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The chiton (Polyplacophora) occupies a significant position in molluscan evolutionary history as one of the most primitive groups within the phylum Mollusca. Acanthochitona defilippii (Tapparone-Canefri 1874) (Chitonida: Acanthochitonidae) is a commonly found intertidal chiton species in South Korea. In this study, we characterized the complete mitochondrial genome of A. defilippii (14,999 bp long), comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A + T rich region (166 bp). The base composition is as follows: 31.82% for A, 11.63% for C, 16.69% for G, and 39.86% for T. We reconstructed a maximum likelihood (ML) tree to elucidate phylogenetic relationships among the eight chitonid families using the nucleotide sequences of all PCGs. The ML tree revealed that A. defilippii clustered with Acanthochitona avicula (BP 100) within the family Acanthochitonidae. Acanthochitonidae formed a sister group with Mopaliidae. The results could provide a valuable understanding the phylogenetic relationships of chitonid species.
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Bioinformatics, the interdisciplinary field that combines biology, computer science, and data analysis, plays a pivotal role in advancing our understanding of life sciences. In the African context, where the diversity of biological resources and healthcare challenges is substantial, fostering bioinformatics literacy and proficiency among students is important. This perspective provides an overview of the state of bioinformatics literacy among African students, highlighting the significance, challenges, and potential solutions in addressing this critical educational gap. It proposes various strategies to enhance bioinformatics literacy among African students. These include expanding educational resources, fostering collaboration between institutions, and engaging students in research projects. By addressing the current challenges and implementing comprehensive strategies, African students can harness the power of bioinformatics to contribute to innovative solutions in healthcare, agriculture, and biodiversity conservation, ultimately advancing the continent's scientific capabilities and improving the quality of life for her people. In conclusion, promoting bioinformatics literacy among African students is imperative for the continent's scientific development and advancing frontiers of biological research.
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The ground beetle Synuchus nitidus (Motschulsky, 1861) (Carabidae: Harpalinae: Sphodrini) is one of the most common species in the forests of South Korea, which has the potential to be utilized as an environmental indicator. Here, we characterized the complete mitochondrial genome (mitogenome) of S. nitidus, which is the first in the harpaline tribe Sphodrini. Its genome is 16,392 bp in length and composed of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and an A + T rich region. In addition, we reconstructed a maximum likelihood tree to elucidate the phylogenetic position of Sphodrini among the seven harpaline tribes using nucleotide sequences of the 13 PCGs. The ML tree supported a monophyletic clade of the subfamily Harpalinae and showed a close relationship between Sphodrini and Lebinii with a low bootstrap value. The complete mitogenome of S. nitidus could be helpful for molecular species identification and exploring phylogenetic relationships among carabids.
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The worm snail Thylacodes adamsii (Mörch, 1859) (Littorinimorpha: Vermetidae) is a sessile gastropod that mainly inhabits rocky shores along the warm temperate to tropical ocean. Herein, the complete mitochondrial genome (mitogenome) of T. adamsii from South Korea was characterized. The genome is 14,913 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The genome organization and base composition of T. adamsii are similar to those of other vermetids. A phylogenetic tree was reconstructed using maximum likelihood based on the nucleotide sequences of the 13 PCGs; this tree supported the monophyly of Vermetidae. The complete mitogenome of T. adamsii can assist with molecular species identification and vermetid phylogenetic research in the future.
