Fish biology has been developed for more than 100 years, but some important breakthroughs have been made in the last decade. Early studies commonly concentrated on morphology, phylogenetics, development, growth, reproduction manipulation, and disease control. Recent studies have mostly focused on genetics, molecular biology, genomics, and genome biotechnologies, which have provided a solid foundation for enhancing aquaculture to ensure food security and improving aquatic environments to sustain ecosystem health. Here, we review research advances in five major areas: (1) biological innovations and genomic evolution of four significant fish lineages including non-teleost ray-finned fishes, northern hemisphere sticklebacks, East African cichlid fishes, and East Asian cyprinid fishes; (2) evolutionary fates and consequences of natural polyploid fishes; (3) biological consequences of fish domestication and selection; (4) development and innovation of fish breeding biotechnologies; and (5) applicable approaches and potential of fish genetic breeding biotechnologies. Moreover, five precision breeding biotechniques are examined and discussed in detail including gene editing for the introgression or removal of beneficial or detrimental alleles, use of sex-specific markers for the production of mono-sex populations, controllable primordial germ cell on-off strategy for producing sterile offspring, surrogate broodstock-based strategies to accelerate breeding, and genome incorporation and sexual reproduction regain-based approach to create synthetic polyploids. Based on these scientific and technological advances, we propose a blueprint for genetic improvement and new breed creation for aquaculture species and analyze the potential of these new breeding strategies for improving aquaculture seed industry and strengthening food security.

Rethinking fish biology and biotechnologies in the challenge era for burgeoning genome resources and strengthening food security

The grass carp has great economic value and occupies an important evolutionary position. Genomic information regarding this species could help better understand its rapid growth rate as well as its unique body plan and environmental adaptation.We assembled the chromosome-level grass carp genome using the PacBio sequencing and chromosome structure capture technique. The final genome assembly has a total length of 893.2 Mb with a contig N50 of 19.3 Mb and a scaffold N50 of 35.7 Mb. About 99.85% of the assembled contigs were anchored into 24 chromosomes. Based on the prediction, this genome contained 30,342 protein-coding genes and 43.26% repetitive sequences. Furthermore, we determined that the large genome size can be attributed to the DNA-mediated transposable elements which accounted for 58.9% of the repetitive sequences in grass carp. We identified that the grass carp has only 24 pairs of chromosomes due to the fusion of two ancestral chromosomes. Enrichment analyses of significantly expanded and positively selected genes reflected evolutionary adaptation of grass carp to the feeding habits. We also detected the loss of conserved non-coding regulatory elements associated with the development of the immune system, nervous system, and digestive system, which may be critical for grass carp herbivorous traits.The high-quality reference genome reported here provides a valuable resource for the genetic improvement and molecular-guided breeding of the grass carp. 

/pdf/chromosome-level-genome-assembly-of-grass-carp-1i462xl2.pdf

Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution

Fish biology has been developed for more than 100 years, but some important breakthroughs have been made in the last decade. Early studies commonly concentrated on morphology, phylogenetics, development, growth, reproduction manipulation, and disease control. Recent studies have mostly focused on genetics, molecular biology, genomics, and genome biotechnologies, which have provided a solid foundation for enhancing aquaculture to ensure food security and improving aquatic environments to sustain ecosystem health. Here, we review research advances in five major areas: (1) biological innovations and genomic evolution of four significant fish lineages including non-teleost ray-finned fishes, northern hemisphere sticklebacks, East African cichlid fishes, and East Asian cyprinid fishes; (2) evolutionary fates and consequences of natural polyploid fishes; (3) biological consequences of fish domestication and selection; (4) development and innovation of fish breeding biotechnologies; and (5) applicable approaches and potential of fish genetic breeding biotechnologies. Moreover, five precision breeding biotechniques are examined and discussed in detail including gene editing for the introgression or removal of beneficial or detrimental alleles, use of sex-specific markers for the production of mono-sex populations, controllable primordial germ cell on-off strategy for producing sterile offspring, surrogate broodstock-based strategies to accelerate breeding, and genome incorporation and sexual reproduction regain-based approach to create synthetic polyploids. Based on these scientific and technological advances, we propose a blueprint for genetic improvement and new breed creation for aquaculture species and analyze the potential of these new breeding strategies for improving aquaculture seed industry and strengthening food security. 

Extraction, purification, structural characteristics, biological activities, and application of the polysaccharides from Nelumbo nucifera Gaertn. (lotus): A review.

Transforming dense MXene (Ti3C2Tx) films into lightweight 3D porous frameworks is crucial for practical applications of 2D MXene materials. However, traditional foaming technologies may compromise the intrinsic properties of MXene films, such as foldability, which is essential for future applications. Here, we report an approach using a common acid-base neutralization reaction to rapidly foam MXene films. The acid solution triggers the generation of porous structures in alkalized MXene films, resulting in a 3D porous MXene film with good foldability, excellent absolute shielding efficiency (25,445 dB cm2 g−1), electrochemical capacitance, and infrared stealth properties. Furthermore, the acid-base neutralization reaction strategy can be applied to foam other 2D material films, such as graphene oxide, broadening the potential for developing innovative foaming modes of 2D materials. This work enhances our understanding of MXene film foaming and lays the foundation for further applications of MXenes. 

