Combination of explainable machine learning and conceptual density functional theory: applications for the study of key solvation mechanisms.

We present explainable machine learning approaches for the accurate prediction and understanding of solvation free energies, enthalpies, and entropies for different salts in various protic and aprotic solvents. As key input features, we use fundamental contributions from the conceptual density functional theory (DFT) of solutions. The most accurate models with the highest prediction accuracy for the experimental validation data set are decision tree-based approaches such as extreme gradient boosting and extra trees, which highlight the non-linear influence of feature values on target predictions. The detailed assessment of the importance of features in terms of Gini importance criteria as well as Shapley Additive Explanations (SHAP) and permutation and reduction approaches underlines the prominent role of anion and cation solvation effects in combination with fundamental electronic properties of the solvents. These results are reasonably consistent with previous assumptions and provide a solid rationale for more recent theoretical approaches.

Artificial neural networks for the prediction of solvation energies based on experimental and computational data.

The knowledge of thermodynamic properties for novel electrolyte formulations is of fundamental interest for industrial applications as well as academic research. Herewith, we present an artificial neural networks (ANN) approach for the prediction of solvation energies and entropies for distinct ion pairs in various protic and aprotic solvents. The considered feed-forward ANN is trained either by experimental data or computational results from conceptual density functional theory calculations. The proposed concept of mapping computed values to experimental data lowers the amount of time-consuming and costly experiments and helps to overcome certain limitations. Our findings reveal high correlation coefficients between predicted and experimental values which demonstrate the validity of our approach.

Characterization and Comparison of Two Complete Plastomes of Rosaceae Species (Potentilla dickinsii var. glabrata and Spiraea insularis) Endemic to Ulleung Island, Korea.

Potentilla dickinsii var. glabrata and Spiraea insularis in the family Rosaceae are species endemic to Ulleung Island, Korea, the latter of which is listed as endangered. In this study, we characterized the complete plastomes of these two species and compared these with previously reported plastomes of other Ulleung Island endemic species of Rosaceae (Cotoneaster wilsonii, Prunus takesimensis, Rubus takesimensis, and Sorbus ulleungensis). The highly conserved complete plastomes of P. dickinsii var. glabrata and S. insularis are 158,637 and 155,524 base pairs with GC contents of 37% and 36.9%, respectively. Comparative phylogenomic analysis identified three highly variable intergenic regions (trnT-UGU/trnL-UAA, rpl32/trnL-UAG, and ndhF/rpl32) and one variable genic region (ycf1). Only 14 of the 75 protein-coding genes have been subject to strong purifying selection. Phylogenetic analysis of 23 representative plastomes within the Rosaceae supported the monophyly of Potentilla and the sister relationship between Potentilla and Fragaria and indicated that S. insularis is sister to a clade containing Cotoneaster, Malus, Pyrus, and Sorbus. The plastome resources generated in this study will contribute to elucidating the plastome evolution of insular endemic Rosaceae on Ulleung Island and also in assessing the genetic consequences of anagenetic speciation for various endemic lineages on the island.

Comparison of Whole Plastome Sequences between Thermogenic Skunk Cabbage Symplocarpus renifolius and Nonthermogenic S. nipponicus (Orontioideae; Araceae) in East Asia.

Symplocarpus, a skunk cabbage genus, includes two sister groups, which are drastically different in life history traits and thermogenesis, as follows: The nonthermogenic summer flowering S. nipponicus and thermogenic early spring flowering S. renifolius. Although the molecular basis of thermogenesis and complete chloroplast genome (plastome) of thermogenic S. renifolius have been well characterized, very little is known for that of S. nipponicus. We sequenced the complete plastomes of S. nipponicus sampled from Japan and Korea and compared them with that of S. renifolius sampled from Korea. The nonthermogenic S. nipponicus plastomes from Japan and Korea had 158,322 and 158,508 base pairs, respectively, which were slightly shorter than the thermogenic plastome of S. renifolius. No structural or content rearrangements between the species pairs were found. Six highly variable noncoding regions (psbC/trnS, petA/psbJ, trnS/trnG, trnC/petN, ycf4/cemA, and rpl3/rpl22) were identified between S. nipponicus and S. renifolius and 14 hot-spot regions were also identified at the subfamily level. We found a similar total number of SSR (simple sequence repeat) motifs in two accessions of S. nipponicus sampled from Japan and Korea. Phylogenetic analysis supported the basal position of subfamily Orontioideae and the monophyly of genus Symplocarpus, and also revealed an unexpected evolutionary relationship between S. nipponicus and S. renifolius.

