Re-evaluation of the taxonomic status of four nominal, western Pacific species of tongue soles (Pleuronectoidei: Cynoglossidae: Cynoglossus), with redescription of C. joyneri Gnther, 1878.

Striking similarities in morphological characters and significant overlap in meristic features have resulted in different hypotheses regarding the taxonomic status of several nominal species of northwestern Pacific tongue soles of the genus Cynoglossus, including C. joyneri Gnther, 1878, C. lighti Norman, 1925, C. tenuis (Oshima, 1927), and C. tshusanensis Chabanaud, 1951. Previous hypotheses have proposed that each taxon is a valid species; or that C. lighti and C. tshusanensis are junior subjective synonyms of C. joyneri; or that C. tenuis is a junior subjective synonym of either C. joyneri or C. lighti. Although several previous investigations concluded that C. lighti is a synonym of C. joyneri, names of both nominal species still appear in contemporary literature indicating that taxonomic status of these nominal species remains unresolved. To clarify the taxonomic status of these four nominal species, detailed study of morphological characters of 138 specimens collected from 22 localities in Japan and China, and re-examination of type specimens of three of these nominal species was conducted. The molecular barcodes of mitochondrial DNA from six representative specimens featuring morphological variation purportedly useful for distinguishing C. lighti from C. joyneri were also analyzed and then compared with sequences reported for C. joyneri in the literature. Lectotypes of C. joyneri and C. lighti differed in only two morphological characters (body depth and position of posterior tip of rostral hook relative to anterior margin of lower eye). However, when these two characters were examined in 138 recently collected non-type specimens, no differences were found among these nominal species. Our results do not support recognizing these as separate species. Results from genetic analyses also support recognizing only a single species among the material examined. Furthermore, overall similarities in morphological features between the holotype of C. tshusanensis and specimens of C. joyneri support recognizing C. tshusanensis as a junior subjective synonym of C. joyneri. Likewise, values for morphological features of C. joyneri examined in the present study also encompass the range of values reported in the original description of C. tenuis. This finding supports conclusions of previous studies that this nominal species is also a junior synonym of C. joyneri. Based on morphological and genetic evidence, we conclude that only a single species, C. joyneri, should be recognized among the four nominal species included in this study. Cynoglossus joyneri is re-described based on data from 492 specimens collected throughout nearly the entire range of the species.

The critical role and molecular mechanisms of ferroptosis in antioxidant systems: a narrative review.

Background and Objective: Ferroptosis is a recently discovered form of cell death which differs from other forms of cell death in terms of morphology, biochemistry, and regulatory mechanisms. Ferroptosis is regulated by a complex system and the precise molecular mechanisms are still being elucidated. Over the past few years, extensive research has revealed that the essence of ferroptosis is iron-dependent accumulation of lipid hydroperoxides induced by oxidative stress, and the System Xc-glutathione (GSH)-glutathione peroxidase 4 (GPX4) pathway is the main ferroptosis prevention system. Meanwhile, other antioxidant systems have also been implicated in regulating ferroptosis, including the transsulfuration pathway, mevalonate pathway, ferroptosis inhibitory protein 1 (FSP1)-Coenzyme Q10 (CoQ10) pathway, dihydroorotate dehydrogenase (DHODH)-dihydroubiquione (CoQH2) pathway, and GTP cyclohydrolase-1 (GCH1)-tetrahydrobiopterin (BH4) pathway. This article reviews the molecular mechanisms of ferroptosis and its critical role in antioxidant systems, aiming to reveal that antioxidation is an important method of inhibiting ferroptosis and to provide a new direction for the treatment of ferroptosis-related diseases. Methods: We searched all original papers and reviews about the molecular mechanisms of ferroptosis in antioxidant systems using PubMed to November 2021. The search terms used included: 'ferroptosis', 'ferroptosis inducers', 'ferroptosis inhibitors', 'ferroptosis and GSH', 'ferroptosis and GPX4', 'ferroptosis and System Xc-', 'SLC7A11', 'P53', 'NRF2 and ferroptosis', 'iron metabolism', 'lipid peroxidation', 'antioxidant systems', 'transsulfuration pathway', 'mevalonate pathway', 'FSP1-CoQ10', 'DHODH-CoQH2', and 'GCH1-BH4'. Key Content and Findings: We first introduced the origin of ferroptosis and its common inhibitors and inducers. Next, we discussed the molecular mechanisms of ferroptosis and its role in antioxidant systems in existing studies. Finally, we briefly summarized the relationship between ferroptosis and diseases. It reveals that antioxidation is an important method of inhibiting ferroptosis. Conclusions: This review discusses the recent rapid progress in the understanding of the molecular mechanisms of ferroptosis and its role in several antioxidant systems.