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This research offers a comprehensive exploration of the microbial communities associated with vector mosquitoes from South Korea. Aedes albopictus, Anopheles sinensis, and Culex molestus are vectors of pathogens, and understanding the intricacies of their microbiome profile is paramount for unraveling their roles in disease transmission dynamics. In this study, we characterized the microbiome of the midguts of adult female vector mosquitoes collected from different locations in South Korea. After DNA extraction from dissected mosquito midguts, we used the Illumina MiSeq next-generation sequencing to obtain sequences spanning the V4 hypervariable region of the bacteria 16S rRNA. Morphological and molecular characterization using 506-bp mitochondrial 16S rRNA was used to identify the mosquito species before amplicon sequencing. Across the three vector mosquitoes surveyed, 21 bacteria genera belonging to 20 families and 5 phyla were discovered. Proteobacteria and Bacteriodota were the major phyla of bacteria associated with the three mosquito species. There were significant differences in the gut microbiome genera composition between the species and little variation in the gut microbiome between individuals of the same mosquito species. Wolbachia is the most dominant genus in Aedes while Aeromonas, Acinetobacter, and unassigned taxa are the most common in An. sinensis. In addition to that, Chromobacterium, Chryseobacterium, and Aeromonas are dominant in Cx. molestus. This study sheds light on the complex interactions between mosquitoes and their microbiome, revealing potential implications for vector competence, disease transmission, and vector control strategies.
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Aedes , Bacterias , Culex , Mosquitos Vectores , ARN Ribosómico 16S , Animales , República de Corea , ARN Ribosómico 16S/genética , Aedes/microbiología , Mosquitos Vectores/microbiología , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Femenino , Culex/microbiología , Anopheles/microbiología , Microbioma Gastrointestinal , Microbiota/genética , ADN Bacteriano/genética , Filogenia , Análisis de Secuencia de ADN , Wolbachia/genética , Wolbachia/aislamiento & purificación , Wolbachia/clasificación , Secuenciación de Nucleótidos de Alto RendimientoRESUMEN
A freshwater mussel, Nodularia breviconcha (Mollusca: Bivalvia: Unionida) is endemic to Korean Peninsula. It has recently been taxonomically reexamined and elevated from a subspecies of N. douglasiae to an independent species. But population genetic studies for the species have rarely been conducted. To explore the population genetic structure of N. breviconcha, the nucleotide sequences of cytochrome oxidase subunit I(COI) and 16S rRNA genes from 135 N. breviconcha individuals, including 52 from this study and 83 from Choi et al. (2020). We found 23 COI and 11 16S rRNA genes haplotypes. Phylogeny, TCS network, Principal coordinates analysis, and spatial analysis of molecular variance performed with COI gene indicated that there are exist three different genetic lineages in the N. breviconcha populations: West lineage, Southwest lineage, and Southeast lineage. According to the time calibrated phylogeny, they are likely to be diverged during the late Miocene (8-6 Ma). Geographical distribution patterns of the three genetic lineages may be related to the formation of Taebaek and Sobaek-Noryeong mountain ranges in the Korean Peninsula occurred during the Miocene (30-10 Ma). The present results of this study will be helpful not only for the conservation, but also for the exploration of the population genetic structure of endemic freshwater mussels in the Korean Peninsula.
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Nodularia , Genes de ARNr , Nodularia/genética , Filogeografía , República de Corea , ARN Ribosómico 16S/genética , Genética de PoblaciónRESUMEN
The mitochondrial genome of a golden orb-web spider Trichonephila clavata (L. Koch, 1878) from South Korea is determined and characterized in detail, which is the second mitochondrial genome reported from this species: the first was published from the Chinese sample by Pan et al. (2016). It was 14,436 bp in length being composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and one control region (CR). It has a base composition of 35.99% for 'A,' 14.88% for 'G,' 9.09% for 'C,' and 40.04% for 'T.' Comparing the South Korean and Chinese mitochondrial genomes, we observed 8% nucleotide sequence differences between their CRs, caused by the different numbers and sorts of possessed tandem repeats, suggesting a promising molecular marker to distinguish South Korean individuals from Chinese ones. The phylogenetic trees using the maximum likelihood (ML) method were reconstructed with nucleotides (without 3rd codon position) and amino acids from 13 PCGs, respectively, which consistently confirmed that T. clavata (Subfamily Nephilinae) from South Korea and China are clustered together, distinctly separated from the other subfamily Araneinae in the monophyletic family Araneidae.
