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

Comparative genomic analysis of immune-related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated Asian carps

BACKGROUND

Ctenopharyngodon idella (grass carp), Mylopharyngodon piceus (black carp), Hypophthalmichthys nobilis (bighead carp), and Hypophthalmichthys molitrix (silver carp), collectively known as the four major domesticated Asian carp, are freshwater fish species from the family Cyprinidae and are widely consumed in China. Current studies on these species primarily focus on immune system regulation and the growth and development of individual species. However, in-depth genomic investigations and comprehensive comparative analysis remained limited.

METHODS

The complete genomes of Ctenopharyngodon idella, Mylopharyngodon piceus and Hypophthalmichthys nobilis were assembled using a hybrid approach that integrated both next- and third-generation sequencing reads, followed by annotation using the MAKER2 pipeline. Based on the high-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus Hypophthalmichthys nobilis, and Hypophthalmichthys molitrix, a comparative genomic analysis was conducted using bioinformatic tools to investigate gene family evolution in these four domesticated Asian carp species.

RESULTS

High-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus, and Hypophthalmichthys nobilis were assembled, achieving over 90% completeness. Immune-related gene families, including MHC class I and NLRC3-like genes, have undergone rapid evolution, with Ctenopharyngodon idella exhibiting significant expansion of NLRC3-like genes. Massive tandem duplication events were identified in trace amine-associated receptors (TAARs), and rapid expansion was observed in TAAR16 and TAAR29. Additionally, a novel TAAR gene cluster was identified in all four Asian carp species. Comparative genomic analysis revealed the expansion of type 1 taste receptor genes, particularly in Ctenopharyngodon idella and Mylopharyngodon piceus.

CONCLUSION

This study has successfully constructed the high-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus, and Hypophthalmichthys nobilis. The comparative genomic analysis revealed the evolution of immune-related genes and chemosensory receptors in the four major domesticated Asian carp species. These findings suggested the enhanced immunity and sensory perception in these species, providing valuable insights into their adaptation, survival and reproduction.

EccDNA Analysis Provides Novel Insights Into the Molecular Mechanism of Firmness of Fish Fillet

Extrachromosomal circular DNAs (eccDNAs) play a significant role in regulating various biological processes, including abnormal muscle development. The molecular functions and impact of eccDNAs in the muscle development of fish are poorly understood. To investigate the potential roles of eccDNAs in the muscle development of fish, we analyzed and compared the expression profile of muscle eccDNAs of crisp grass carp, fed a faba bean meal-based diet, and ordinary grass carp, fed a practical diet. Using the Circle-seq strategy, we found the eccDNA abundance in crisp grass carp (211,920 eccDNAs) was significantly higher than that in ordinary grass carp (25,857 eccDNAs), suggesting that the faba bean diet likely independently influences eccDNA production. Compared to ordinary grass carp, crisp grass carp exhibited 10,565 upregulated and 129 downregulated eccDNAs, indicating eccDNAs were possibly associated with the muscle development of grass carp. GO and KEGG enrichment analyses indicated that the upregulated eccDNAs were related to muscle fiber development, cellular structure, and cell junctions. Based on our results, we speculated that the overexpression of genes involved in muscle fiber, calcium metabolism, and collagen driven by eccDNAs likely contributes to the observed increase in muscle fiber density, calcium levels, and collagen content in crisp grass carp, thereby enhancing muscle hardness. Notably, eccDNAs were identified as potential innate immunostimulants capable of eliciting immune responses in fish. In summary, our findings demonstrate that eccDNAs are aberrantly expressed in the muscles of fish fed a faba bean diet, offering novel insights into the molecular mechanisms underlying muscle hardening in fish.

The First Genome-Wide Survey Analysis of the Tibetan Plateau Tetraploid Schizothorax curvilabiatus Reveals Its Microsatellite Characteristics and Phylogenetic Relationships

Background/Objectives: Schizothorax curvilabiatus, a typical highland polyploid species within the subfamily Schizothoracinae, holds economic value and ecological research significance. Currently, there are no related genomic studies. To obtain its genetic information and lay the foundation for subsequent whole-genome map construction, this study conducted a genome survey analysis, preliminary genome assembly, microsatellite identification, repeat sequence annotation, mitochondrial genome characterization, and phylogenetic relationship research. Methods: DNA was sequenced on a DNBSEQ-T7 platform to obtain paired-end genomic data. The genome was analyzed using GCE, and the draft genome was assembled with SOAPdenovo. Microsatellites were identified using MISA, and the mitochondrial genome was assembled with NOVOPlasty. Genome features were analyzed, and phylogenetic trees were constructed using PhyloSuite and MEGA. Results: The genome size was estimated at 2.53 Gb, with a heterozygosity of 6.55% and 47.66% repeat sequences. A 1.324 Gb preliminary genome draft was obtained, with repeat sequences comprising 47.17%, the majority being DNA transposons (24.64%). Dinucleotide repeats were most abundant (46.91%), followed by mononucleotide repeats (38.31%), with A/T and AC/GT being the most frequent. A complete mitochondrial genome of 16,589 bp was assembled, and a 939 bp D-loop was annotated. Phylogenetic relationships among genera in the Schizothoracinae subfamily were also clarified. Conclusions: This study provides the latest molecular data for analysis of the S. curvilabiatus genome and its related populations, and for the first time offers genomic resources for research on genomic adaptive evolution and polyploidization in high-altitude environments.

Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologies

Xenocypris davidi is a benthic fish species widely distributed in the water systems south of the Yellow River in China, playing a significant role in aquatic ecosystems. Despite its ecological and economic importance, genomic resources for X. davidi are limited, hindering a comprehensive understanding of its evolutionary adaptations and genetic improvements. This study presents the first chromosome-level genome assembly of X. davidi, utilizing PacBio long-reads, Illumina short reads, and Hi-C sequencing data. The genome assembly spans 1.05 Gb with a scaffold N50 length of 33.99 Mb, and 95.12% of the genome sequence was successfully anchored onto 24 pseudochromosomes. We identified 27,360 protein-coding genes, of which 26,672 were functionally annotated. This genome sequence provides a valuable resource for exploring the molecular basis of agronomic traits in X. davidi and will facilitate its genetic enhancement.

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity

BACKGROUND

In this study, we present an in-depth analysis of the Eurasian minnow (Phoxinus phoxinus) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chromosome-level genome assembly (2n = 50) by integrating high-fidelity (HiFi) long reads and chromosome conformation capture data (Hi-C).

RESULTS

We achieved a haploid size of 940 megabase pairs (Mbp) for haplome 1 and 929 Mbp for haplome 2 with high scaffold N50 values of 36.4 Mb and 36.6 Mb and BUSCO scores of 96.9% and 97.2%, respectively, indicating a highly complete genome assembly. We detected notable heterozygosity (1.43%) and a high repeat content (approximately 54%), primarily consisting of DNA transposons, which contribute to genome rearrangements and variations. We found substantial structural variations within the genome, including insertions, deletions, inversions, and translocations. These variations affect genes enriched in functions such as dephosphorylation, developmental pigmentation, phagocytosis, immunity, and stress response. In the annotation of protein-coding genes, 30,980 messenger RNAs and 23,497 protein-coding genes were identified with a high completeness score, which further underpins the high contiguity of our genome assemblies. We performed a gene family evolution analysis by comparing our proteome to 10 other teleost species, which identified immune system gene families that prioritize histone-based disease prevention over NB-LRR-related-based immune responses. Additionally, demographic analysis indicates historical fluctuations in the effective population size of P. phoxinus, likely correlating with past climatic changes.

CONCLUSIONS

This annotated, phased reference genome provides a crucial resource for resolving the taxonomic complexity within the genus Phoxinus and highlights the importance of haplotype-phased assemblies in understanding haplotype diversity in species characterized by high heterozygosity.

Tryptophan supplements in high-carbohydrate diets by improving insulin response and glucose transport through PI3K-AKT-GLUT2 pathways in blunt snout bream (Megalobrama amblycephala)

The aim of this experiment was to elucidate the metabolic ramifications of tryptophan supplementation in the context of high-carbohydrate diet-feeding, which is important for improving feeding strategies in aquaculture in order to improve fish carbohydrate metabolism. Juvenile blunt snout bream with an initial mean body mass of 55.0±0.5 g were allocated to consume one of three experimental diets: CN, a normal diet with carbohydrate content of 30% (w/w); HC, a diet with high carbohydrate content of 43% (w/w); and HL, a high-carbohydrate diet to which 0.8% L-tryptophan (L-trp) had been added. These diets were fed for 8 weeks, and the effects of the carbohydrate and tryptophan contents of the diets were assessed. Histological analysis using Hematoxylin and Eosin (H&E) and Oil Red O staining revealed that high-carbohydrate intake was associated with abnormal hepatocyte morphology and excessive liver lipid accumulation, which were notably ameliorated by tryptophan supplementation. A significant increase in plasma glucose, glucagon, AGEs (advanced glycation end products), triglycerides, total cholesterol, and a significant decrease in insulin and hepatic glycogen after a high-carbohydrate diet in terms of plasma indices, compared to the control group. Almost all of them were restored to the normal level in the HL group. The present study might preliminarily suggest that tryptophan supplementation ameliorates the imbalance in glucose metabolism of this species induced by a high-carbohydrate diet. Transcriptomics showed that glucose metabolism under high carbohydrate was mainly regulated by the PI3K-AKT signaling pathway. The mRNA expression and protein levels of GLUT2 also varied with this pathway, which would suggest that sustained activation of this pathway with the addition of tryptophan accelerates glucose transport and insulin secretion under high-carbohydrate diet. Subsequent GTT and ITT experiments have also demonstrated that tryptophan improves glucose tolerance and insulin tolerance in blunt snout bream on a high-carbohydrate diet. In conclusion, these findings elucidate the positive regulatory effect of tryptophan on the PI3K-AKT-GLUT2 pathway under a high carbohydrate diet and provide a theoretical basis for the subsequent rational application of high carbohydrate diets in the future.