The complete mitochondrial genome of Pseudorhombus dupliocellatus (Pleuronectiformes: Paralichthyidae).

The Pseudorhombus dupliocellatus belongs to family Paralichthyidae of Pleuronectiformes. In this study, the complete mitochondrial genome of P. dupliocellatus is determined and described. The mitogenome is 16 621 bp in length and consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, a control region, and a L-strand replication origin. The arrangement of the mitogenome is identical to that of the typical teleost. The overall base composition is 26.9%, 25.3%, 31.0%, and 16.8% for A, T, C, and G, respectively, with a slight bias on A+T content (52.2%). The phylogenetic tree of 13 species all in Pleuronectiformes demonstrated that P. dupliocellatus, as well as the other Paralichthyidae fishes containing Paralichthys olivaceus and Pseudorhombus cinnamoneus, clustered in a clade and had a closer relationship with Pleuronectidae species than Bothidae ones. This study is expected to contributing to the systematic evolution of Paralichthyidae and further Pleuronectiformes.

The complete mitochondrial genome sequence of Cynoglossus abbreviatus (Pleuronectiformes: Cynoglossidae) with control region translocation and tRNA-Gln gene inversion.

Cynoglossus abbreviatus (Cynoglossidae, Soleoidei) is characterized by a bilaterally asymmetrical with both eyes on the left side. In this study, the complete mitogenome of this tongue sole has been reported for the first time. The gene order in C. abbreviatus mitogenome possesses a novel rearrangement like other tonguefish. The tRNA-Gln gene moves from the light strand to the heavy strand, accompanied by tRNA-Ile gene shuffling, leaving a large non-coding region (88 bp) between these two tRNAs. Additionally, the control region translocates to the place between ND1 and tRNA-Gln genes. The total length is 16,417 bp, with 30.9%, 29.5%, 24.9% and 14.7% for A, T, C and G, respectively (60.4% for AT content). These molecular data will provide useful information about the mechanism of gene reorganization in Cynoglossidae mitogenome and further phylogenetic study on Pleuronectiformes.

The complete mitochondrial genome sequence of Brachirus orientalis (Pleuronectiformes: Soleidae).

The oriental sole Brachirus orientalis (Pleuronectiformes: Soleidae) is characterized by both eyes on the right side of the body and orbicular-ovate body. In this paper, the complete mitochondrial genome sequence of this sole was first determined. The total length is 16,602 bp, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes (12S and 16S), as well as a putative control region and a putative L-strand replication origin (OL). Gene contents, locations, and arrangements are identical to those of typical bony fishes. Overall base composition of the mitogenome is 30.4%, 28.6%, 15.3%, and 25.7% for A, C, G, and T, with a high A + T content (56.1%). The determination of B. orientalis complete mitogenome sequence could contribute to phylogenetic study on Soleidae and Pleuronectiformes.

The complete mitochondrial genome of Zebrias quagga (Pleuronectiformes: Soleidae).

