Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus.

BACKGROUND: The shuttles hoppfish (mudskipper), Periophthalmus modestus, is one of the mudskippers, which are the largest group of amphibious teleost fishes, which are uniquely adapted to live on mudflats. Because mudskippers can survive on land for extended periods by breathing through their skin and through the lining of the mouth and throat, they were evaluated as a model for the evolutionary sea-land transition of Devonian protoamphibians, ancestors of all present tetrapods. RESULTS: A total of 39.6, 80.2, 52.9, and 33.3 Gb of Illumina, Pacific Biosciences, 10X linked, and Hi-C data, respectively, was assembled into 1,419 scaffolds with an N50 length of 33 Mb and BUSCO score of 96.6%. The assembly covered 117% of the estimated genome size (729 Mb) and included 23 pseudo-chromosomes anchored by a Hi-C contact map, which corresponded to the top 23 longest scaffolds above 20 Mb and close to the estimated one. Of the genome, 43.8% were various repetitive elements such as DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. Ab initio and homology-based gene prediction identified 30,505 genes, of which 94% had homology to the 14 Actinopterygii transcriptomes and 89% and 85% to Pfam familes and InterPro domains, respectively. Comparative genomics with 15 Actinopterygii species identified 59,448 gene families of which 12% were only in P. modestus. CONCLUSIONS: We present the high quality of the first genome assembly and gene annotation of the shuttles hoppfish. It will provide a valuable resource for further studies on sea-land transition, bimodal respiration, nitrogen excretion, osmoregulation, thermoregulation, vision, and mechanoreception.

Production of juvenile masu salmon (Oncorhynchus masou) from spermatogonia-derived sperm and oogonia-derived eggs via intraperitoneal transplantation of immature germ cells.

No effective cryopreservation technique exists for fish eggs and embryos; thus, the cryopreservation of germ cells (spermatogonia or oogonia) and subsequent generation of eggs and sperm would be an alternative solution for the long-term preservation of piscine genetic resources. Nevertheless, in our previous study using rainbow trout, we showed that recipients transplanted with XY spermatogonia or XX oogonia produced unnatural sex-biased F1 offspring. To overcome these obstacles, we transplanted immature germ cells (XX oogonia or XY spermatogonia; frozen for 33 days) into the body cavities of triploid hatchlings, and the transplanted germ cells possessed a high capacity for differentiating into eggs and sperm in the ovaries and testes of recipients. Approximately 30% of triploid recipients receiving frozen germ cells generated normal salmon that displayed the donor-derived black body color phenotype, although all triploid salmon not receiving transplants were functionally sterile. Furthermore, F1 offspring obtained from insemination of the oogonia-derived eggs and spermatogonia-derived sperm show a normal sex ratio of 1:1 (female:male). Thus, this method presented a critical technique for practical conservation projects for other teleost fish species and masu salmon.

Characterization of the complete mitochondrial genome of the white grouper Epinephelus aeneus (Perciformes, Serranidae) and a comparative analysis with other Serranidae species.

The complete mitochondrial genome of the white grouper Epinephelus aeneus, which belongs to the family Serranidae, was determined. The complete mitochondrial genome measured 16,578 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. The mitochondrial gene arrangement of E. aeneus was typical of vertebrates. Phylogenetic analysis conducted using the mitochondrial genomes of 13 related species showed that E. aeneus clustered with other Serranidae species. This mitochondrial genome provides an important resource for addressing taxonomic issues and developing conservation strategies.

Complete mitochondrial genome of the double-lined fusileer, Pterocaesio digramma (Perciformes, Caesionidae): mitogenome characterization and phylogenetic analysis.

The complete mitochondrial genome of the double-lined fusileer, Pterocaesio digramma, which belongs to the family Caesionidae was determined. The complete mitochondrial genome has a length of 16,504 bp and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. P. digramma has a mitochondrial gene arrangement that is typical of vertebrates. Phylogenetic analysis using mitochondrial genomes of 15 related species revealed that P. digramma formed a well-supported monophyletic group with the other Caesionidae and Lutjanidae species.