Wasabi Gone Wild? Origin and Characterization of the Complete Plastomes of Ulleung Island Wasabi (Eutrema japonicum; Brassicaceae) and Other Cultivars in Korea.

Korean wasabi occurs naturally on the young oceanic, volcanic Ulleung Island off the east coast of the Korean Peninsula. Although the Ulleung Island wasabi is reported as Eutrema japonicum and has been suggested to be morphologically identical to cultivars in Korea, very little is known about its taxonomic identity and relationship with other cultivars. In this study, we sequenced the complete chloroplast DNA sequences of three naturally occurring Ulleung Island wasabi plants and six cultivars ('Daewang', 'Daruma', 'Micado', 'Orochi', 'Green Thumb', and 'Shogun') from continental Korea and determined the taxonomic identity of Korean wasabi on Ulleung Island. The size and organization of the complete chloroplast genomes of the nine accessions were nearly identical to those of previously reported wasabi cultivars. In addition, phylogenetic analysis based on the complete plastomes suggested that Ulleung Island wasabi most likely comprises various wasabi cultivars with three chlorotypes ('Shogun', 'Green Thumb', and a unique Chusan type). Based on the complete plastomes, we identified eight chlorotypes for the major wasabi cultivars and the Ulleung Island wasabi. Two major groups (1-'Mazuma' and 'Daruma', and 2-'Fujidaruma'/'Shimane No. 3'/Ulleung Island wasabi/five cultivars in Korea) were also identified based on mother line genealogical history. Furthermore, different types of variations (mutations, insertions/deletions (indels), mononucleotide repeats, and inversions) in plastomes were identified to distinguish different cultivar lines and five highly divergent hotspots. The nine newly obtained complete plastomes are valuable organelle genomic resources for species identification and infraspecific phylogeographic studies on wild and cultivated wasabi.

Development of metabolomic biomarkers to discriminate the geographical origin of Korean and Russian snow crabs using CE-TOF/MS.

The quantity of snow crabs (Chionoecetes opilio) harvested in Korea is subject to seasonal restrictions; therefore, snow crabs are imported from Russia. Metabolites in snow crabs from two geographic origins were compared. The metabolites were subjected to metabolomic analysis to prevent fraudulent sales of marine products from a particular country. Capillary electrophoresis time-of-flight mass spectrometry was used. Seventy-seven target metabolites were identified using a mass spectral library. Through orthogonal partial least squares discriminant analysis, the top 25 biomarker candidates were evaluated based on p-values and fold changes. A total of 246 peaks (187 and 59 in the cation and anion modes, respectively) were identified. Among the biomarker candidates, 2-oxovaleric acid, asymmetric dimethylarginine, hypotaurine, and allo-threonine were selected as final biomarkers to unequivocally determine the geographic origin. Overall, metabolic analyses allowed us to differentiate snow crabs from different geographic origins. This method could also be extended of other marine products.

Chloroplast Genome Provides Insights into Molecular Evolution and Species Relationship of Fleabanes (Erigeron: Tribe Astereae, Asteraceae) in the Juan Fernández Islands, Chile.

Erigeron represents the third largest genus on the Juan Fernández Islands, with six endemic species, five of which occur exclusively on the younger Alejandro Selkirk Island with one species on both islands. While its continental sister species is unknown, Erigeron on the Juan Fernández Islands appears to be monophyletic and most likely evolved from South American progenitor species. We characterized the complete chloroplast genomes of five Erigeron species, including accessions of E. fernandezia and one each from Alejandro Selkirk and Robinson Crusoe Islands, with the purposes of elucidating molecular evolution and phylogenetic relationships. We found highly conserved chloroplast genomes in size, gene order and contents, and further identified several mutation hotspot regions. In addition, we found two positively selected chloroplast genes (ccsA and ndhF) among species in the islands. The complete plastome sequences confirmed the monophyly of Erigeron in the islands and corroborated previous phylogenetic relationships among species. New findings in the current study include (1) two major lineages, E. turricola-E. luteoviridis and E. fernandezia-E. ingae-E. rupicola, (2) the non-monophyly of E. fernandezia occurring on the two islands, and (3) the non-monophyly of the alpine species E. ingae complex.