Zebrias quagga (Soleoidei, Soleidae) is a sort of small and medium-sized commercial flatfish, characterized by both eyes on the right side of the body and with a dark brown short tentacle on each eye. In this paper, the complete mitogenome sequence of Z. quagga was first determined, which is 17,045 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, as well as a control region (CR) and a L-strand replication origin (OL). Gene contents, locations, and orders are identical to those of typical teleostean mtDNA. The nucleotide composition of the whole mitogenome is 28.8%, 29.3%, 15.8%, and 26.1% for A, C, G, and T, respectively, with a slight bias of A+T content (54.9%). This result is expected to contribute to a better understanding the phylogenetic study of Soleidae and Pleuronectiformes.

The complete mitochondrial genome of Cynoglossus puncticeps (Pleuronectiformes: Cynoglossidae).

Cynoglossus puncticeps (Soleoidei Cynoglossidae) is characterized by both eyes on the left side of the body. Here we report the mitogenome of this tonguesole for the first time, which is 17,142 bp in length, and the gene order has been reorganized. The tRNA-Gln gene translocated from the light strand (L-strand) to the heavy strand (H-strand), accompanied by tRNA-Ile gene shuffling. In addition, the putative control region translocated downstream to the position between the ND1 and the tRNA-Gln genes, leaving a 25-bp trace fragment in the original location. In addition, two tandem arrays were found: one was a 17-bp motif with 40.2 copies, and the other was 73-bp with 3.0 copies.

The complete mitochondrial genome of Paraplagusia blochii (Pleuronectiformes: Cynoglossidae).

Paraplagusia blochii (Cynoglossidae, Soleoidei) is characterized by both eyes on the left side of the body with a short rostral hook reaching only to hind margin of lower eye. Here we first report the mitogenome of this tongue sole, which is 16,611 bp in length, and the gene order has been reorganized. Specifically, the tRNA-Gln gene encoded by the light strand (L-strand) has been translocated to the heavy strand (H-strand), accompanied by the tRNA-Ile gene shuffling. In addition, the putative control region has been translocated downstream to a position between the ND1 and tRNA-Gln genes, leaving a 24-bp trace fragment in the original position. Nevertheless, the rest gene arrangement is identical to that of the typical fish. The determination of the complete mitogenome sequence of P. blochii could contribute to a better understanding the molecular mechanisms of gene reorganization in fish mitogenome and phylogenetic study of Soleidae and Pleuronectiformes.

The complete mitochondrial genome of Zebrias crossolepis (Pleuronectiformes: Soleidae).

Zebrias crossolepis belongs to the family Soleidae of Pleuronectiformes. This species and its congeners are characterized by eyes on right side and a compressed body with only anterior half of caudal fin margin connected with dorsal and anal fins. In this article, we determined and described the complete mitogenome of Z. crossolepis. The genome is 16,734 bp in length, and is typically consist of 37 genes, including 13 protein-coding, two ribosomal RNA, 22 transfer RNA genes, as well as a putative control region and an L-strand replication origin. The gene organization is identical to that of typical bony fishes. The overall base composition is 28.3, 26.4, 30.0, and 15.3% for A, T, C, and G, respectively, with a slight bias on AT content (54.7%). This result is expected to contribute to understanding the systematic evolution of the genus Zebrias and further phylogenetic studies of Soleidae and Pleuronectiformes.

The complete mitochondrial genome of Cynoglossus zanzibarensis (Pleuronectiformes: Cynoglossidae).

Cynoglossus zanzibarensis (Cynoglossidae, Soleoidei) is characterized by both eyes on the left side of the body. Here we report the mitogenome of this tonguesole for the first time, which is 16,569 bp in length, with gene order reorganized. The tRNA-Gln gene is translocated from the light strand (L-strand) to the heavy strand (H-strand), accompanied by shuffling of tRNA-Ile and tRNA-Met genes with a 160-bp intergenic spacer between tRNA-Gln and tRNA-Ile. The putative control region is translocated downstream to the place between the ND1 and the tRNA-Gln genes, leaving a 25-bp trace fragment in the original position. The rest of the gene arrangement is identical to that of the typical fish.

