more accurately estimated by environmental DNA analysis than by traditional survey, in which it is difficult to identify the species. Real-time PCR analysis using environmental DNA is an effective monitoring method that can determine both the distribution and the monthly change in biomass of B. californica in Korea.
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Anneissia intermedia (A.H. Clark, 1916) is a common crinoid found in waters along the coastlines of China, Japan, and Korea. In this study, we determined the complete mitogenome of A. intermedia. The genome was found to be 15,874 bp in length and consists of 13 protein-coding genes, 22 tRNAs, and 2 rRNAs. With the exception of Antedon mediterranea, the gene order and genetic characteristics of the A. intermedia mitogenome are identical with those of the mitogenomes of other crinoids. The complete mitogenome of A. intermedia will contribute to enhance our understanding of the phylogeny of crinoids.
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The complete mitochondrial genome of Yuukianura szeptyckii Deharveng & Weiner 1984 was sequenced, assembled, and annotated. The mitochondrial genome of Y. szeptyckii has a length of 15,771 bp and contains 13 protein-coding genes (PCGs), 22 transfer (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. Y. szeptyckii was closely clustered with the following species of Neanuridae: Bilobella aurantiaca and Friesea grisea.
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The complete mitochondrial genome of Allonychiurus kimi (Lee, 1973) was sequenced, assembled, and annotated. The mitochondrial genome of A. kimi is 14,386 bp in length and contains 13 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes. A. kimi was closely clustered with the following species of the family Onychiuridae: Onychiurus orientalis, Orthonychiurus forlsomi, and Tetrodontophora bielanensis.
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Iksookimia yongdokensis (Actinopterygii, Cypriniformes, Cobitidae) is known as endemic freshwater fish species in Korea. The total length of I. yongdokensis mitogenome is 16,640 bp, consisting of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and 1 control region (D-loop). The gene arrangement and content were identical with previously recorded mitogenomes of Iksookimia species. Phylogenetic analysis using PCGs and rRNA was examined by maximum likelihood method indicated that genus Iksookimia is taxonomically not stable status according to Iksookimia species and Cobitis species were grouped together.
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In this study, we determined the complete mitochondrial genome sequences of cyprinid freshwater fish, Microphysogobio jeoni, belonging to the subfamily Gobioninae in the order Cypriniformes. The complete mitogenome of M. jeoni was 16,602 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. The gene order was identical with other Microphysogobio species. The overall nucleotide composition of M. jeoni was A + T: 56.1% and G + C: 43.9%, with slightly AT bias. In the phylogenetic tree, M. jeoni and other congeneric species clearly formed a monophyletic clade, and each species distinguished against each other well.
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In this study, the complete mitochondrial genome sequences of Iksookimia hugowolfeldi, Korean loach species, was determined using next-generation sequencing analysis. The complete mitogenome of I. hugowolfeldi has 16,634 bp in length and consists of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and one control region (D-loop). Both gene orders and characteristics were exactly accord with mitochondrial genome of other species those belong to the family Cobitidae. Phylogenetic analysis revealed that the establishment of taxonomic relationship between Iksookimia and Cobitis has still uncompleted because of the not distinguished as monophyletic status.
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The Korean catfish, Liobagrus somjinensis, was recorded in 2010 as a new species of genus Liobagrus. The complete mitochondrial DNA sequence of L. somjinensis was sequenced by next-generation sequencing (NGS) analysis. The assembled mitogenome was 16,526 bp in length and encoded 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs. The gene arrangement, content, and total size were clearly identical with the congeneric species, L. mediadiposalis. Phylogenetic analysis based on nucleotide dataset, consisting PCGs and rRNA genes revealed the taxonomical relationship in species level among the genus Liobagrus.
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In this study, the mitogenome sequences of Korean indigenous stag beetle, Dorcus koreanus, was completely determined by next-generation sequencing analysis. The complete mitogenome of D. koreanus has 15,421 bp in length and consists of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and one control region. The gene orders and content were identical with previously recorded mitogenomes of Lucanidae species. Phylogenetic analysis based on mitogenome dataset, consisting PCGs was revealed the taxonomical position in the family Lucanidae.
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A new species of the genus Henricia Gray, 1840 that belongs to the family Echinasteridae is described from South Korea. Henricia epiphysialis sp. nov. has epiphyseal ossicles at the ends of the abactinal and lateral plates, and the abactinal and lateral spines form a hooked crown. The partial sequence of the mitochondrial COXI gene (537 bp) of H. epiphysialis sp. nov. was obtained, and the new species was morphologically and genetically compared with other related Henricia species.
