Expression of Tshb and Tshr in the ricefield eel Monopterus albus: Potential paracrine/autocrine roles in gonads.

Thyroid stimulating hormone (TSH), a glycoprotein synthesized and secreted from thyrotrophs of the pituitary gland, is composed of a glycoprotein hormone common alpha subunit (CGA) and a specific beta subunit (TSHB). The major biological function of TSH is to stimulate thyroidal follicles to synthesize and secrete thyroid hormones through activating its cognate receptor, the thyroid stimulating hormone receptor (TSHR). In the present study, polyclonal antisera against ricefield eel Tshb and Tshr were generated respectively, and the expression of Tshb and Tshr was examined at mRNA and protein levels. RT-PCR analysis showed that tshb mRNA was expressed mainly in the pituitary as well as in some extrapituitary tissues including the ovary and testis. Tshr mRNA was also expressed in a tissue-specific manner, with transcripts detected in tissues including the kidney, ovary, and testis. The immunoreactive Tshb signals in the pituitary were shown to be localized to the inner areas of adenohypophysis which are close to the neurohypophysis of adult ricefield eels. Tshb-immunoreatvie cells in the pituitary of ricefield eel larvae were firstly observed at hatching. The expression of immunoreactive Tshb and Cga was also detected in ricefield eel ovary and testis together with Tshr. In the ovary, immunoreactive Tshb, Cga, and Tshr were observed in oocytes and granulosa cells. In the testis, immunoreactive Tshb was mainly observed in Sertoli cells while immunoreactive Cga and Tshr were detected in germ cells as well as somatic cells. Results of the present study suggest that Tsh may be synthesized both in the ovary and testis locally, which may play paracrine and/or autocrine roles in gonadal development in ricefield eels.

Stable Production of a Recombinant Single-Chain Eel Follicle-Stimulating Hormone Analog in CHO DG44 Cells.

This study aimed to produce single-chain recombinant Anguillid eel follicle-stimulating hormone (rec-eel FSH) analogs with high activity in Cricetulus griseus ovary DG44 (CHO DG44) cells. We recently reported that an O-linked glycosylated carboxyl-terminal peptide (CTP) of the equine chorionic gonadotropin (eCG) ß-subunit contributes to high activity and time-dependent secretion in mammalian cells. We constructed a mutant (FSH-M), in which a linker including the eCG ß-subunit CTP region (amino acids 115-149) was inserted between the ß-subunit and α-subunit of wild-type single-chain eel FSH (FSH-wt). Plasmids containing eel FSH-wt and eel FSH-M were transfected into CHO DG44 cells, and single cells expressing each protein were isolated from 10 and 7 clones. Secretion increased gradually during the cultivation period and peaked at 4000-5000 ng/mL on day 9. The molecular weight of eel FSH-wt was 34-40 kDa, whereas that of eel FSH-M increased substantially, with two bands at 39-46 kDa. Treatment with PNGase F to remove the N glycosylation sites decreased the molecular weight remarkably to approximately 8 kDa. The EC50 value and maximal responsiveness of eel FSH-M were approximately 1.23- and 1.06-fold higher than those of eel FSH-wt, indicating that the mutant showed slightly higher biological activity. Phosphorylated extracellular-regulated kinase (pERK1/2) activation exhibited a sharp peak at 5 min, followed by a rapid decline. These findings indicate that the new rec-eel FSH molecule with the eCG ß-subunit CTP linker shows potent activity and could be produced in massive quantities using the stable CHO DG44 cell system.

Protein expression patterns and metal metabolites in a protogynous hermaphrodite fish, the ricefield eel (Monopterus albus).