Chromosome-Level Assembly and Annotation of the Endangered Red-Wing Fish (Distoechodon macrophthalmus)

Background/Objectives: The red-wing fish (Distoechodon macrophthalmus), an endangered species native to Yunnan, is endemic to Chenghai Lake. The natural population of this species has suffered a sharp decline due to the invasion of alien fish species. Fortunately, the artificial domestication and reproduction of D. macrophthalmus have been successful and this species has become an economic species locally. However, there is still little research on D. macrophthalmus. Methods: In this study, a high-quality genome of D. macrophthalmus was assembled and annotated. The genome was sequenced and assembled using the PacBio platform and Hi-C method. Results: The genome size is 1.01 Gb and N50 is 37.99 Mb. The assembled contigs were anchored into 24 chromosomes. BUSCO analysis revealed that the genome assembly has 95.6% gene coverage completeness. A total of 455.62 Mb repeat sequences (48.50% of the assembled genome) and 30,424 protein-coding genes were identified in the genome. Conclusions: This study provides essential genomic data for further research on the evolution and conservation of D. macrophthalmus. Meanwhile, the high-quality genome assembly also provides insights into the genomic evolution of the genus Distoechodon.

Chromosome-level genome assembly of the mud carp (Cirrhinus molitorella) using PacBio HiFi and Hi-C sequencing

The mud carp (Cirrhinus molitorella) is an important economic farmed fish, mainly distributed in South China and Southeast Asia due to its strong adaptability and high yield. Despite its economic importance, the paucity of genomic information has constrained detailed genetic research and breeding efforts. In this study, we utilized PacBio HiFi long-read sequencing and Hi-C technologies to generate a meticulously assembled chromosome-level genome of the mud carp. This assembly spans 1,033.41 Mb, with an impressive 99.82% distributed across 25 chromosomes. The contig N50 and scaffold N50 are 33.29 Mb and 39.86 Mb, respectively. The completeness of the mud carp genome assembly is highlighted by a BUSCO score of 98.05%. We predict 25,865 protein-coding genes, with a BUSCO score of 96.54%, and functional annotations for 91.83% of these genes. Approximately 52.21% of the genome consists of repeat elements. This high-fidelity genome assembly is a vital resource for advancing molecular breeding, comparative genomics, and evolutionary studies of the mud carp and related species.

Genetic improvement and genomic resources of important cyprinid species: status and future perspectives for sustainable production

Cyprinid species are the most cultured aquatic species around the world in terms of quantity and total value. They account for 25% of global aquaculture production and significantly contribute to fulfilling the demand for fish food. The aquaculture of these species is facing severe concerns in terms of seed quality, rising feed costs, disease outbreaks, introgression of exotic species, environmental impacts, and anthropogenic activities. Numerous researchers have explored biological issues and potential methods to enhance cyprinid aquaculture. Selective breeding is extensively employed in cyprinid species to enhance specific traits like growth and disease resistance. In this context, we have discussed the efforts made to improve important cyprinid aquaculture practices through genetic and genomic approaches. The recent advances in DNA sequencing technologies and genomic tools have revolutionized the understanding of biological research. The generation of a complete genome and other genomic resources in cyprinid species has significantly strengthened molecular-level investigations into disease resistance, growth, reproduction, and adaptation to changing environments. We conducted a comprehensive review of genomic research in important cyprinid species, encompassing genome, transcriptome, proteome, metagenome, epigenome, etc. This review reveals that considerable data has been generated for cyprinid species. However, the seamless integration of this valuable data into genetic selection programs has yet to be achieved. In the upcoming years, genomic techniques, gene transfer, genome editing tools are expected to bring a paradigm shift in sustainable cyprinid aquaculture production. The comprehensive information presented here will offer insights for the cyprinid aquaculture research community.

Anti-infective immune functions of type IV interferon in grass carp ( Ctenopharyngodon idella): A novel antibacterial and antiviral interferon in lower vertebrates

Type IV interferon (IFN-υ) is a recently discovered cytokine crucial for host defense against viral infections. However, the role and mechanisms of IFN-υ in bacterial infections remain unexplored. This study investigated the antibacterial and antiviral functions and mechanisms of grass carp ( Ctenopharyngodon idella) IFN-υ (CiIFN-υ) both in vivo and in vitro. The CiIFN-υ gene was first identified and characterized in grass carp. Subsequently, the immune expression of CiIFN-υ significantly increased following bacterial challenge, indicating its response to bacterial infections. The eukaryotic recombinant expression plasmid of CiIFN-υ was then constructed and transfected into fathead minnow (FHM) cells. Supernatants were collected and incubated with four bacterial strains, followed by plate spreading and colony counting. Results indicated that CiIFN-υ exhibited more potent antibacterial activity against gram-negative bacteria compared to gram-positive bacteria and aggregated gram-negative bacteria but not gram-positive bacteria. In vivo experiments further confirmed the antibacterial function, showing high survival rates, low tissue edema and damage, reduced tissue bacterial load, and elevated proinflammatory response at the early stages of bacterial infection. In addition, the antiviral function of CiIFN-υ was confirmed through in vitro and in vivo experiments, including crystal violet staining, survival rates, tissue viral burden, and RT-qPCR. This study highlights the antibacterial function and preliminary mechanism of IFN-υ, demonstrating that IFN-υ possesses dual functions against bacterial and viral infections.