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A white-spotted flower chafer Protaetia brevitarsis seulensis widely distributed in Asian countries is traditionally used in oriental medicine. This study explored gene expression abundance with respect to wing development and metamorphosis in P. b. seulensis based on the large-scale RNA-seq data. The transcriptome assembly consists of 23,551 high-quality transcripts which are approximately 96.7% covered. We found 265 wing development genes, 19 metamorphosis genes, and 1,314 candidates. Of the 1,598 genes, 1,594 are included exclusively in cluster 4 with similar gene co-expression patterns. The network centrality analyses showed that wing development- and metamorphosis-related genes have a high degree of betweenness centrality and are expressed most highly in eggs, moderately in pupa and adults, and lowest in larva. This study provides some meaningful clues for elucidating the genetic modulation mechanism of wing development and metamorphosis in P. b. seulensis.
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Escarabajos , Perfilación de la Expresión Génica , Animales , Larva , RNA-Seq , TranscriptomaRESUMEN
The blotched nerite Nerita albicilla (Linnaeus 1758) is distributed in intertidal areas of the Indo-Pacific. In South Korea, it has been found only in the southernmost region of Jeju Island so far. Owing to its limited distribution, it can be a promising intertidal species helpful for monitoring global climate change effects in the Korean Peninsula. We performed population genetic analyses based on 393 COI haplotypes from 697 N. albicilla, including 167 from this study and 530 from public databases. The results showed that there are two distinct genetic lineages in N. albicilla: PAIO (Palearctic, Australasia, Indo-Malay, and Oceania) and Afrotropic lineages. DNA barcoding gap analyses indicated that the two lineages could be differentiated into two different species: N. albicilla (PAIO) and N. originalis sp. nov. (Afrotropic) (3.96%). Additionally, it was revealed that their divergence time was ca. 5.96 Ma and dramatic diversification of COI haplotypes occurred during the late Pliocene and Pleistocene. The results of MDA, BSP, and neutrality test implied recent population size expansion, which was estimated to be ca. 250 Ka. Finally, we discussed whether the observation of N. originalis sp. nov. in South Korea is due to the northward migration through ocean currents caused by global warming or due to artificial activity through marine transportation.
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ADN Mitocondrial , Variación Genética , Filogenia , ADN Mitocondrial/genética , Densidad de Población , República de CoreaRESUMEN
Background: Grasshoppers (Acridoidea, Orthoptera) are the dominant herbivores in grassland ecosystems worldwide. They can increase rangeland productivity by stimulating plant growth and accelerating nutrient cycling. This article presents a comprehensive checklist of grasshoppers in Mongolia. Until then, the available information was very scattered, based on old studies of Mongolian grasshoppers, recorded in a few international catalogues and databases, individual records and research work on agroecosystem communities. However, the available information on the composition of the Orthopteran fauna in Mongolia was sometimes unclear or non-existent and these dubious data were excluded from the present study. In addition, the grasshopper distribution analysis used the standardised personal collection of D. Altanchimeg. We also present a list of grasshoppers, as well as their distribution and abundance, in countries adjacent to Mongolia, such as Russia, China and South Korea. The surveys covered six types of natural zones: high mountain, taiga, forest-steppe, steppe, desert steppe and desert; desert steppe and steppe zones are the most widely distributed. We hope to have contributed significantly to the study of the distribution of grasshopper species in all these natural zones. New information: In this study, a total of three families of Acridoidea belonging to eight subfamilies, 17 tribes, 52 genera and 128 species are reported for the various natural zones. The recorded species belong to eight subfamilies: Gomphocerinae are the most numerous with 56 species recorded, followed by Oedipodinae (51 species), Thrinchinae (nine species), Melanoplinae (six species), Calliptaminae (three species), Dericorythinae, Acridinae, Egnatiinae (one species each).