BACKGROUND: The ricefield eel Monopterus albus undergoes a natural sex change from female to male during its life cycle, and previous studies have shown the potential mechanisms of this transition at the transcriptional and protein levels. However, the changes in protein levels have not been fully explored, especially in the intersexual stage. RESULTS: In the present study, the protein expression patterns in the gonadal tissues from five different periods, the ovary (OV), early intersexual stage gonad (IE), middle intersexual stage gonad (IM), late intersexual stage gonad (IL), and testis (TE), were determined by untargeted proteomics sequencing. A total of 5125 proteins and 394 differentially expressed proteins (DEPs) were detected in the gonadal tissues. Of the 394 DEPs, there were 136 between the OV and IE groups, 20 between the IM and IE groups, 179 between the IL and IM groups, and 59 between the TE and IL groups. Three candidate proteins, insulin-like growth factor 2 mRNA-binding protein 3 isoform X1 (Igf2bp3), triosephosphate isomerase (Tpi), and Cu-Zn superoxide dismutase isoform X1 [(Cu-Zn) Sod1], were validated by western blotting to verify the reliability of the data. Furthermore, metal metabolite-related proteins were enriched in the IL vs. IM groups and TE vs. IL groups, which had close relationships with sex change, including Cu2+-, Ca2+-, Zn2+- and Fe2+/Fe3+-related proteins. Analysis of the combined transcriptome data revealed consistent protein/mRNA expression trends for two metal metabolite-related proteins/genes [LOC109953912 and calcium Binding Protein 39 Like (cab39l)]. Notably, we detected significantly higher levels of Cu2+ during the sex change process, suggesting that Cu2+ is a male-related metal metabolite that may have an important function in male reproductive development. CONCLUSIONS: In summary, we analyzed the protein profiles of ricefield eel gonadal tissues in five sexual stages (OV, IE, IM, IL, and TE) and verified the plausibility of the data. After preforming the functional enrichment of metal metabolite-related DEPs, we detected the contents of the metal metabolites Zn2+, Cu2+, Ca2+, and Fe2+/Fe3+ at these five stages and screened for (Cu-Zn) Sod1 and Mmp-9 as possible key proteins in the sex reversal process.

Hidden in the depths, discovery of a new spiny sucker eel of the genus Lipogenys Goode and Bean 1895 (Teleostei, Notacanthiformes, Notacanthidae) in the eastern North Atlantic Ocean.

This study describes Lipogenys hyalinumvelum, a new species of the genus Lipogenys found on the Portuguese coast on the northeastern Atlantic during a crustacean survey. Information on the classification history and known distribution of the genus Lipogenys is provided. Dichotomous keys to the genera of Notacanthidae and the species of Lipogenys, based on morphology, are provided. The specimens were analysed using both morphological and molecular methods, including DNA sequencing of the COI and 16S genes. The distinct genetic characteristics support the recognition of the present specimens as a new species. The hyaline color of the flap at the posterior edge of the operculum is a characteristic that differentiates L. hyalinumvelum from Lipogenys gillii and provides the etymology of the species name.

Planococcus notacanthi sp. nov., isolated from the skin of a deep-sea snub-nosed spiny eel.

A novel bacterial strain, APC 4016T, was previously isolated from the skin of a snub-nosed spiny eel, Notacanthus chemnitzii, from a depth of 1000 m in the northern Atlantic Ocean. Cells were aerobic, cocci, motile, Gram-positive to Gram-variable staining, and gave rise to orange-pigmented colonies. Growth occurred at 4-40 °C (optimum, 25-28 °C), pH 5.5-12 (optimum, pH 7-7.5), and 0-12 % (w/v) NaCl (optimum, 1 %). 16S rRNA gene phylogenetic analysis confirmed that strain APC 4016T belonged to the genus Planococcus and was most closely related to Planococcus okeanokoites IFO 12536T (98.98 % 16S similarity). However, digital DNA-DNA hybridization and average nucleotide identity values between these two strains were low, at 20.1 and 83.8 %, respectively. Major (>10 %) cellular fatty acids of strain APC 4016T were iso-C14 : 0, anteiso-C15 : 0 and C16 : 1-ω-Alc. The predominant respiratory quinones were menaquinones 5, 6, 7 and 8. The major cellular polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine, and three unknown lipids were also present. The draft genome sequence is 3.6 Mb with a G+C content of 45.25 mol%. This strain was previously shown to have antimicrobial activity and to encode bacteriocin and secondary metabolite biosynthetic gene clusters. Based on the phylogenetic analysis and its distinct phenotypic characteristics, strain APC 4016T is deemed to represent a novel species of the genus Planococcus, and for which the name Planococcus notacanthi sp. nov. is proposed. The type strain of this species is APC 4016T (=DSM 115753T=NCIMB 15463T).

Gills de novo assembly reveals oxidative stress, unfolded protein, and immune response on red cusk-eel (Genypterus chilensis) under thermal stress.