Chromosome-level genome assembly and annotation of the Spinibarbus caldwelli

Spinibarbus caldwelli is an important freshwater economic fish in China. Owing to uncontrolled fishing, wild resources of S. caldwelli have decreased rapidly and may be on the verge of extinction. In this study, utilizing single-molecule real-time (SMRT) sequencing technology and chromatin interaction mapping (Hi-C) technologies, we assembled the first chromosome-scale genome for S. caldwelli about 1.77 Gb in size, with a contig N50 length of 11.83 Mb and scaffold N50 length of 33.91 Mb. In total 1.72 Gb (97.01%) of the contig sequences were anchored onto fifty chromosomes with the longest scaffold being 56.20 Mb. Furthermore, proximately 49.41% of the genome was composed of repetitive elements. In total, 49,377 protein-coding genes were predicted, of which 47,724 (96.65%) genes have been functionally annotated. The high-quality chromosome-level reference genome and annotation are vital for supporting basic genetic studies and will be contribute to genetic structure, functional elucidation, evolutionary inquiry, and germplasm conservation for S. caldwelli.

Genome-wide identification of Gα family in grass carp (Ctenopharyngodon idella) and reproductive regulation functional characteristics of Cignaq

BACKGROUND

The Gα family plays a crucial role in the complex reproductive regulatory network of teleosts. However, the characterization and function of Gα family members, especially Gαq, remain poorly understood in teleosts. To analyze the characterization, expression, and function of grass carp (Ctenopharyngodon idella) Gαq, we identified the Gα family members in grass carp genome, and analyzed the expression, distribution, and signal transduction of Gαq/gnaq. We also explored the role of Gαq in the reproductive regulation of grass carp.

RESULTS

Our results showed that the grass carp genome contains 27 Gα genes with 46 isoforms, which are divided into four subfamilies: Gαs, Gαi/o, Gαq/11, and Gα12/13. The expression level of Cignaq in the testis was the highest and significantly higher than in other tissues, followed by the hypothalamus and brain. The luteinizing hormone receptor (LHR) was mainly localized to the nucleus in grass carp oocytes, with signals also present in follicular cells. In contrast, Gαq signal was mainly found in the cytoplasm of oocytes, with no signal in follicular cells. In the testis, Gαq and LHR were co-localized in the cytoplasm. Furthermore, the grass carp Gαq recombinant protein significantly promoted Cipgr expression.

CONCLUSIONS

These results provided preliminary evidence for understanding the role of Gαq in the reproductive regulation of teleosts.

Whole-Genome Sequencing Analyses Reveal the Evolution Mechanisms of Typical Biological Features of Decapterus maruadsi

Decapterus maruadsi is a typical representative of small pelagic fish characterized by fast growth rate, small body size, and high fecundity. It is a high-quality marine commercial fish with high nutritional value. However, the underlying genetics and genomics research focused on D. maruadsi is not comprehensive. Herein, a high-quality chromosome-level genome of a male D. maruadsi was assembled. The assembled genome length was 716.13 Mb with contig N50 of 19.70 Mb. Notably, we successfully anchored 95.73% contig sequences into 23 chromosomes with a total length of 685.54 Mb and a scaffold N50 of 30.77 Mb. A total of 22,716 protein-coding genes, 274.90 Mb repeat sequences, and 10,060 ncRNAs were predicted, among which 22,037 (97%) genes were successfully functionally annotated. The comparative genome analysis identified 459 unique, 73 expanded, and 52 contracted gene families. Moreover, 2804 genes were identified as candidates for positive selection, of which some that were related to the growth and development of bone, muscle, cardioid, and ovaries, such as some members of the TGF-β superfamily, were likely involved in the evolution of typical biological features in D. maruadsi. The study provides an accurate and complete chromosome-level reference genome for further genetic conservation, genomic-assisted breeding, and adaptive evolution research for D. maruadsi.

JunD functions as a transcription factor of IL-10 to regulate bacterial infectious inflammation in grass carp (Ctenopharyngodon idella)

IL-10 is a key anti-inflammatory mediator ensuring the protection of a host from excessive inflammation in response to pathogen infections, whose transcription or expression levels are tightly linked to the onset and progression of infectious diseases. An AP-1 family member called CiJunD was shown to be a transcription factor of IL-10 in grass carp (Ctenopharyngodon idella) in the current study. CiJunD protein harbored the conserved Jun and bZIP domains. Mutant experiments demonstrated that CiJunD bound to three specific sites on IL-10 promoter, i.e., 5'-ATTATTCATA-3', 5'-AGATGAGACATCT-3', and 5'-ATTATTCATC-3', mainly relying on the bZIP domain, and initiated IL-10 transcription. Expression data from the grass carp spleen infected by Aeromonas hydrophila and lipopolysaccharide (LPS) challenged spleen leukocytes indicated that the expressions of CiJunD and IL-10 were positively correlated, while the expression of pro-inflammatory cytokines, such as IL-1β, IL-6, IL-8, IFN-γ, and TNF-α, showed an overall downward trend when CiJunD and IL-10 peaked. The ability of CiJunD to down-regulate the production of pro-inflammatory cytokines and up-regulate the expression of IL-10, both with and without LPS stimulation, was confirmed by overexpression experiments. Meanwhile, the subcellular fractionation assay revealed that the nuclear translocation of CiJunD was significantly enhanced after the LPS challenge. Moreover, in vivo administration of grass carp with Oxamflatin, a potent agonist of JunD activity, could promote IL-10 but suppress the expression of pro-inflammatory cytokines. Intriguingly, tissue inflammation lesions and the survival rates of grass carp infected with A. hydrophila were also significantly improved by Oxamflatin administration. This work sheds light on the regulation mechanism by JunD of IL-10 expression and bacterial infectious inflammation for the first time, and it may present a viable method for preventing infectious diseases in fish by regulating IL-10 expression and inflammatory response.