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The long-necked woodwasp superfamily Xiphydrioidea belongs to the suborder Symphyta (Hymenoptera). Here we newly characterize the complete mitochondrial genome of the South Korean Euxiphydria potanini (Xiphydriidae) using next-generation sequencing: 16,500 bp long with 84.27% A + T content and 37 typical mitochondrial genes including those encoding 13 PCGs, 2 rRNAs, 22 tRNAs, and one A + T rich region. We compare the patterns of symphytan mitochondrial gene arrangement with those of an ancestral insect form and found some synapomorphic rearrangements in phylogenetic context. We use a variety of nucleotide and amino acid sequence alignments (thirteen mtPCGs and/or eight nDNAs) alongside step-by-step exclusions of long-branched taxa to elucidate the phylogenetic position of Xiphydrioidea and phylogenetic relationships among the seven symphytan superfamilies, except for Anaxyeloidea of which no mtgenome was available. The monophyly of symphytan superfamilies (with weak support for Pamphilioidea), sister-group relationship of Xiphydrioidea and Cephoidea, and Symphyta being paraphyletic to Apocrita, etc. are consistently supported by maximum likelihood and Bayesian inference trees. We also discuss the problematic phylogenetic positions of Orussoidea and Siricoidea and propose a hypothetical scenario of morphological character transition during hymenopteran evolution based on morphological key characteristics, such as the cenchrus and the wasp-waist.
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Genoma Mitocondrial , Himenópteros , Avispas , Animales , Genoma Mitocondrial/genética , Himenópteros/genética , Filogenia , Teorema de Bayes , Avispas/genética , NucleótidosRESUMEN
We present the complete mitochondrial genome of a Malaria vector Mosquito Anopheles sinensis Wiedemann, 1828 from South Korea. The mitochondrial genome is about 15,421 bp long and contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and an A-T rich region. The present data were compared with those from China with respect to PCG sequence differences, tRNA structure, gene order, and control region (CR) structure. An. sinensis mitochondrial genomes from northeast Asia share identical gene composition and gene order. In contrast, they have distinct differences in the CR within the range 8.75% (51/583 bp) to 9.95% (58/583 bp). The phylogenetic analysis showed that An. sinensis from South Korea was clustered together with those from China, but there existed distinct genetic distance between the two. Likewise, mitochondrial genome sequences from other Anopheles species were employed to infer phylogenetic relationships among the members of the genus Anopheles. This study further promotes the enrichment of An. sinensis mitochondrial genome data, providing useful information for their mitochondrial genetic differences along with geographical distances in northeast Asia.
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Methyl benzoate (MBe) is a volatile organic molecule found in various plants; it is used as an insect semiochemical. MBe also has a biorational insecticidal effect against various agricultural and urban arthropod pests. The present study was the first to assess the larvicidal potential of MBe against fourth-instar larvae of the mosquitoes Aedes albopictus (Skuse) and Culex pipiens (L.). A positive association was observed between MBe concentrations and larval mortality in both the species. The highest mortality recorded was 100% for Ae. albopictus and 56% for Cx. pipiens after 24 h of exposure to 200 ppm MBe. The lethal median concentration (LC50) values of MBe against fourth-instar larvae of Ae. albopictus and Cx. pipiens were 61 ppm and 185 ppm, respectively. These results suggest that MBe has great potential for use as an environmentally friendly larvicidal agent for mosquito control.
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Aedes , Culex , Insecticidas , Aceites Volátiles , Compuestos Orgánicos Volátiles , Animales , Benzoatos/farmacología , Insecticidas/química , Insecticidas/farmacología , Larva , Aceites Volátiles/química , Compuestos Orgánicos Volátiles/farmacologíaRESUMEN
The chiton Liolophura japonica (Lischke 1873) is distributed in intertidal areas of the northwestern Pacific. Using COI and 16S rRNA, we found three genetic lineages, suggesting separation into three different species. Population genetic analyses, the two distinct COI barcoding gaps albeit one barcoding gap in the 16S rRNA, and phylogenetic relationships with a congeneric species supported this finding. We described L. koreana, sp. nov. over ca. 33°24' N (JJ), and L. sinensis, sp. nov. around ca. 27°02'-28°00' N (ZJ). We confirmed that these can be morphologically distinguished by lateral and dorsal black spots on the tegmentum and the shape of spicules on the perinotum. We also discuss species divergence during the Plio-Pleistocene, demographic expansions following the last interglacial age in the Pleistocene, and augmentation of COI haplotype diversity during the Pleistocene. Our study sheds light on the potential for COI in examining marine invertebrate species discrimination and distribution in the northwestern Pacific.