The heat waves on the South Pacific coast could lead to thermal stress in native fish. The red cusk-eel (Genypterus chilensis) is relevant for Chilean artisanal fisheries and aquaculture diversification. This study examined the effect of high-temperature stress in the gills of G. chilensis in control (14 °C) and high-temperature stress (19 °C) conditions. High-temperature stress induces a significant increase in gills cortisol levels. Additionally, oxidative damage was observed in gills (protein carbonylation and lipoperoxidation). RNA-seq data was used to build the first transcriptome assembly of gills in this species (23,656 annotated transcripts). A total of 1138 down-regulated and 1531 up-regulated transcripts were observed in response to high-temperature stress in gills. The enrichment analysis showed immune response and replication enriched processes (on down-regulated transcripts), and processes related to the folding of proteins, endoplasmic reticulum, and transporter activity (on up-regulated transcripts). The present study showed how gills could be affected by high-temperature stress.

Chromosome-level genome assembly and annotation of eel goby (Odontamblyopus rebecca).

The eel gobies fascinate researchers with many important features, including its unique body structure, benthic lifestyle, and degenerated eyes. However, genome assembly and exploration of the unique genomic composition of the eel gobies are still in their infancy. This has severely limited research progress on gobies. In this study, multi-platform sequencing data were generated and used to assemble and annotate the genome of O. rebecca at the chromosome-level. The assembled genome size of O. rebecca is 918.57 Mbp, which is similar to the estimated genome size (903.03 Mbp) using 17-mer. The scaffold N50 is 41.67 Mbp, and 23 chromosomes were assembled using Hi-C technology with a mounting rate of 99.96%. Genome annotation indicates that 53.29% of the genome is repetitive sequences, and 22,999 protein-coding genes are predicted, of which 21,855 have functional annotations. The chromosome-level genome of O. rebecca will not only provide important genomic resources for comparative genomic studies of gobies, but also expand our knowledge of the genetic origin of their unique features fascinating researchers for decades.

A new snake eel species of the genus Ophichthus (Anguilliformes: Ophichthidae) from the southeast coast of India, Bay of Bengal, with the taxonomic account of Ophichthus chilkensis.

A new species of the ophichthid eel of the family Ophichthidae is described based on five specimens collected from the Mudasalodai fish landing center, off Cuddalore coast, southeast coast of India, Bay of Bengal. Ophichthus naevius sp. nov. is distinguished from its congeners by having a unique color pattern: dorsal body with numerous dense dark spots or patches, ventral body pale yellowish green, dorsal-fin origin just before pectoral-fin tip, vertebral formula: 12-14/52-53/134-138, and teeth on jaw uniserial and pointed. The study also reports the range extension and molecular evidence of Ophichthus chilkensis from South India. Molecular analyses were performed for both species, and their phylogenetic relationship suggests that the new species exhibits 10.2% genetic divergence with its congener Ophichthus sangjuensis, followed by Ophichthus brevicaudatus (10.4%), and Ophichthus sp. 1 (11.8%) also forms the closest clade in both Bayesian inference and maximum likelihood (ML) tree. Similarly, according to the topology of the ML tree, the species O. chilkensis forms a clade with Ophichthus sp. 5, Ophichthus remiger, Ophichthus frontalis, Ophichthus sp. 6, and Ophichthus rex, suggesting that it would be the genetically closest congener.

Neuropeptide B (NPB) and NPB receptor 2b (NPBWR2b) in the ricefield eel Monopterus albus: expression and potential involvement in the regulation of gonadotropins.

The neuropeptide B/W signaling system is composed of neuropeptide B (NPB), neuropeptide W (NPW), and two cognate receptors, NPBWR1 and NPBWR2, which are involved in diverse physiological processes, including the central regulation of neuroendocrine axes in vertebrates. The components of this signaling system are not well conserved during vertebrate evolution, implicating its functional diversity. The present study characterized the ricefield eel neuropeptide B/W system, generated a specific antiserum against the neuropeptide B/W receptor, and examined the potential roles of the system in the regulation of adenohypophysial functions. The ricefield eel genome contains npba, npbb, and npbwr2b but lacks the npw, npbwr1, and npbwr2a genes. The loss of npw and npbwr1 probably occurred at the base of ray-finned fish radiation and that of npbwr2a species specifically in ray-finned fish. Npba and npbb genes are produced through whole-genome duplication (WGD) in ray-finned fish. The ricefield eel npba was expressed in the brain and some peripheral tissues, while npbb was predominantly expressed in the brain. The ricefield eel npbwr2b was also expressed in the brain and in some peripheral tissues, such as the pituitary, gonad, heart, and eye. Immunoreactive Npbwr2b was shown to be localized to Lh and Fsh cells but not to Gh or Prl cells in the pituitary of ricefield eels. Npba upregulated the expression of fshb and cga but not lhb mRNA in pituitary fragments of ricefield eels cultured in vitro. The results of the present study suggest that the NPB system of ricefield eels may be involved in the neuroendocrine regulation of reproduction.