Re-identification and characterization of grass carp Ctenopharyngodon idella TLR20

Toll-like receptors (TLRs) play a crucial role in the recognition of microbial-associated molecular patterns in the innate immune system. Fish TLRs have undergone significant gene expansion to adapt to complex aquatic environments. Among them, TLR20 from the TLR11 family actively responds to viral and bacterial invasions. Previous studies have reported two TLR20s in grass carp (Ctenopharyngodon idella), and in this study, we revised this conclusion. Based on the latest grass carp genome, we identified a new TLR20 member. These three TLR20s are arranged in tandem on chromosome 9, indicating that they are generated by gene duplication events. They were renamed CiTLR20.1 to CiTLR20.3 based on their chromosomal positions. The CiTLR20s in C. idella exhibit higher similarities with those in Danio rerio, Cyprinus carpio, and Megalobrama amblycephala, and lower similarities with those in other distantly related fish species. Selective pressure analysis revealed low conservation and negative evolution of TLR20s during evolution. The 3D structures of the three TLR20s showed significant differences, reflecting functional variations and different downstream adaptor molecule recruitment. Transcriptome data revealed tissue distribution differences of TLR20s, with TLR20.1 showing relatively low expression levels in all the tissues, while TLR20.2 and TLR20.3 showed higher expression in the head kidney, spleen, and gill. Additionally, TLR20.2 and TLR20.3 actively responded to GCRV-II infection, with higher upregulation of TLR20.2 in response to Aeromonas hydrophila challenge. In conclusion, this study corrected the number of grass carp TLR20 members and analyzed TLR20 from an evolutionary and structural perspective, exploring its role in antiviral and antibacterial defense. This study provides reference for future research on fish TLR20.

TLR7 neo-functionalizes to sense dsRNA and trigger antiviral and antibacterial immunity in non-tetrapod vertebrates

TLR7 plays a crucial role in sensing viral ssRNA and initiating immune responses. Piscine TLR7 also responds to dsRNA challenge. dsRNA exists in almost all the viruses at specific stages. However, the mechanism on sensing dsRNA by TLR7 remains unknown. In the present study, we employed Ctenopharyngodon idella TLR7 (CiTLR7) to systematically explore the immune functions and mechanisms in teleost. CiTLR7 can directly bind not only ssRNA but also dsRNA at different patches in lysosome, recruit MyD88 as adaptor, and activate the downstream IFN pathway via SLC15A4/TASLa/TASLb/IRF5/IRF7 complex for antiviral and antibacterial infections and AP-1 pathway for pro-inflammatory cytokines. The key binding sites for dsRNA are L29 and L811 in CiTLR7. Further, we found that the function on recognizing dsRNA by TLR7 emerges in pisciformes and loses in tetrapods in evolution. This is the first report on sensing both ssRNA and dsRNA by a TLR member.

SPLASH: A statistical, reference-free genomic algorithm unifies biological discovery

Today's genomics workflows typically require alignment to a reference sequence, which limits discovery. We introduce a unifying paradigm, SPLASH (Statistically Primary aLignment Agnostic Sequence Homing), which directly analyzes raw sequencing data, using a statistical test to detect a signature of regulation: sample-specific sequence variation. SPLASH detects many types of variation and can be efficiently run at scale. We show that SPLASH identifies complex mutation patterns in SARS-CoV-2, discovers regulated RNA isoforms at the single-cell level, detects the vast sequence diversity of adaptive immune receptors, and uncovers biology in non-model organisms undocumented in their reference genomes: geographic and seasonal variation and diatom association in eelgrass, an oceanic plant impacted by climate change, and tissue-specific transcripts in octopus. SPLASH is a unifying approach to genomic analysis that enables expansive discovery without metadata or references.

PacBio Full-Length Transcriptome of a Tetraploid Sinocyclocheilus multipunctatus Provides Insights into the Evolution of Cavefish

Sinocyclocheilus multipunctatus is a second-class nationally protected wild animal in China. As one of the cavefish, S. multipunctatus has strong adaptability to harsh subterranean environments. In this study, we used PacBio SMRT sequencing technology to generate a first representative full-length transcriptome for S. multipunctatus. Sequence clustering analysis obtained 232,126 full-length transcripts. Among all transcripts, 40,487 were annotated in public databases, while 70,300 microsatellites, 2384 transcription factors, and 16,321 long non-coding RNAs were identified. The phylogenetic tree showed that S. multipunctatus shows a closer relationship to Carassius auratus and Cyprinus carpio, phylogenetically diverging from the common ancestor ~14.74 million years ago (Mya). We also found that between 15.6 and 17.5 Mya, S. multipunctatus also experienced an additional whole-genome duplication (WGD) event, which may have promoted the species evolution of S. multipunctatus. Meanwhile, the overall rates of evolutionary of polyploid S. multipunctatus were significantly higher than those of the other cyprinids, and 220 positively selected genes (PSGs) were identified in two sub-genomes of S. multipunctatus. These PSGs are likely to fulfill critical roles in the process of adapting to diverse cave environments. This study has the potential to facilitate future investigations into the genomic characteristics of S. multipunctatus and provide valuable insights into revealing the evolutionary history of polyploid S. multipunctatus.