Gene rearrangements in the mitochondrial genome of Cynoglossus bilineatus (Pleuronectiformes: Cynoglossidae).

Cynoglossus bilineatus (Cynoglossidae, Soleoidei) is characterized by both eyes on the left side of the body and with a rounded snout and a short rostral hook. Here we first report the mitogenome of this tongue sole, which is 16,454 bp in length, and gene rearrangements have been observed. Particularly, the tRNA-Gln gene encoded by the light strand (L-strand) has translocated to the heavy strand (H-strand), along with the tRNA-Ile gene shuffling. In addition, the putative control region has translocated downstream to a position between the ND1 and tRNA-Gln genes, leaving a 26-bp intergenic spacer in its original position. However, the arrangement of the rest genes is identical to that of the typical teleost. This result could contribute to a better understanding the molecular mechanisms of gene rearrangement in fish mitogenome as well as phylogenetic study of Cynoglossidae and Pleuronectiformes.

Concerted Evolution of Duplicate Control Regions in the Mitochondria of Species of the Flatfish Family Bothidae (Teleostei: Pleuronectiformes).

Mitogenomes of flatfishes (Pleuronectiformes) exhibit the greatest diversity of gene rear-rangements in teleostean fishes. Duplicate control regions (CRs) have been found in the mito-genomes of two flatfishes, Samariscus latus (Samaridae) and Laeops lanceolata (Bothidae), which is rare in teleosts. It has been reported that duplicate CRs have evolved in a concerted fashion in fishes and other animals, however, whether concerted evo-lution exists in flatfishes remains unknown. In this study, based on five newly sequenced and six previously reported mitogenomes of lefteye flounders in the Bothidae, we explored whether duplicate CRs and concerted evolution exist in these species. Results based on the present study and previous reports show that four out of eleven bothid species examined have duplicate CRs of their mitogenomes. The core regions of the duplicate CRs of mitogenomes in the same species have identical, or nearly identical, sequences when compared to each other. This pattern fits the typical characteristics of concerted evolution. Additionally, phylogenetic and ancestral state reconstruction analysis also provided evidence to support the hypothesis that duplicate CRs evolved concertedly. The core region of concerted evolution is situated at the conserved domains of the CR of the mitogenome from the termination associated sequences (TASs) to the conserved sequence blocks (CSBs). Commonly, this region is con-sidered to regulate mitochondrial replication and transcription. Thus, we hypothesize that the cause of concerted evolution of the duplicate CRs in the mtDNAs of these four bothids may be related to some function of the conserved sequences of the CRs during mitochondrial rep-lication and transcription. We hope our results will provide fresh insight into the molecular mechanisms related to replication and evolution of mitogenomes.

Tandem Duplication and Random Loss for mitogenome rearrangement in Symphurus (Teleost: Pleuronectiformes).

BACKGROUND: The mitochondrial genomes (mitogenomes) of flatfishes (Pleuronectiformes) exhibit highly diversified types of large-scale gene rearrangements. We have reported that the mitogenomes of Crossorhombus azureus (Bothidae), Samariscus latus (Samaridae) and Cynoglossus fishes (Cynoglossidae) show different types of gene rearrangements. RESULTS: In the present study, the complete mitogenomes of two Symphurus species (Cynoglossidae), Symphurus plagiusa and Symphurus orientalis, were determined. The gene order in the S. plagiusa mitogenome is the same as that of a typical vertebrate (without any gene rearrangements). Surprisingly, large-scale gene rearrangements have occurred in S. orientalis. In the rearranged fragment from the control region (CR) to the WANCY tRNA cluster (tRNA cluster of tRNA-W, tRNA-A, tRNA-N, tRNA-C and tRNA-Y) in the S. orientalis mitogenome, tRNA-V and tRNA-M have been translocated to the 3' end of the 16S rRNA gene, with six large intergenic spacers over 20 bp in length. In addition, an origin for light-strand replication (OL) structure that is typically located in the WANCY region was absent in both the S. plagiusa and S. orientalis mitogenomes. It is generally recognized that a sequence in the WANCY region that encodes tRNAs forms a hairpin structure (OL-like structure) and can act as the OL when the typical locus is lost. Moreover, an additional OL-like structure was identified near the control region in the S. plagiusa mitogenome. CONCLUSIONS: The positions of the intergenic spacers and the rearranged genes of the S. orientalis mitogenome strongly indicate that the mechanism underlying the rearrangement of this mitogenome was Tandem Duplication and Random Loss. Additionally, two OL-like regions substituting for the typical locus were found in the S. plagiusa mitogenome. We speculate that the ancestral mitogenomes of S. plagiusa and S. orientalis also had this characteristic, such that if both OL-like structures functioned during mitochondrial replication, they could initiate duplicate replications of the light strand (L-strand), leading to duplication of the region between the two structures. We consider that this mechanism may account for the gene duplication that occurred during the gene rearrangement process in the evolution of the ancestral mitogenome to the S. orientalis mitogenome.