FoxH1 Represses the Promoter Activity of cyp19a1a in the Ricefield Eel (Monopterus albus).

Forkhead box H1 (FoxH1) is a sexually dimorphic gene in Oreochromis niloticus, Oplegnathus fasciatus, and Acanthopagrus latus, indicating that it is essential for gonadal development. In the present study, the molecular characteristics and potential function of FoxH1 and the activation of the cyp19a1a promoter in vitro were evaluated in Monopterus albus. The levels of foxh1 in the ovaries were three times higher than those in the testes and were regulated by gonadotropins (Follicle-Stimulating Hormone and Human Chorionic Gonadotropin). FoxH1 colocalized with Cyp19a1a in the oocytes and granulosa cells of middle and late vitellogenic follicles. In addition, three FoxH1 binding sites were identified in the proximal promoter of cyp19a1a, namely, FH1 (-871/-860), FH2 (-535/-524), and FH3 (-218/-207). FoxH1 overexpression significantly attenuated the activity of the cyp19a1a promoter in CHO cells, and FH1/2 mutation increased promoter activity. Taken together, these results suggest that FoxH1 may act as an important regulator in the ovarian development of M. albus by repressing cyp19a1a promoter activity, which provides a foundation for the study of FoxH1 function in bony fish reproductive processes.

Establishment of cell-lines stably expressing recombinant Japanese eel follicle-stimulating hormone and luteinizing hormone using CHO-DG44 cells: fully induced ovarian development at different modes.

The gonadotropins (Gth), follicle-stimulating hormone (Fsh) and luteinizing hormone (Lh), play central roles in gametogenesis in vertebrates. However, available information on their differential actions in teleost, especially in vivo, is insufficient. In this study, we established stable CHO-DG44 cell lines expressing long-lasting recombinant Japanese eel Fsh and Lh with extra O-glycosylation sites (Fsh-hCTP and Lh-hCTP), which were produced in abundance. Immature female eels received weekly intraperitoneal injections of Gths. Fsh-hCTP induced the entire ovarian development by 8 weeks from the beginning of injection; thus, the ovaries of most fish were at the migratory nucleus stage while the same stage was observed in eels after 4 weeks in the Lh-hCTP-treated group. In contrast, all pretreated and saline-injected eels were in the pre-vitellogenic stage. Gonadosomatic indices in the Fsh-hCTP-treated group were significantly higher than those in the Lh-hCTP group at the migratory nucleus stage because of the significantly higher frequency of advanced ovarian follicles. Ovarian mRNA levels of genes related to E2 production (cyp11a1, cyp17a1, cyp19a1, hsd3b, fshr, and lhr) were measured using real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR). All genes were induced by both Fsh-hCTP and Lh-hCTP, with a peak at either the mid- or late vitellogenic stages. Transcript abundance of cyp19a1 and fshr in the Lh-hCTP group were significantly higher than those in the Fsh-hCTP group, whereas no difference in the expression of other genes was observed between the groups. Fluctuations in serum levels of sex steroid hormones (estradiol-17ß, 11-ketotestosterone, and testosterone) in female eels were comparable in the Fsh-hCTP and Lh-hCTP groups, thus increasing toward the maturational phase. Furthermore, the fecundity of the eels induced to mature by Fsh-hCTP was significantly higher than that induced by Lh-hCTP. These findings indicate that Fsh and Lh can induce ovarian development in distinctively different modes in the Japanese eel.

A chromosome-level reference genome assembly of the Reeve's moray eel (Gymnothorax reevesii).

Due to potentially hostile behaviors and elusive habitats, moray eels (Muraenidae) as one group of apex predators in coral reefs all across the globe have not been well investigated. Here, we constructed a chromosome-level genome assembly for the representative Reeve's moray eel (Gymnothorax reevesii). This haplotype genome assembly is 2.17 Gb in length, and 97.87% of the sequences are anchored into 21 chromosomes. It contains 56.34% repetitive sequences and 23,812 protein-coding genes, of which 96.77% are functionally annotated. This sequenced marine species in Anguilliformes makes a good complement to the genetic resource of eel genomes. It not only provides a genetic resource for in-depth studies of the Reeve's moray eel, but also enables deep-going genomic comparisons among various eels.