Chromosome-level genome assembly of Bactrocera correcta provides insights into its adaptation and invasion mechanisms

Bactrocera correcta is an invasive polyphagous pest with significant ecological and economic implications. Understanding its genetic characteristics and the molecular mechanisms that drive its rapid adaptation to new environments requires genomic information. In this study, we successfully assembled the chromosome-level genome of B. correcta using PacBio long-read sequencing, Illumina sequencing, and chromatin conformation capture (Hi-C) methods. The final genome assembly spans a total length of 702.65 Mb. We managed to anchor approximately 86.88% of the assembled contigs into 6 linkage groups, ranging from 17.97 Mb to 166.49 Mb. Additionally, our analysis predicted a total of 21,015 genes, with repetitive sequences accounting for 58.22% of the genome. We further identified retroelements and DNA transposons as the major contributors to the larger size of the B. correcta genome, constituting 36.06% and 30.92% of the repetitive sequences, respectively. Our divergence time estimation placed B. correcta's split from other Bactrocera species at around 5.99-16.71 million years ago. Through gene family analyses, we discovered significant expansions in sensing-related gene families (IR, GR), heat shock proteins (HSP60), and resistance-related gene families (ABC) in B. correcta compared to its closest relatives. Transcriptomic analysis revealed substantial upregulation of HSP genes, especially those from the HSP20 subfamily, in response to high temperatures. The availability of this reference genome serves as a foundation for the identification of precise target genes in B. correcta, facilitating molecular prevention and control strategies.

An Atlas of Grass Carp IgM+ B Cells in Homeostasis and Bacterial Infection Helps to Reveal the Unique Heterogeneity of B Cells in Early Vertebrates

Teleost B cells are primitive lymphocytes with both innate and adaptive immune functions. However, the heterogeneity and differentiation trajectory of teleost B cells remain largely unknown. In this study, the landscape of grass carp IgM+ (gcIgM+) B cells was revealed by single-cell RNA sequencing. The results showed that gcIgM+ B cells mainly comprise six populations: (im)mature B cells, innate B cells, proliferating B cells, plasma cells, CD22+ cells, and CD34+ cells, among which innate B cells and proliferating B cells were uncommon B cell subsets with, to our knowledge, new characteristics. Remarkably, three functional IgMs were discovered in grass carp, and a significant percentage of gcIgM+ B cells, especially plasma cells, expressed multiple Igμ genes (Igμ1, Igμ2, and/or Igμ3). More importantly, through single-cell sorting combined with Sanger sequencing, we found that distinct VHDJH recombination patterns of Igμ genes were present in single IgM+ B cells, indicating that individual teleost B cells might produce multiple Abs by coexpressing rearranged IgM subclass genes. Moreover, the percentage of IgM1highIgM2highIgM3high plasma cells increased significantly after bacterial infection, suggesting that individual plasma cells might tend to produce multiple IgMs to resist the infection in teleost fish. In summary, to our knowledge, this study not only helps to uncover the unique heterogeneity of B cells in early vertebrates but also provided significant new evidence supporting the recently proposed "one cell-multiple Abs" paradigm, challenging the classical rule of "one cell-one Ab."

[WITHDRAWN] SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery

The authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2022/497555. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi: https://doi.org/10.1101/2022.06.24.497555.

Circular RNAs in ferroptosis: regulation mechanism and potential clinical application in disease

Ferroptosis, an iron-dependent non-apoptotic form of cell death, is reportedly involved in the pathogenesis of various diseases, particularly tumors, organ injury, and degenerative pathologies. Several signaling molecules and pathways have been found to be involved in the regulation of ferroptosis, including polyunsaturated fatty acid peroxidation, glutathione/glutathione peroxidase 4, the cysteine/glutamate antiporter system Xc-, ferroptosis suppressor protein 1/ubiquinone, and iron metabolism. An increasing amount of evidence suggests that circular RNAs (circRNAs), which have a stable circular structure, play important regulatory roles in the ferroptosis pathways that contribute to disease progression. Hence, ferroptosis-inhibiting and ferroptosis-stimulating circRNAs have potential as novel diagnostic markers or therapeutic targets for cancers, infarctions, organ injuries, and diabetes complications linked to ferroptosis. In this review, we summarize the roles that circRNAs play in the molecular mechanisms and regulatory networks of ferroptosis and their potential clinical applications in ferroptosis-related diseases. This review furthers our understanding of the roles of ferroptosis-related circRNAs and provides new perspectives on ferroptosis regulation and new directions for the diagnosis, treatment, and prognosis of ferroptosis-related diseases.

An efficient, fast and inexpensive method for genomic DNA extraction of fish tissue

BACKGROUND

DNA extraction is an essential step for many genetic techniques like PCR and other molecular analyses. Based on the method of extraction and type of tissue used, the quality of extracted DNA for genetic studies varies. An appropriate extraction method is evaluated by the high concentration and purity of DNA. Thus, this study aimed to find a more efficient and effective method of DNA extraction from fish tissues and compare it to commercially available kits.