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Genus Zacco specimens collected in this study were classified genetically as five species, Zacco platypus, Z. temminckii, Z. koreanus and two unidentified species, using DNA barcoding analysis based on 655 bp of mitochondrial cytochrome c oxidase subunit I (COI) gene. Two of unidentified species (Z. sp.1 and Z. sp.2) were considered to be unrecorded or new species of genus Zacco according to genetic distances between Zacco species. In addition, we determined a natural hybrid based on polymorphic base at the diagnostic positions displayed on nuclear recombination activating gene 1 (RAG1) gene (965 bp), and estimated paternal and maternal species of natural hybrid comparing phylogenetic tree between COI and RAG1, and Z. sp.1â × Z. koreanusâ, Z. sp.2â × Z. koreanusâ and Z. koreanusâ × Z. sp.1â individuals were confirmed. The habitat of natural hybrids of Z. koreanus between Z. sp.1 and Z. sp.2 was identified as Geum and Yeongsan River, respectively. In our data, only F1 hybrid generation was identified; however, generations after F1 hybrid or backcross were not demonstrated.
Asunto(s)
Núcleo Celular/genética , Cyprinidae/clasificación , ADN/genética , Mitocondrias/genética , Animales , Cruzamiento , Quimera , Cyprinidae/genética , Código de Barras del ADN Taxonómico , Femenino , Genes RAG-1/genética , Variación Genética , Masculino , Filogenia , República de CoreaRESUMEN
The bryozoan, Bugula neritina, is one of the most widespread sessile marine invasive species. Since its first discovery in Korea in 1978, the gradual increase in the distribution and abundance of this species resulted in a significant damage to growth of aquaculture. Environmental DNA (eDNA) is a potentially useful tool for species detection including rare, invasive and threatened native species. In this study, species-specific primers and probe were designed to amplify a 185-bp region based on mitochondrial COI of B. neritina for monitoring, and tested on environmental samples from 35 harbors of Korea in 2017. Among 35 sites monitored, B. neritina colonies were detected in 27 sites during field survey. However, B. neritina DNA was detected in all examined eDNA isolated from seawater. These results suggested that eDNA-based methods coupled with simple seawater sampling could be suitable for determining the distribution and abundance of B. neritina as complementary traditional monitoring.
Asunto(s)
Briozoos , Monitoreo del Ambiente/métodos , Especies Introducidas , Animales , Cartilla de ADN , República de Corea , Especificidad de la EspecieRESUMEN
The pregnancy and abortion process involves a complex mechanism with various immune cells present in the implantation sites and several hormones associated with pregnancy, such as leptin, ghrelin and nesfatin-1. However, the mechanism underlying spontaneous abortion by maternal T helper 17 (Th17) present in the implantation sites and nesfatin-1, which is of anorexigenic hormones, is not fully understood so far. Therefore, the purpose of this study was to examine the possible roles of Th17 cells present in the implantation sites and nesfatin-1 expressed in the uterus on spontaneous abortion using the CBA/j × DBA/2 mouse model. Th17 transcription factor, ROR-γt mRNA expression was significantly increased in the abortion sites compared with the implantation sites of abortion model mice on day 14.5 and 19.5 of pregnancy. In addition, the expression levels of IL(-1)7A mRNA were significantly higher in abortion sites than in implantation sites on day 14.5 and 19.5. Moreover, the nesfatin-1/NUCB2 protein and mRNA levels were increased in abortion sites compared with levels in implantation sites of both normal pregnant and abortion model mice on day 14.5 of pregnancy. Interestingly, nesfatin- 1/NUCB2 serum levels were not changed throughout the whole pregnancy in abortion model mice, but its serum level was dramatically increased on day 14.5, and then rapidly decreased on day 19.5 in normal pregnant mice. In this study, we showed for the first time the expression of nesfatin-1/NUCB2 mRNA and protein in implantation sites during pregnancy. The present results suggest that Th17 cells in the uterus may play an important role in the period of implantation and for maintenance of pregnancy. Furthermore, the present results suggest that Th17 cells in implantation sites may be a key regulator for maintenance of pregnancy and provides evidence that activation of these cells may be regulated by nesfatin-1/NUCB2. Further study is needed to elucidate the role of nesfatin-1 expressed in the uterus during pregnancy.