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The land snail Ellobium chinense (L. Pfeiffer, 1855) (Eupulmonata, Ellobiida, Ellobiidae), which inhabits the salt marshes along the coastal areas of northwestern Pacific, is an endangered species on the IUCN Red List. Over recent decades, the population size of E. chinense has consistently decreased due to environmental interference caused by natural disasters and human activities. Here, we provide the first assessment of the genetic diversity and population genetic structures of northwestern Pacific E. chinense. The results analyzed with COI and microsatellites revealed that E. chinense population exhibit metapopulation characteristics, retaining under the influence of the Kuroshio warm currents through expansion of the Late-Middle and Late Pleistocene. We also found four phylogenetic groups, regardless of geographical distributions, which were easily distinguishable by four unidirectional and stepwise adenine-to-guanine transitions in COI (sites 207-282-354-420: A-A-A-A, A-A-G-A, G-A-G-A, and G-G-G-G). Additionally, the four COI hotspots were robustly connected with a high degree of covariance between them. We discuss the role of these covariate guanines which link to form four consecutive G-quadruplexes, and their possible beneficial effects under positive selection pressure.
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Complejo IV de Transporte de Electrones/genética , G-Cuádruplex , Gastrópodos/clasificación , Gastrópodos/genética , Guanina , Animales , Complejo IV de Transporte de Electrones/química , Gastrópodos/anatomía & histología , Variación Genética , Genética de Población , Guanina/química , Humanos , Repeticiones de Microsatélite , Filogenia , FilogeografíaRESUMEN
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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A giant water bug Lethocerus deyrollei (Hemiptera: Belostomatidae) is a large, predatory, and nocturnal hemipteran insect, which has been considered threatened and thus enrolled as an endangered species in South Korea and Japan. Here, we characterized the complete mitochondrial genome of L. deyrollei, which has a circular form with 19,295 bp in length, which is the longest when compared to those of the 111 hemipteran species reported so far. Its longest genome size is due to the extremely extended CR (4686 bp), which is much longer than those of China and Japan. It consisted of a total of 37 genes (13 PCGs, 22 tRNA genes, and two rRNA genes) and one control region (CR). The genome composition and gene order were identical to those previously reported from the same species of China and Japan with over 99.7% sequence similarities except for CR and trnI. The nucleotide composition was highly A + T biased, accounting for 71% of the whole mitochondrial genome, as in other species of Nepoidea. Based on the aa sequences of 13 PCGs, we reconstructed a maximum likelihood tree, which indicated that the three mitochondrial genomes of L. deyrollei from South Korea, China, and Japan are grouped, and also Lethocerus, Belostomatidae, Nepoidea, Nepomorpha, Heteroptra are strong monophyletic groups, respectively.
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The mitochondrial genome of the Endangered freshwater snail Koreoleptoxis nodifila (Caenogastropoda: Semisulcospiridae) from South Korea is determined and characterized in detail. It is 15,737 bp in length being composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one control region. It has a base composition of 31.23% for A, 16.29% for G, 17.84% for C, and 34.64% for T. The phylogenetic trees reconstructed based on the maximum-likelihood (ML) method and Bayesian inference (BI) confirmed that K. nodifila belongs to the Semisulcospiridae clade in the monophyletic caeonogastropod superfamily Cerithioidea.
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The complete mitochondrial genome of a two-spotted cricket Gryllus bimaculatus (Orthoptera: Gryllidae) from South Korea is determined and characterized in this study. The circular genome is 16,075 bp long, which consists of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and an A + T-rich region. It has a base composition of A (40.35%), G (9.09%), C (16.80%), and T (33.76%). The gene order is identical to the ancestral gene arrangement pattern generally shown in arthropods, with the exception of an inversion of trnN-trnS1-trnE into trnE-trnS1-trnN. The maximum likelihood (ML) tree supports that G. bimaculatus is a distinct member of the monophyletic family Gryllidae.