Characterization of the complete mitochondrial genome of the Butterfly whiptail, Pentapodus setosus (Spariformes, Nemipteridae) and phylogenetic analysis.

The complete mitochondrial genome of Pentapodus setosus which belongs to the family Nemipteridae was first determined. The complete mitochondrial genome was 16,836 bp in length with 37 genes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of 11 related species revealed that P. setosus formed a well-supported monophyletic group with the other Nemipteridae species. This mitochondrial genome provides a useful information for resolving the taxonomic issues.

Complete mitochondrial genome of the orange-spotted trevally, Carangoides bajad (Perciformes, Carangidae) and a comparative analysis with other Carangidae species.

The complete mitochondrial genome of the orange-spotted trevally, Carangoides bajad, which belongs to the family Carangidae was determined. The complete mitochondrial genome has a length of 16,556 bp and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Carangoides bajad has a mitochondrial gene arrangement that is typical of vertebrates. Phylogenetic analysis using mitochondrial genomes of 13 related species revealed that C. bajad formed a well-supported monophyletic group with the other Carangidae species.

Characterization of the complete mitochondrial genome of the fork-tailed threadfin bream, Nemipterus furcosus (Spariformes, Nemipteridae) and phylogenetic analysis.

The complete mitochondrial genome of the fork-tailed threadfin bream, Nemipterus furcosus, which belongs to the family Nemipteridae was first determined. The complete mitochondrial genome was 16,882 bp in size and encoded of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Nemipterus furcosus has a mitochondrial gene arrangement that is typical of vertebrates. Phylogenetic analysis using mitochondrial genomes of 11 related species revealed that N. furcosus formed a well-supported monophyletic group with the other Nemipteridae species. This mitochondrial genome provides a useful information for addressing taxonomic issues.

The complete mitochondrial genome of Cynoglossus interruptus and its novel rearrangement (Pleuronectiformes: Cynoglossidae).

The complete mitochondrial genome was determined for the Cynoglossus interruptus belonging to the family Cynoglossidae. The length of the complete mitochondrial genome is 17,262 bp, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. The gene rearrangement related to tRNAGln and a control region gene were found, forming the gene order of CR-Ile-Gln-Met. Phylogenetic analysis using mitochondrial genomes of 12 species showed that C. interruptus formed a well-supported monophyletic group with other Cynoglossus species.

Characterization of the complete mitochondrial genome of Dactylopterus volitans (Syngnathiformes, Dactylopteridae).

The complete mitochondrial genome was determined for the flying gurnard Dactylopterus volitans belonging to the family Dactylopteridae. The total length of the D. volitans mitochondrial genome is 16,632 bp, which consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using mitochondrial genomes of 20 species showed that D. volitans formed a well-supported monophyletic group with other Dactylopteridae species.

Gene rearrangements in the mitochondrial genome of robust tonguefish, Cynoglossus robustus (Pleuronectiformes: Cynoglossidae) and a comparative analysis with other Cynoglossus fishes.

The complete mitochondrial genome was determined for the Robust tonguefish Cynoglossus robustus belonging to the family Cynoglossidae. The length of the complete mitochondrial genome is 16,720 bp, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Rearrangements of the tRNAGln and a control region gene were found and tRNAGln is translocated from the light to the heavy strand. Phylogenetic analysis using mitochondrial genomes of 12 species showed that C. robustus formed a well-supported monophyletic group with other Cynoglossus species.

A Brain Atlas of the Long Arm Octopus, Octopus minor.