The complete mitochondrial genome of Liachirus melanospilos (Pleuronectiformes: Soleidae).

Liachirus melanospilos (Pleuronectiformes: Soleidae) is characterized by both eyes on the right side of the body and pale brown color with black dots, small irregular, brown spots and large vague ocelli. In this study, the complete mitogenome sequence of this carpet sole has been determined. The total length is 17,001 bp, including 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes (12S and 16S), as well as one control region and one L-strand replication origin (OL). Gene contents, locations and arrangements are identical to those of typical bony fishes. The nucleotide composition of the genome is 30.9%, 27.8%, 15.9% and 25.5% for A, C, G and T, respectively, with a slight bias of A + T content (56.4%). The determination of L. melanospilos complete mitogenome sequence could contribute to a better understanding of the systematic evolution of Soleidae and Pleuronectiformes.

The complete mitochondrial genome sequence of Aesopia cornuta (Pleuronectiformes: Soleidae).

Aesopia cornuta belongs to the family Soleidae of Pleuronectiformes, and the morphological characters are much similar to those of Zebrias. In this article, we sequenced, characterized, and compared the complete mitogenome of A. cornuta for the first time. The genome is 16,737 base pairs in length, and is typically consist of 37 genes, including 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA, as well as a putative L-strand replication origin and a putative control region. The gene organization is identical to that of typical bony fishes. The overall base composition is 29.1, 28.3, 26.8 and 15.8% for C, A, T and G, respectively, with a slight AT bias of 55.1%. This result is expected to contribute to understanding the systematic evolution of the genus Aesopia and further taxonomic and phylogenetic studies of Soleidae and Pleuronectiformes.

The complete mitochondrial genome sequence of Cynoglossus sinicus (Pleuronectiformes: Cynoglossidae).

Cynoglossidae (tongue soles) mitogenomes have been found to be translocated in their control region and a tRNA gene inversed, but no gene rearrangement in Soleidae, the closest family to Cynoglossidae, has been detected. In order to explore whether or not mitogenomes of tongue soles bear other gene-rearrangement types, we determined another tongue sole mitogenome of Cynoglossus sinicus. The total length of this mitogenome is 16,478 bp, and the tRNA-Gln gene is translocated from the light strand (L-strand) to the heavy strand (H-strand), accompanied by shuffling of tRNA-Gln, Ile and Met genes with a 143 bp intergenic spacer between tRNA-Gln and Ile. The control region (CR) might translocate to the position between the ND1 and the tRNA-Gln genes. The order of the rest genes is identical to that of the typical fish.

A novel model of double replications and random loss accounts for rearrangements in the Mitogenome of Samariscus latus (Teleostei: Pleuronectiformes).