Development of biomarkers to distinguish different origins of red seabreams (Pagrus major) from Korea and Japan by fatty acid, amino acid, and mineral profiling.

Red seabream (Pagrus major) has been one of the most popular fish in East Asia since early times. However, the discharge of nuclear wastewater into the sea following the Fukushima nuclear disaster in Japan has led to violations of the country of origin labeling. Therefore, the aim of the present study was to determine the origin of fish based on fatty acid, amino acid, and mineral analyses, and to develop biomarkers that can discriminate between Japanese and Korean red seabream. To identify the differences between the two groups, 29 fatty acid families, 17 amino acids, and 4 minerals were analyzed in 60 fish samples (standard sample collected in autumn), and fatty acid profiles were analyzed using heatmap with hierarchical clustering analysis and orthogonal projections to latent structures discriminant analysis. The top 10 fatty acids that were different between the two groups were selected from all seasonal fish samples by combining variable importance in projection scores and p-values. According to the receiver operating characteristic curve analysis results, we proposed percentage linoleic acid (C18:2n-6, cis) as a candidate biomarker with excellent sensitivity and specificity. This study introduces a strategy to identify the origins of red seabream using linoleic acid obtained from fatty acid analysis.

Phylogenetic relationships and genetic diversity of the Korean endemic Phedimus latiovalifolius (Crassulaceae) and its close relatives.

Phedimus latiovalifolius (Y.N.Lee) D.C.Son & H.J.Kim is exclusively distributed in the high mountains in the Korean Peninsula, mainly along the Baekdudaegan mountain range. Despite its morphological and distributional distinction from other Phedimus Raf. species, its taxonomic identity and phylogenetic relationship with congeneric species remain unclear. This study employs genotyping-by-sequencing-derived genome-wide single nucleotide polymorphisms to establish the monophyly of P. latiovalifolius and its relationship with closely related species. Genetic diversity and population differentiation of P. latiovalifolius are also assessed to provide baseline genetic information for future conservation and management strategies. Our phylogenetic analyses robustly demonstrate the monophyletic nature of P. latiovalifolius, with P. aizoon (L.) 't Hart identified as its closest sister lineage. There is no genetic evidence supporting a hybrid origin of P. latiovalifolius from P. aizoon involving either P. ellacombeanus (Praeger) 't Hart or P. kamtschaticus (Fisch.) 't Hart. Population genetic analyses reveal two major groups within P. latiovalifolius. A higher genetic variation is observed in P. ellacombeanus than in the congeneric species. Notably, most of the genetic variation exists within P. latiovalifolius populations. Given its distribution and the potential role of Baekdudaegan as an East Asian Pleistocene refugia, P. latiovalifolius could be considered rare and endemic, persisting in the refugium across glacial/interglacial cycles.

Potential metabolomic biomarkers for evaluation of adriamycin efficacy using a urinary 1H-NMR spectroscopy.

A metabolomics approach using proton nuclear magnetic resonance (NMR) was applied to investigate metabolic alterations following adriamycin (ADR) treatment for gastric adenocarcinoma. After BALB/c-nu/nu mice were implanted with human gastric adenocarcinoma, ADR (1 or 3 mg kg(-1) per day) was intraperitoneally administered for 5 days. Urine was collected on days 2 and 5 and analyzed by NMR. The levels of trimethylamine oxide (TMAO, ×0.3), hippurate (×0.3) and taurine (×0.6) decreased significantly (P < 0.05), whereas the levels of 3-indoxylsulfate (×12.6), trigonelline (×1.5), citrate (×2.5), trimethylamine (TMA, ×2.0) and 2-oxoglutarate (×2.3) increased significantly (P < 0.05) in the tumor model. After ADR treatment, TMAO, hippuarte and taurine were increased significantly on day 5 compared with those of the tumor model. The levels of 2-oxoglutarate, 3-indoxylsulfate, trigonelline, TMA and citrate, which increased in the tumor model, significantly decreased to those of normal control by ADR treatment. Furthermore, the ratio between TMA and TMAO was dramatically altered in both tumor and ADR-treated groups. Overall, metabolites such as TMAO, TMA, 3-indoxylsulfate, hippurate, trigonelline, citrate and 2-oxoglutarate related to the tricarboxylic acid (TCA) cycle might be considered as therapeutic targets to potentiate the efficacy of ADR. Thus, these results suggest that the metabolomics analysis of tumor response to ADR treatment may be applicable for demonstrating the efficacy of anticancer agent, ADR and treatment adaptation.