Cephalopods have the most advanced nervous systems and intelligent behavior among all invertebrates. Their brains provide comparative insights for understanding the molecular and functional origins of the human brain. Although brain maps that contain information on the organization of each subregion are necessary for a study on the brain, no whole brain atlas for adult cephalopods has been constructed to date. Here, we obtained sagittal and coronal sections covering the entire brain of adult Octopus minor (Sasaki), which belongs to the genus with the most species in the class Cephalopoda and is commercially available in East Asia throughout the year. Sections were stained using Hematoxylin and Eosin (H&E) to visualize the cellular nuclei and subregions. H&E images of the serial sections were obtained at 30~70-µm intervals for the sagittal plain and at 40~80-µm intervals for the coronal plain. Setting the midline point of the posterior end as the fiducial point, we also established the distance coordinates of each image. We found that the brain had the typical brain structure of the Octopodiformes. A number of subregions were discriminated by a Hematoxylin-positive layer, the thickness and neuronal distribution pattern of which varied markedly depending upon the region. We identified more than 70 sub-regions based on delineations of representative H&E images. This is the first brain atlas, not only for an Octopodiformes species but also among adult cephalopods, and we anticipate that this atlas will provide a valuable resource for comparative neuroscience research.

Correction to: Development of 21 polymorphic microsatellite markers for the black-banded sea krait, Laticauda semifasciata (Elapidae: Laticaudinae), and cross-species amplification for two other congeneric species.

Unfortunately, one of the co-author's family name has been incorrectly published in the original online publication. The correct family name should be Tsai.

Development of 21 polymorphic microsatellite markers for the black-banded sea krait, Laticauda semifasciata (Elapidae: Laticaudinae), and cross-species amplification for two other congeneric species.

The genus Laticauda (Reptilia: Elapidae), commonly known as sea kraits, is venomous marine amphibious snakes distributed throughout the south and southeast Asian islands and mostly found in coastal waters. To facilitate genetic studies, we have developed microsatellite loci for L. semifasciata using the 454 GS-FLX pyrosequencing technique. A total of 65,680 sequences containing a minimum of five repeat motifs were identified from 451,659 reads. Among 80 loci containing more than nine repeat units, 34 primer sets (42.5%) produced strong PCR products, of which 21 were polymorphic among 36 samples of L. semifasciata. All loci exhibited high genetic variability, with an average of 7.38 alleles per locus, and the mean observed and expected heterozygosities were 0.73 and 0.76, respectively. The cross-species amplification of these loci in two laticaudine species, L. colubrina and L. laticaudata, revealed a high transferability (78.6%) and polymorphism (59.5%) of the loci. Our work demonstrated the utility of next-generation 454 sequencing as the rapid and cost-effective method for development of microsatellite markers. The high level of polymorphism in these microsatellite loci will be useful for the detection of population subdivision and the study of migration, gene flow, relatedness and philopatry of L. semifasciata and other laticaudine species.

Complete mitochondrial genome of Cheilio inermis (Labriformes, Labridae).

In the present report, we describe the first sequencing and assembly of the complete mitochondrial genome of Cheilio inermis. The mitochondrial genome of C. inermis, with 16,494 bp in length, has the typical vertebrate mitochondrial gene arrangement. It contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. All the tRNA genes typically formed a cloverleaf secondary structure. Phylogenetic analysis using mitochondrial genomes of 11 species showed that C. inermis formed monophyletic group with other Labridae species.

Complete mitochondrial genome of Parupeneus barberinus (Perciformes, Mullidae): mitogenome characterization and phylogenetic analysis.

Parupeneus barberinus is a tropical/subtropical reef-dwelling marine fish belonging to the family Mullidae. Herein, we report the first sequencing and assembly of the complete mitochondrial genome of P. barberinus. The complete mitochondrial genome is 16,560 bp long and has the typical vertebrate mitochondrial gene arrangement, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of 18 species showed that P. barberinus is clustered with P. multifasciatus and P. chrysopleuron and rooted with other Mullidae species. This mitochondrial genome provides potentially important resources for addressing taxonomic issues and studying molecular evolution.