Specific Signal Transduction of Constitutively Activating (D576G) and Inactivating (R476H) Mutants of Agonist-Stimulated Luteinizing Hormone Receptor in Eel.

We investigated the mechanism of signal transduction using inactivating (R476H) and activating (D576G) mutants of luteinizing hormone receptor (LHR) of eel at the conserved regions of intracellular loops II and III, respectively, naturally occurring in mammalian LHR. The expression of D576G and R476H mutants was approximately 58% and 59%, respectively, on the cell surface compared to those of eel LHR-wild type (wt). In eel LHR-wt, cAMP production increased upon agonist stimulation. Cells expressing eel LHR-D576G, a highly conserved aspartic acid residue, exhibited a 5.8-fold increase in basal cAMP response; however, the maximal cAMP response by high-agonist stimulation was approximately 0.62-fold. Mutation of a highly conserved arginine residue in the second intracellular loop of eel LHR (LHR-R476H) completely impaired the cAMP response. The rate of loss in cell-surface expression of eel LHR-wt and D576G mutant was similar to the agonist recombinant (rec)-eel LH after 30 min. However, the mutants presented rates of loss higher than eel LHR-wt did upon rec-eCG treatment. Therefore, the activating mutant constitutively induced cAMP signaling. The inactivating mutation resulted in the loss of LHR expression on the cell surface and no cAMP signaling. These data provide valuable information regarding the structure-function relationship of LHR-LH complexes.

Transcription factors Dmrt1a, Foxl2, and Nr5a1a potentially interact to regulate cyp19a1a transcription in ovarian follicles of ricefield eel (Monopterus albus).

Aromatase (encoded by Cyp19a1) in the ovarian follicular cells catalyzes the production of estradiol from testosterone, which plays important roles in the ovarian development of vertebrates. In the present study, the interaction of Dmrt1, Foxl2, and Nr5a1a on the regulation of cyp19a1a transcription in ovarian follicles was examined in a teleost, the ricefield eel Monopterus albus. The expression of dmrt1a, foxl2, and nr5a1a was detected in ovarian follicular cells together with cyp19a1a at the mRNA and/or protein levels. Sequence analysis identified one conserved Foxo binding site in the proximal promoter region of ricefield eel cyp19a1a. Transient transfection assay showed that Foxl2 may bind to the conserved Foxo site to activate cyp19a1a transcription and act synergistically with Nr5a1a. Mutation of either the conserved Nr5a1 site or Foxo site abolished or significantly decreased the synergistic effects of Nr5a1a and Foxl2 on cyp19a1a transcription. The sequence between Region III and I-box of Nr5a1a was critical to this synergistic effect. Dmrt1a modulated the Foxl2- and Nr5a1a-induced activation of cyp19a1a transcription and their synergistic effects in a biphasic manner, with inhibitory roles observed at lower doses (10-50 ng) but release of the inhibition or even potentiating effects observed at higher doses (100-200 ng). Collectively, data of the present study suggest that the interaction of Dmrt1a, Foxl2, and Nr5a1a in the ovarian follicular cells may facilitate the adequate expression of cyp19a1a and the production of estradiol, and contribute to the development and maturation of ovarian follicles in ricefield eels and other vertebrates as well.

A new species of the congrid eel genus Conger (Anguilliformes: Congridae) from the southwest coast of India.

A new species of Conger eel is described from a single specimen (569 mm total length) collected off Kanyakumari, Southwest coast of India, Arabian Sea. The following characters distinguish the new species from other congeners: dorsal-fin origin behind the pectoral-fin tip; head larger, 18.5% TL; longer predorsal length 24.0% TL; relatively shorter trunk, uniserial teeth at the posterior end of vomerine patch; body blackish to dark brown; pectoral fin completely darker; cephalic pores rim whitish; SO pores 3; IO pores 6; pectoral rays 19; total vertebrae 141+. Genetic analysis of the mitochondrial COI gene revealed that the new species is closely related to Conger verreauxi Kaup, 1856 and Conger macrocephalus Kanazawa, 1958, with a genetic divergence of 5.7% and 5.9% respectively.

Genetic diversity of Toll-like receptor 9 in swamp eels (Monopterus albus).