METHODS AND RESULTS

A total of 200 fish tissue samples were extracted using each method and then validated with restriction enzymes and PCR amplification. The result revealed that the mean quantity of the isolated genomic DNA, when measured by Nanodrop for grass and common carp, was estimated at (624.41 ± 34.51) µg/ml and (651.27 ± 46.31) µg/ml, respectively, and the purity of this DNA was about (1.83 ± 0.04) and (1.88 ± 0.03) respectively, as compared to commercial extraction kits. Furthermore, gel electrophoresis was performed on the PCR-ready DNA, and the results were confirmed with restriction enzymes and PCR amplification. Based on results obtained from restriction enzymes and PCR analysis, it was determined that no significant inhibitors existed for the enzymes that were used in molecular biology reactions.

CONCLUSION

As a result, this technique provides an efficient and versatile alternative to the traditional method for obtaining bulk amounts of highly qualified DNA from fish tissue and can be easily used for subsequent analyses such as PCR and several molecular experiments on other fish species.

Contribution bias of parental genomes to the hybrid lineages of black Amur bream and topmouth culter revealed by low-coverage whole-genome sequencing

Interspecific hybridization has the potential to increase animal genetic diversity, enable the introgression of advantageous genetic variation, and even create hybrid lineages. Using the low-coverage whole-genome sequencing data of black Amur bream (Megalobrama terminalis [SJ]), topmouth culter (Culter alburnus [QZ]), and their hybrid progeny, we focused on the sequence variation and contribution bias to the genomic composition of the hybrid lineages of SJ♀ × QZ♂ [ZJ] and QZ♀ × SJ♂ [FJ]. Both mash-based genetic distance analysis and variant analysis based on various reference genomes revealed that the hybrid lineages' genomes are more prone to QZ composition. Furthermore, we assess the degree of subgenomic intermixing between parents QZ and SJ in the FJ and ZJ hybrid lineages. In the Jaccard index-zero genomic area, 89.41% of the genomic region in ZJ and 90.23% in FJ are entirely from one of the parental genomes. This genomic area is primarily from QZ, regardless of FJ or ZJ. In FJ, the proportion is 55.70%; in ZJ, the proportion is 54.60%. Using the reference-free variant discovery tool, we identified two InDel markers (Both were SSR-type InDel markers) and one (T/A)-type SNP marker that displayed differences in agarose electrophoresis. Our current findings suggest that parental genomic contribution bias leads to an imbalance in the genomic composition of hybrid lineages. The genomic composition bias is connected to species but not maternal effects, giving insights into the development of vertebrate genomes shortly after hybridization.

Comparative study on antibacterial characteristics of the multiple liver expressed antimicrobial peptides (LEAPs) in teleost fish

Antimicrobial peptides are important components of the host innate immune system, forming the first line of defense against infectious microorganisms. Among them, liver-expressed antimicrobial peptides (LEAPs) are a family of antimicrobial peptides that widely exist in vertebrates. LEAPs include two types, named LEAP-1 and LEAP-2, and many teleost fish have two or more LEAP-2s. In this study, LEAP-2C from rainbow trout and grass carp were discovered, both of which are composed of 3 exons and 2 introns. The antibacterial functions of the multiple LEAPs were systematically compared in rainbow trout and grass carp. The gene expression pattern revealed that rainbow trout and grass carp LEAP-1, LEAP-2A, LEAP-2B and/or LEAP-2C were differentially expressed in various tissues/organs, mainly in liver. After bacterial infection, the expression levels of LEAP-1, LEAP-2A, LEAP-2B and/or LEAP-2C in the liver and gut of rainbow trout and grass carp increased to varying degrees. Moreover, the antibacterial assay and bacterial membrane permeability assay showed that rainbow trout and grass carp LEAP-1, LEAP-2A, LEAP-2B and LEAP-2C all have antibacterial activities against a variety of Gram-positive and Gram-negative bacteria with varying levels through membrane rupture. Furthermore, cell transfection assay showed that only rainbow trout LEAP-1, but not LEAP-2, can lead to the internalization of ferroportin, the only iron exporter on cell surface, indicating that only LEAP-1 possess iron metabolism regulation activity in teleost fish. Taken together, this study systematically compared the antibacterial function of LEAPs in teleost fish and the results suggest that multiple LEAPs can enhance the immunity of teleost fish through different expression patterns and different antibacterial activities to various bacteria.

Genome-wide survey reveals the phylogenomic relationships of Chirolophisjaponicus Herzenstein, 1890 (Stichaeidae, Perciformes)

Fish are the largest vertebrate group, consisting of more than 30 000 species with important ecological and economical value, while less than 3% of fish genomes have been published. Herein, a fish, Chirolophisjaponicus, was sequenced using the next-generation sequencing. Approximately 595.7 megabase pair of the C.japonicus genome was assembled (49 901 contigs with 42.61% GC contents), leading to a prediction of 46 729 protein-coding gene models. A total of 554 136 simple sequence repeats was identified in the whole genome of C.japonicus, and dinucleotide microsatellite motifs were the most abundant, accounting for 59.49%. Phylogenomic analysis of 16 genomes based on the 694 single-copy genes suggests that C.japonicus is closely related with Anarrhichthysocellatus, Cebidichthysviolaceus, and Pholisgunnellus. The results provide more thorough genetic information of C.japonicus and a theoretical basis and reference for further genome-wide analysis.