Biomarker Development for Identifying Mud Loach (Misgurnus mizolepis) Origin Country Using Untargeted Metabolite Profiling.

Mud loach (Misgurnus mizolepis) has long been consumed in Korea. Recently, Chinese mud loaches were replaced with expensive Korean mud loaches, owing to taste and preference. Such issues occur in aquatic food distribution processes, leading to inferior food delivery. Previously, a study was conducted to confirm the origin of mud loaches using genetic analysis. However, untargeted metabolites profiling of mud loaches has not been reported. Untargeted metabolomics provides information on the overall metabolic profiling of a sample, allowing the identification of new metabolites. Here, we analyzed the metabolites of mud loaches of different geographical origins using liquid chromatography (LC)-quadrupole-time-of-flight mass spectrometry (MS). Orthogonal partial least squares discriminant analysis from LC/MS datasets showed a clear distinction between Korean and Chinese mud loaches, and univariate statistical analysis showed significantly different metabolites between them. N-acetylhistidine and anserine were selected as biomarkers for geographical origin discrimination using the receiver operating characteristic curve. N-acetylhistidine and anserine levels were significantly higher in Chinese than in Korean mud loaches. These results indicate that metabolic analysis can be used to discriminate between the geographical origins of mud loaches, curtailing the inadvertent substitution of mud loaches from different regions.

Analysis of metabolite differences between South Korean and Chinese yellow goosefish (Lophius litulon) using capillary electrophoresis time-of-flight mass spectrometry.

The yellow goosefish is a benthic fish that belongs to the family Lophiidae and order Lophiiformes and is distributed in the Yellow and East China Seas. This study aimed to distinguish between yellow goosefish from different geographical origins by analyzing their metabolites. Capillary electrophoresis time-of-flight mass spectrometry was used to analyze metabolite profiles in the muscle tissues of yellow goosefish to distinguish between Korean and Chinese yellow goosefish. In total, 271 putative metabolites were extracted using 50% acetonitrile in water. Principal component analysis and orthogonal partial least squares discriminant analysis (OPLS-DA) were used to distinguish different geographical origins using the metabolite profiles obtained. The R2 and Q2 values of the OPLS-DA model were 0.856 and 0.695, respectively, indicating that the model was well-fitted and had good predictability. The heat map revealed that nucleic acid and amino compounds differed between the Korean and Chinese fish, and the variable importance in the projection scores obtained from OPLS-DA showed that there were geographical differences in the primary metabolites (5'-methylthioadenosine, adenosine, uridine 5-diphosphate, guanosine 5-diphosphate, urea, homocarnosine, O-acetylcarnitine, cycloleucine, cycloleucine S-adenosylmethionine, S-adenosylhomocysteine, ethanolamine, myo-inositol 1-phosphate), which were identified as potential candidate biomarkers.

New insights into the phylogenetic relationships among wild onions (Allium, Amaryllidaceae), with special emphasis on the subgenera Anguinum and Rhizirideum, as revealed by plastomes.

The genus Allium, with over 900 species, is one of the largest monocotyledonous genera and is widely accepted with 15 recognized subgenera and 72 sections. The robust subgeneric and sectional relationships within Allium have long been not resolved. Based on 76 species of Allium (a total of 84 accessions), we developed a highly resolved plastome phylogenetic framework by integrating 18 newly sequenced species (20 accessions) in this study and assessed their subgeneric and sectional relationships, with special emphasis on the two subgenera Anguinum and Rhizirideum. We retrieved the three major evolutionary lines within Allium and found that the two subgenera Anguinum and Rhizirideum are monophyletic whereas others are highly polyphyletic (e.g., Allium, Cepa, Polyprason, and Melanocrommyum). Within the subgenus Anguinum, two strongly supported sublineages in East Asian and Eurasian-American were found. Allium tricoccum in North America belonged to the Eurasian clade. The distinct taxonomic status of A. ulleungense and its sister taxon were further determined. In subg. Rhizirideum, the Ulleung Island endemic A. dumebuchum shared its most recent common ancestor with the species from Mongolia and the narrow Korean endemic A. minus. Two Ulleung Island endemics were estimated to originate independently during the Pleistocene. In addition, a separate monotypic sectional treatment of the east Asian A. macrostemon (subg. Allium) and sister relationship between A. condensatum and A. chinense was suggested.

Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics.

Although the monophyly of Phedimus has been strongly demonstrated, the species relationships among approximately 20 species of Phedimus have been difficult to determine because of the uniformity of their floral characteristics and extreme variation of their vegetative characters, often accompanied by high polyploid and aneuploid series and diverse habitats. In this study, we assembled 15 complete chloroplast genomes of Phedimus species from East Asia and generated a plastome-based backbone phylogeny of the subgenus Aizoon. As a proxy for nuclear phylogeny, we reconstructed the nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) phylogeny independently. The 15 plastomes of subg. Aizoon were highly conserved in structure and organization; hence, the complete plastome phylogeny fully resolved the species relationships with strong support. We found that P. aizoon and P. kamtschaticus were polyphyletic and morphologically distinct or ambiguous species, and they most likely evolved from the two species complex. The crown age of subg. Aizoon was estimated to be 27 Ma, suggesting its origin to be in the late Oligocene; however, the major lineages were diversified during the Miocene. The two Korean endemics, P. takesimensis and P. zokuriensis, were inferred to have originated recently during the Pleistocene, whereas the other endemic, P. latiovalifolium, originated in the late Miocene. Several mutation hotspots and seven positively selected chloroplast genes were identified in the subg. Aizoon.

Phylogenomic insight into dysploidy, speciation, and plastome evolution of a small Mediterranean genus Reichardia (Cichorieae; Asteraceae).

Reichardia Roth is a small Mediterranean genus comprising ten homogeneous species with basic chromosome numbers of 7, 8, and 9. To assess the plastid genome evolution and differentiation of Reichardia species, we assembled the complete plastome sequences of seven Reichardia and two Launaea species and conducted various phylogenomic analyses comparatively with nuclear ribosomal DNA ITS sequences. Reichardia and Launaea plastomes were highly conserved in gene content and order, containing 130 genes. Plastid phylogenomic reconstruction strongly suggested that Reichardia was a sister to Launaea, and its common ancestor initially diverged into two major lineages: the first containing species with n = 8 chromosomes exclusively, and the other with n = 9, 8, and 7 chromosomes. Although the ancestral Reichardia karyotype was suggested to most likely be n = 9 from ancestral chromosome number reconstruction, the pattern of descending dysploidy indicated by the phylogenetic trees based on nuclear ribosomal DNA ITS was less evident in the trees based on the plastome. Possible reasons for these findings are discussed.

Infrageneric Plastid Genomes of Cotoneaster (Rosaceae): Implications for the Plastome Evolution and Origin of C. wilsonii on Ulleung Island.

Cotoneaster is a taxonomically and ornamentally important genus in the family Rosaceae; however, phylogenetic relationships among its species are complicated owing to insufficient morphological diagnostic characteristics and hybridization associated with polyploidy and apomixis. In this study, we sequenced the complete plastomes of seven Cotoneaster species (C. dielsianus, C. hebephyllus, C. integerrimus, C. mongolicus, C. multiflorus, C. submultiflorus, and C. tenuipes) and included the available complete plastomes in a phylogenetic analysis to determine the origin of C. wilsonii, which is endemic to Ulleung Island, Korea. Furthermore, based on 15 representative lineages within the genus, we carried out the first comparative analysis of Cotoneaster plastid genomes to gain an insight into their molecular evolution. The plastomes were highly conserved, with sizes ranging from 159,595 bp (C. tenuipes) to 160,016 bp (C. hebephyllus), and had a GC content of 36.6%. The frequency of codon usage showed similar patterns among the 15 Cotoneaster species, and 24 of the 35 protein-coding genes were predicted to undergo RNA editing. Eight of the 76 common protein-coding genes, including ccsA, matK, ndhD, ndhF, ndhK, petA, rbcL, and rpl16, were positively selected, implying their potential roles in adaptation and speciation. Of the 35 protein-coding genes, 24 genes (15 photosynthesis-related, seven self-replications, and three others) were found to harbor RNA editing sites. Furthermore, several mutation hotspots were identified, including trnG-UCC/trnR-UCU/atpA and trnT-UGU/trnL-UAA. Maximum likelihood analysis based on 57 representative plastomes of Cotoneaster and two Heteromeles plastomes as outgroups revealed two major lineages within the genus, which roughly correspond to two subgenera, Chaenopetalum and Cotoneaster. The Ulleung Island endemic, C. wilsonii, shared its most recent common ancestor with two species, C. schantungensis and C. zabelii, suggesting its potential origin from geographically close members of the subgenus Cotoneaster, section Integerrimi.

