A chromosomelevel genome assembly of the Asian arowana, Scleropages formosus

Asian arowana (Scleropages formosus), an ancient teleost belonging to the Order Osteoglossomorpha, has been a valuable ornamental fish with some varieties. However, its biological studies and breeding germplasm have been remarkably limited by the lack of a reference genome. To solve these problems, here we report high-quality genome sequences of three common varieties of Asian arowana (the golden, red and green arowana). We firstly generated a chromosome-level genome assembly of the golden arowana, on basis of the genetic linkage map constructed with the restriction site-associated DNA sequencing (RAD-seq). In addition, we obtained draft genome assemblies of the red and green varieties. Finally, we annotated 22,016, 21,256 and 21,524 protein-coding genes in the genome assemblies of golden, red and green varieties respectively. Our data were deposited in publicly accessible repositories to promote biological research and molecular breeding of Asian arowana

Study on aging parameters and effect of rice wine based on aging device

Rice wine is a kind of low alcohol and high nutrition four season drinking wine made from water and glutinous rice. Generally, new rice wine needs to undergo a natural aging process for about 1 year. In order to solve the problems of long natural aging period and poor aging effect of rice wine, a set of rice wine aging device was designed and a comprehensive method was used to age the rice wine. By orthogonal experiments, the optimal aging process parameters were determined, which were temperature 55 °C, aging time 12 days, and hydrogen peroxide addition 4 mL/200 mL. The results show that the content of ethyl acetate and ethyl lactate in rice wine are 0.44 g/L and 0.80 g/L respectively and the content of total acid and total sugar reaches 6.9 g/L and 230.2 g/L respectively. Compared with naturally aged rice wine, it is verified that the effect of artificial aging can achieve the effect of natural aging for one year. This experiment provides a new method for the study of artificial aging of rice wine

Research on the Morphology Reconstruction of Deep Cryogenic Treatment on PtRu/nitrogen-Doped Graphene Composite Carbon Nanofibers

To improve the performance of PtRu/nitrogen-doped graphene composite carbon nanofibers, the composite carbon nanofibers were thermally compensated by deep cryogenic treatment (DCT), which realized the morphology reconstruction of composite carbon nanofibers. The effects of different DCT times were compared: 12 h, 18 h, and 24 h. The morphology reconstruction mechanism was explored by combining the change of inner chain structure and material group. The results showed that the fibers treated for 12 h had better physical and chemical properties, where the diameter is evenly distributed between 500 and 800 nm. Combined with Fourier infrared analysis, the longer the cryogenic time, the more easily the water vapor and nitrogen enter polymerization reaction, causing changes of chain structure and degradation performance. With great performance of carbonization and group transformation, the PtRu/nitrogen-doped graphene composite carbon nanofibers can be used as an efficient direct alcohol fuel cell catalyst and promote its commercialization

Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes

Limbs originated from paired fish fins are an important innovation in Gnathostomata. Many studies have focused on limb development-related genes, of which the T-box transcription factor 4 gene (tbx4) has been considered as one of the most essential factors in the regulation of the hindlimb development. We previously confirmed pelvic fin loss in tbx4-knockout zebrafish. Here, we report a high-quality genome assembly of the Japanese eel (Anguilla japonica), which is an economically important fish without pelvic fins. The assembled genome is 1.13 Gb in size, with a scaffold N50 of 1.03 Mb. In addition, we collected 24 tbx4 sequences from 22 teleost fishes to explore the correlation between tbx4 and pelvic fin evolution. However, we observed complete exon structures of tbx4 in several pelvic-fin-loss species such as Ocean sunfish (Mola mola) and ricefield eel (Monopterus albus). More interestingly, an inversion of a special tbx4 gene cluster (brip1-tbx4-tbx2b- bcas3) occurred twice independently, which coincides with the presence of fin spines. A nonsynonymous mutation (M82L) was identified in the nuclear localization sequence (NLS) of the Japanese eel tbx4. We also examined variation and loss of hindlimb enhancer B (HLEB), which may account for pelvic fin loss in Tetraodontidae and Diodontidae. In summary, we generated a genome assembly of the Japanese eel, which provides a valuable genomic resource to study the evolution of fish tbx4 and helps elucidate the mechanism of pelvic fin loss in teleost fishes. Our comparative genomic studies, revealed for the first time a potential correlation between the tbx4 gene cluster and the evolutionary development of toxic fin spines. Because fin spines in teleosts are usually venoms, this tbx4 gene cluster may facilitate the genetic engineering of toxin-related marine drugs

Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes

Naturally derived toxins from animals are good raw materials for drug development. As a representative venomous teleost, Chinese yellow catfish (Pelteobagrus fulvidraco) can provide valuable resources for studies on toxin genes. Its venom glands are located in the pectoral and dorsal fins. Although with such interesting biologic traits and great value in economy, Chinese yellow catfish is still lacking a sequenced genome. Here, we report a high-quality genome assembly of Chinese yellow catfish using a combination of next-generation Illumina and third-generation PacBio sequencing platforms. The final assembly reached 714 Mb, with a contig N50 of 970 kb and a scaffold N50 of 3.65 Mb, respectively. We also annotated 21,562 protein-coding genes, in which 97.59% were assigned at least one functional annotation. Based on the genome sequence, we analyzed toxin genes in Chinese yellow catfish. Finally, we identified 207 toxin genes and classified them into three major groups. Interestingly, we also expanded a previously reported sex-related region (to ≈6 Mb) in the achieved genome assembly, and localized two important toxin genes within this region. In summary, we assembled a high-quality genome of Chinese yellow catfish and performed high-throughput identification of toxin genes from a genomic view. Therefore, the limited number of toxin sequences in public databases will be remarkably improved once we integrate multi-omics data from more and more sequenced species

Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii

Background: As one of the most popular and valuable commercial marine fishes in China and East Asian countries, the Chinese black porgy (Acanthopagrus schlegelii), also known as the blackhead seabream, has some attractive characteristics such as fast growth rate, good meat quality, resistance to diseases, and excellent adaptability to various environments. Furthermore, the black porgy is a good model for investigating sex changes in fish due to its protandrous hermaphroditism. Here, we obtained a high-quality genome assembly of this interesting teleost species and performed a genomic survey on potential genes associated with the sex-change phenomenon. Findings: We generated 175.4 gigabases (Gb) of clean sequence reads using a whole-genome shotgun sequencing strategy. The final genome assembly is approximately 688.1 megabases (Mb), accounting for 93% of the estimated genome size (739.6 Mb). The achieved scaffold N50 is 7.6 Mb, reaching a relatively high level among sequenced fish species. We identified 19 465 protein-coding genes, which had an average transcript length of 17.3 kb. By performing a comparative genomic analysis, we found 3 types of genes potentially associated with sex change, which are useful for studying the genetic basis of the protandrous hermaphroditism. Conclusions: We provide a draft genome assembly of the Chinese black porgy and discuss the potential genetic mechanisms of sex change. These data are also an important resource for studying the biology and for facilitating breeding of this economically important fish.</p

Golden_arowana_chromosomes_gene_annotation

This "gff" format file contains the gene annotation of golden arowana chromosomes

Three_varieties_of_arowana_gene_annotation_gff

This '.zip' file contains the three "gff" format annotation files of the genome assemblies of golden, red and green arowana varieties, respectively