Complete mitochondrial genome of the Korean torrent catfish Liobagrus andersoni (Siluriformes, amblycipitidae).

The Korean torrent catfish (Liobagrus andersoni), an endemic species in Korea, is a member of the family Amblycipitidae. Herein, we report the first sequencing and assembly of the complete mitochondrial genome of L. andersoni. The complete mitochondrial genome is 16,514 bp long, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using mitochondrial genomes of 21 species showed that L. andersoni was clustered with L. marginatoides and L. nigricauda. This mitochondrial genome provides potentially important resources for addressing taxonomic issues and studying molecular evolution.

Complete mitochondrial genome of the Pacific cod, Gadus macrocephalus (Gadiformes, Gadidae).

The Pacific cod Gadus macrocephalus is a commercially important species belonging to the family Gadidae. In this study, we performed the first sequencing and assembly of the complete mitochondrial genome of G. macrocephalus. The complete mitochondrial genome is 16,567 bp long, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using the mitochondrial genomes of 15 species showed that G. macrocephalus clusters with G. ogac. This mitochondrial genome provides potentially important resources for performing population genetic analysis and addressing phylogenetic issues.

The complete mitochondrial genome of Gymnogobius heptacanthus (Perciformes, gobiidae).

Gymnogobius heptacanthus is a small intertidal species belonging to the family Gobiidae. Herein, we report the first sequencing and assembly of the complete mitochondrial genome of G. heptacanthus. The complete mitochondrial genome is 16,529 bp long and has the typical vertebrate mitochondrial gene arrangement, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of 12 species showed that G. heptacanthus is clustered with G. urotaenia and G. petschiliensis and rooted with other Gobiidae species. This mitochondrial genome provides potentially important resources for addressing taxonomic issues and studying molecular evolution.

Complete mitochondrial genome of the Korean oily shinner Sarcocheilichthys nigripinnis morii (Cypriniformes, cyprinidae): mitogenome characterization and phylogenetic analysis.

The Korean oily shinner (Sarcocheilichthys nigripinnis morii) is a subspecies belonging to the subfamily Gobioninae in the family Cyprinidae and is endemic to Korea. Herein, we report the first sequencing and assembly of the complete mitochondrial genome of S. nigripinnis morii. The complete mitochondrial genome is 16,679 bp long, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using mitogenomes of 16 species showed that S. nigripinnis morii was clustered with S. nigripinnis and S. variegatus microoculus and grouped with the other Cyprinidae species.

Mitogenomic circumscription of a novel percomorph fish clade mainly comprising "Syngnathoidei" (Teleostei).

Percomorpha, comprising about 60% of modern teleost fishes, has been described as the "(unresolved) bush at the top" of the tree, with its intrarelationships still being ambiguous owing to huge diversity (>15,000 species). Recent molecular phylogenetic studies based on extensive taxon and character sampling, however, have revealed a number of unexpected clades of Percomorpha, and one of which is composed of Syngnathoidei (seahorses, pipefishes, and their relatives) plus several groups distributed across three different orders. To circumscribe the clade more definitely, we sampled several candidate taxa with reference to the previous studies and newly determined whole mitochondrial genome (mitogenome) sequences for 16 percomorph species across syngnathoids, dactylopterids, and their putatively closely-related fishes (Mullidae, Callionymoidei, Malacanthidae). Unambiguously aligned sequences (13,872 bp) from those 16 species plus 78 percomorphs and two outgroups (total 96 species) were subjected to partitioned Bayesian and maximum likelihood analyses. The resulting trees revealed a highly supported clade comprising seven families in Syngnathoidei (Gasterosteiformes), Dactylopteridae (Scorpaeniformes), Mullidae in Percoidei and two families in Callionymoidei (Perciformes). We herein proposed to call this clade "Syngnathiformes" following the latest nuclear DNA studies with some revisions on the included families.