Characterization of the complete chloroplast genome sequence of Potentilla gageodoensis (rosaceae), endemic to the continental islands of Korea.

This study reports the complete chloroplast genome sequence of a continental island endemic, Potentilla gageodoensis. The total plastome size was 156,397 bp, comprising one large single-copy (LSC; 85,768 bp), one small single-copy (SSC; 18,589 bp), and two inverted repeat (IR) regions (IRa and IRb, each with 26,020 bp). The overall GC content was 36.92%, and the plastome contained 131 genes, comprising 84 protein-coding genes with two pseudogenes (infA and ycf1), 37 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic analysis performed using 27 representative Rosoideae plastomes suggests that the genus Potentilla is not monophyletic and that P. gageodoensis is sister to the clade containing four taxa of Potentilla (P. freyniana, P. freyniana var. chejuensis, P. stolonifera, and P. stolonifera var. quelpaertensis). The present study reveals the taxonomic distinction of P. gageodoensis from its congeneric species in Korea and the plastome sequence obtained from this study can be used to study phylogenetic relationships and taxonomic status.

Analysis of metabolites of red seabream (Pagrus major) from different geographical origins by capillary electrophoresis time-of-flight mass spectrometry.

Red seabream (Pagrus major), a migratory fish, is characterized by high protein levels in the muscle. South Korean and Japanese red seabreams have a general distribution pattern; however, distinguishing them based on their geographical origin is difficult. In this study, we used capillary electrophoresis time-of-flight mass spectrometry (CE-TOF/MS) to analyze the red seabream muscle metabolome to investigate how can distinguish the origin of the fish. The metabolites were extracted using 50% acetonitrile in water. Chromatographic separation was successfully used to classify the metabolite profiles of Japanese and South Korean red seabream. Principal component analysis and hierarchical cluster analysis showed good ability to categorize the samples according to their origin. Amino acids showed the greatest quantitative difference in South Korean and Japanese muscle samples. Specifically, the L-alanine, L-glutamic acid, L-isoleucine, dimethylglycine, and L-valine levels in Japanese red seabream samples were significantly higher than those in South Korean samples. In contrast, the levels of trimethylamine N-oxide and inosine monophosphate in South Korean muscle samples were significantly higher than those in Japanese red muscle samples. The monitored metabolite profiles suggest that South Korean and Japanese red seabreams can be identified on the basis of amino acid levels.

Characterization of the complete mitochondrial genome of demersal flatfish Eopsetta grigorjewi (Pleuronectiformes: Pleuronectidae) from South Korea.

Eopsetta grigorjewi (Pleuronectiformes: Pleuronectidae) is a demersal flatfish found in South Korea, Japan, Taiwan, China, and the Yellow Sea. E. grigorjewi complete mitochondrion DNA (mtDNA) consists of 16,921 bp and a 54% A + T content. It includes 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA), 13 protein-coding genes, and 1 non-coding regulatory area. ND2, ND3, ND4, COII, COIII, ATPase6, and CytB all have incomplete stop codon genes. The evolutionary analysis of 13 species from the same family indicated a close relationship. This work will be valuable for future research on molecular evolution and the creation of biomarker databases for determining the originality of E. grigorjewi.

Complete mitochondrial genome of scorpionfish Scorpaena neglecta (Actinopterygii).

Scorpaena neglecta (Temminck and Schlegel, 1843) is a marine fish, in the family Scorpaenidae, order Scorpaeniformes, class Actinopterygii of the phylum Chordata. The first species of Scorpaena with a complete mitochondrial genome is described in the present study. The circular mitochondrial genome of S. neglecta has 17,202 bp with 54.75% A + T content and encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), and two ribosomal RNA (rRNA). The phylogenetic tree indicates S. neglecta clustered into one branch and is closely related to other Scorpaenidae species. The mitochondrial genome structure and gene content of S. neglecta will support the study of evolution and phylogenetic relationships among Scorpaenidae species.