BACKGROUND: Although more than one thousand complete mitochondrial DNA (mtDNA) sequences have been determined in teleostean fishes, only a few gene rearrangements have been observed, and genome-scale rearrangements are even rarer. However, flatfishes (Pleuronectiformes) have been identified as having diverse types of mitochondrial gene rearrangements. It has been reported that tongue soles and the blue flounder mitogenomes exhibit different types of large-scale gene rearrangements. RESULTS: In the present study, the complete mitochondrial genome of another flatfish, Samariscus latus, was sequenced, and genome-scale rearrangements were observed. The genomic features of this flounder are different from those of any other studied vertebrates, including flatfish species too. The mitogenome of S. latus is characterized by the duplication and translocation of the control region (CR). The genes located between the two CRs are divided into two clusters in which their relative orders are maintained. CONCLUSIONS: We propose a "Double Replications and Random Loss" model to explain the rearrangement events in S. latus mitogenome. This model consists of the following steps. First, the CR was duplicated and translocated. Subsequently, double replications of the mitogenome were successively initiated from the two CRs, leading to the duplication of the genes between the two CRs. Finally, one of each pair of duplicated genes was lost in a random event.

The complete mitochondrial genome sequence of Heteromycteris japonicus (Pleuronectiformes: Soleidae).

The bamboo sole Heteromycteris japonicus (Pleuronectiformes: Soleidae) is characterized by both eyes on the right side of the body and a rostral hook. In this article, the complete mitochondrial genome sequence of this sole was first determined. The total length is 17,111 bp, including 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes (12 S and 16 S), as well as a putative control region and a putative L-strand replication origin (OL). Gene contents, locations and arrangements are identical to those of typical bony fishes. Overall base composition of the mitogenome is 29.2%, 27.5%, 16.3% and 27.1% for A, C, G and T, with a high A + T content (56.3%). The determination of H. japonicus mitogenome sequence could contribute to understanding the systematic evolution of the genus Heteromycteris and further phylogenetic study on Soleidae and Pleuronectiformes.

The complete mitochondrial genome of Solea ovata (Pleuronectiformes: Soleidae).

Solea ovata (Pleuronectiformes: Soleidae) is characterized by eyes on right side and an ovata body with small ctenoid scales on both sides. In this article, the complete mitogenome of Solea ovata was first determined. The total length is 16,782 bp, containing 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes (12S and 16S), as well as a putative control region and a L-strand replication origin (OL). Except eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. Overall base composition is 29.2% A, 29.4% C, 15.9% G, and 25.5% T with a slight AT bias of 54.7%. The determination of S. ovata complete mitogenome could contribute to understanding the systematic evolution of the genus Solea and further phylogenetic study on Soleidae and Pleuronectiformes.

Complete mitogenome sequences of four flatfishes (Pleuronectiformes) reveal a novel gene arrangement of L-strand coding genes.

BACKGROUND: Few mitochondrial gene rearrangements are found in vertebrates and large-scale changes in these genomes occur even less frequently. It is difficult, therefore, to propose a mechanism to account for observed changes in mitogenome structure. Mitochondrial gene rearrangements are usually explained by the recombination model or tandem duplication and random loss model. RESULTS: In this study, the complete mitochondrial genomes of four flatfishes, Crossorhombus azureus (blue flounder), Grammatobothus krempfi, Pleuronichthys cornutus, and Platichthys stellatus were determined. A striking finding is that eight genes in the C. azureus mitogenome are located in a novel position, differing from that of available vertebrate mitogenomes. Specifically, the ND6 and seven tRNA genes (the Q, A, C, Y, S1, E, P genes) encoded by the L-strand have been translocated to a position between tRNA-T and tRNA-F though the original order of the genes is maintained. CONCLUSIONS: These special features are used to suggest a mechanism for C. azureus mitogenome rearrangement. First, a dimeric molecule was formed by two monomers linked head-to-tail, then one of the two sets of promoters lost function and the genes controlled by the disabled promoters became pseudogenes, non-coding sequences, and even were lost from the genome. This study provides a new gene-rearrangement model that accounts for the events of gene-rearrangement in a vertebrate mitogenome.