Chromosome-Level Assembly of Male Opsariichthys bidens Genome Provides Insights into the Regulation of the GnRH Signaling Pathway and Genome Evolution

The hook snout carp Opsariichthys bidens is an important farmed fish in East Asia that shows sexual dimorphism in growth, with males growing faster and larger than females. To understand these complex traits and improve molecular breeding, chromosome-level genome assembly of male O. bidens was performed using Illumina, Nanopore, and Hi-C sequencing. The 992.9 Mb genome sequences with a contig N50 of 5.2 Mb were anchored to 38 chromosomes corresponding to male karyotypes. Of 30,922 functionally annotated genes, 97.5% of BUSCO genes were completely detected. Genome evolution analysis showed that the expanded and contracted gene families in the male O. bidens genome were enriched in 76 KEGG pathways, and 78 expanded genes were involved in the GnRH signaling pathway that regulates the synthesis and secretion of luteinizing hormone and glycoprotein hormones, further acting on male growth by inducing growth hormone. Compared to the released female O. bidens genome, the number of annotated genes in males was much higher (23,992). The male chromosome LG06 exhibited over 97% identity with the female GH14/GH38. Male-specific genes were identified for LG06, where structural variation, including deletions and insertions, occurred at a lower rate, suggesting a centric fusion of acrocentric chromosomes GH14 and GH38. The genome-synteny analysis uncovered significant inter-chromosome conservation between male O. bidens and grass carp, the former originating from ancestral chromosome breakage to increase the chromosome number. Our results provide a valuable genetic resource for studying the regulation of sexual dimorphism, sex-determining mechanisms, and molecular-guided breeding of O. bidens.

Animal board invited review: Widespread adoption of genetic technologies is key to sustainable expansion of global aquaculture

•

The extent of application of genetic technologies to aquaculture production varies widely by species and geography.

•

Achieving a more universal application of seed derived from scientifically based breeding programmes is an important goal in order to meet increasing global demands for seafood production.

•

This article reviews the status of genetic technologies across the world’s top 10 highly produced species.

•

Opportunities and barriers to achieving broad-scale uptake of genetic technologies in global aquaculture are discussed.

•

A future outlook for potential disruptive genetic technologies and how they might affect global aquaculture production is given.

Aquaculture production comprises a diverse range of species, geographies, and farming systems. The application of genetics and breeding technologies towards improved production is highly variable, ranging from the use of wild-sourced seed through to advanced family breeding programmes augmented by genomic techniques. This technical variation exists across some of the most highly produced species globally, with several of the top ten global species by volume generally lacking well-managed breeding programmes. Given the well-documented incremental and cumulative benefits of genetic improvement on production, this is a major missed opportunity. This short review focusses on (i) the status of application of selective breeding in the world’s most produced aquaculture species, (ii) the range of genetic technologies available and the opportunities they present, and (iii) a future outlook towards realising the potential contribution of genetic technologies to aquaculture sustainability and global food security.

Molecular and Functional Analyses of the Primordial Costimulatory Molecule CD80/86 and Its Receptors CD28 and CD152 (CTLA-4) in a Teleost Fish

The moderate activation of T cells in mammals requires the costimulatory molecules, CD80 and CD86, on antigen-presenting cells to interact with their respective T cell receptors, CD28 and CD152 (CTLA-4), to promote costimulatory signals. In contrast, teleost fish (except salmonids) only possess CD80/86 as their sole primordial costimulatory molecule. However, the mechanism, which underlies the interaction between CD80/86 and its receptors CD28 and CD152 still requires elucidation. In this study, we cloned and identified the CD80/86, CD28, and CD152 genes of the grass carp (Ctenopharyngodon idella). The mRNA expression analysis showed that CD80/86, CD28, and CD152 were constitutively expressed in various tissues. Further analysis revealed that CD80/86 was highly expressed in IgM⁺ B cells. Conversely, CD28 and CD152 were highly expressed in CD4⁺ and CD8⁺ T cells. Subcellular localization illustrated that CD80/86, CD28, and CD152 are all located on the cell membrane. A yeast two-hybrid assay exhibited that CD80/86 can bind with both CD28 and CD152. In vivo assay showed that the expression of CD80/86 was rapidly upregulated in Aeromonas hydrophila infected fish compared to the control fish. However, the expression of CD28 and CD152 presented the inverse trend, suggesting that teleost fish may regulate T cell activation through the differential expression of CD28 and CD152. Importantly, we discovered that T cells were more likely to be activated by A. hydrophila after CD152 was blocked by anti-CD152 antibodies. This suggests that the teleost CD152 is an inhibitory receptor of T cell activation, which is similar to the mammalian CD152. Overall, this study begins to define the interaction feature between primordial CD80/86 and its receptors CD28 and CD152 in teleost fish, alongside providing a cross-species understanding of the evolution of the costimulatory signals throughout vertebrates.