Rapid foaming of dense MXene films induced by acid-base neutralization reaction

The edible silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis), which are two of the "Four Domesticated Fish" of China, are cultivated intensively worldwide. Here, we constructed 837- and 845-Mb draft genome assemblies for the silver carp and the bighead carp, respectively, including 24,571 and 24,229 annotated protein-coding genes. Genetic maps, anchoring 71.7% and 83.8% of all scaffolds, were obtained for the silver and bighead carp, respectively. Phylogenetic analysis showed that the bighead carp formed a clade with the silver carp, with an estimated divergence time of 3.6 million years ago; the time of divergence between the silver carp and zebrafish was 50.7 million years ago. An East Asian cyprinid genome-specific chromosome fusion took place ~9.2 million years after this clade diverged from the clade containing the common carp and Sinocyclocheilus. KEGG and GO analyses indicated that the expanded gene families in the silver and bighead carp were associated with diseases, the immune system and environmental adaptations. Genomic regions differentiating the silver and bighead carp populations were detected based on the whole-genome sequences of 42 individuals. Genes associated with the divergent regions were associated with reproductive system development and the development of primary female sexual characteristics. Thus, our results provided a novel systematic genomic analysis of the East Asian cyprinids, as well as the evolution and speciation of the silver carp and bighead carp.

Whole genome sequencing of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) provide novel insights into their evolution and speciation

Lotus (family: Nelumbonaceae) are perennial aquatic plants that represent one of the most ancient basal dicots. In the present study, we resequenced 296 lotus accessions from various geographical locations and germplasms to explore their genomic diversity and population structure. This germplasm set consisted of four accessions of American wild lotus and 292 accessions of Asian lotus, which were divided into four subgroups: wild, rhizome, flower and seed. Total single nucleotide polymorphisms (SNPs) suggested that the wild lotus had the highest variant number (7 191 010). Population structure and genome diversity analysis indicated that the American wild lotus demonstrated a distant genetic relationship with the Asian lotus. Furthermore, the seed and rhizome lotus groups had not originated from a single source but rather had a more complex multisource origin. Besides that, the seed lotus showed higher genetic diversity, which might have been due to the gene flow from the flower lotus to seed lotus by artificial crossing, and the rhizome lotus showed a much lower genetic diversity than the other groups. The present study provides SNP markers for lotus genomic diversity analysis, which will be useful for guiding lotus breeding.

Resequencing of 296 cultivated and wild lotus accessions unravels its evolution and breeding history

A fucan sulfate (HfFS) was isolated from the sea cucumber Holothuria floridana after proteolysis-alkaline treatment and purified with anion-exchange chromatography. The molecular weight (Mw) of HfFS was determined to be 443.4 kDa, and the sulfate content of HfFS was 30.4%. The structural analysis of the peroxidative depolymerized product (dHfFS-1) showed that the primary structure of HfFS was mainly composed of a distinct pentasaccharide repeating unit -[l-Fuc2S4S-α(1,3)-l-Fuc-α(1,3)-Fuc-α(1,3)-l-Fuc2S-α(1,3)-l-Fuc2S-α(1,3)-]n-. Then, the “bottom-up” strategy was employed to confirm the structure of HfFS, and a series of fucooligosaccharides (disaccharides, trisaccharides, and tetrasaccharides) were purified from the mild acid-hydrolyzed HfFS. The structures identified through 1D/2D NMR spectra showed that these fucooligosaccharides could be derivates from the pentasaccharide units, while the irregular sulfate substituent also exists in the units. Anticoagulant activity assays of native HfFS and its depolymerized products (dHf-1~dHf-6) in vitro suggested that HfFS exhibits potent APTT-prolonging activity and the potencies decreased with the reduction in molecular weights, and HfFS fragments (dHf-4~dHf-6) with Mw less than 11.5 kDa showed no significant anticoagulant effect. Overall, our study enriched the knowledge about the structural diversity of FSs in different sea cucumber species and their biological activities.

https://www.mdpi.com/1660-3397/20/6/377/pdf?version=1654251578

A Fucan Sulfate with Pentasaccharide Repeating Units from the Sea Cucumber Holothuria floridana and Its Anticoagulant Activity

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Whole genome sequencing of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) provide novel insights into their evolution and speciation

Resequencing of 296 cultivated and wild lotus accessions unravels its evolution and breeding history

A Fucan Sulfate with Pentasaccharide Repeating Units from the Sea Cucumber Holothuria floridana and Its Anticoagulant Activity