The swamp eel, Monopterus albus, is an important aquaculture species in Asia (mainly China) whose production has seriously suffered from infectious diseases. In spite of the critical requirement for aquaculture practices, to date there is scant information on its immune defence. Here, the genetic characteristics of Toll-like receptor 9 (TLR9), which plays crucial roles in the initiation of host defence against microbial invasion, were analysed. It exhibits a striking lack of genetic variation resulting from a recent demographic bottleneck. A comparison with the homologue of M. javanensis revealed that replacement but not silent differences have nonrandomly accumulated in the coding sequences at the early stage following their split from a common ancestor. Furthermore, the replacements relevant to the type II functional divergence have mainly occurred in structural motifs mediating ligand recognition and receptor homodimerization. These results provide hints to understand the diversity-based strategy of TLR9 in the arms race against pathogens. Furthermore, the findings reported here give credence to the importance of basic immunology knowledge, especially for the key elements, in genetic engineering and breeding for disease resistance in the eel and other fishes.

A new deep-water conger eel of the genus Rhynchoconger (Anguilliformes: Congridae) from the south-west coast of India, Arabian Sea.

A new species of deep-water conger eel, Rhynchoconger bicoloratus sp. nov., is described herein based on three specimens collected from the deep-sea trawlers landing at Kalamukku fishing harbour, off Kochi, Arabian Sea, from a depth beyond 200 m. The new species is distinguished from its congeners by having the following combination of characters: head larger than trunk, rictus at posterior margin of pupil, dorsal fin origin slightly before the pectoral fin insertion, eye diameter 1.7-1.9 times in snout length, ethmovomerine teeth patch broader than long with 41-44 recurved pointed teeth in six or seven rows, vomerine teeth patch pentagonal shaped with single tooth on posterior end, 35 pre-anal vertebrae, body bicoloured, peritoneum and stomach black. Genetically, the new species differs from its congeners with a divergence of 12.9%-20.1% in the mitochondrial COI gene.

Genome structures resolve the early diversification of teleost fishes.

Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts are the largest and most diversified group of extant vertebrates, but relationships among their three oldest extant lineages remain unresolved. On the basis of seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (arapaima, elephantnose fish) in a monophyletic sister group to all other teleosts, i.e., the Clupeocephala lineage (zebrafish, medaka). This finding resolves more than 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.

A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus.

Despite increasing sequencing efforts, numerous fish families still lack a reference genome, which complicates genetic research. One such understudied family is the sand lances (Ammodytidae, literally: "sand burrower"), a globally distributed clade of over 30 fish species that tend to avoid tidal currents by burrowing into the sand. Here, we present the first annotated chromosome-level genome assembly of the great sand eel (Hyperoplus lanceolatus). The genome assembly was generated using Oxford Nanopore Technologies long sequencing reads and Illumina short reads for polishing. The final assembly has a total length of 808.5 Mbp, of which 97.1% were anchored into 24 chromosome-scale scaffolds using proximity-ligation scaffolding. It is highly contiguous with a scaffold and contig N50 of 33.7 and 31.3 Mbp, respectively, and has a BUSCO completeness score of 96.9%. The presented genome assembly is a valuable resource for future studies of sand lances, as this family is of great ecological and commercial importance and may also contribute to studies aiming to resolve the suprafamiliar taxonomy of bony fishes.

Pseudo-chromosome-length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation.

High hydrostatic pressure, low temperature, and scarce food supply are the major factors that limit the survival of vertebrates in extreme deep-sea environments. Here, we constructed a high-quality genome of the deep-sea Muddy arrowtooth eel (MAE, Ilyophis brunneus, captured below a depth of 3,500 m) by using Illumina, PacBio, and Hi-C sequencing. We compare it against those of shallow-water eel and other outgroups to explore the genetic basis that underlies the adaptive evolution to deep-sea biomes. The MAE genome was estimated to be 1.47 Gb and assembled into 14 pseudo-chromosomes. Phylogenetic analyses indicated that MAE diverged from its closely related shallow-sea species, European eel, ∼111.9 Mya and experienced a rapid evolution. The genome evolutionary analyses primarily revealed the following: (i) under high hydrostatic pressure, the positively selected gene TUBGCP3 and the expanded family MLC1 may improve the cytoskeleton stability; ACOX1 may enhance the fluidity of cell membrane and maintain transport activity; the expansion of ABCC12 gene family may enhance the integrity of DNA; (ii) positively selected HARS likely maintain the transcription ability at low temperatures; and (iii) energy metabolism under a food-limited environment may be increased by expanded and positively selected genes in AMPK and mTOR signaling pathways.