Ming Li

The Chinese bahaba (Bahaba taipingensis) is a critically endangered species found in the coastal waters of the South China Sea, which has garnered significant attention due to its ecological, economic, and medicinal value. In this study, we present a high-quality genome assembly of the Chinese bahaba. By employing a combination of Hifi, Nanopore UL and Hi-C data, we assembled 686.86 Mb genome sequences, consisting of 83 contigs with a contig N50 of 30.02 Mb. Then, the initial assembly was further anchored onto 24 chromosomes, of which only 2 chromosomes have gaps. The enrichment analysis of expanded gene families revealed the immune system characteristics in Sciaenidae fish and Chinese bahaba. Notably, the fibrinogen complex of expanded gene families in Chinese bahaba, along with multiple GO terms related to ion binding, suggested potential roles in coagulation processes. An analysis of selection pressure revealed 47 fast-evolving genes, including tcn2 and cd44, which may participate in hematopoiesis. The RNA-seq data from 9 tissues indicated the higher expression level of col1a1 and col1a2 in swim bladder, which may contribute to the massive collagen deposition. The assembled genome and transcriptome will provide insights into the genetic basis of key biological traits, population genetics, and evolutionary history.

Phosphorylation is a post-translational modification that contributes to versatile protein functions in spermatogenesis, and the variations they generate usually results in abnormal spermatogenesis or sperm dysfunction. The sex-reversal phenomenon exists in Chinese tongue sole under certain conditions such that individuals with a ZW genotype can acquire a male phenotype and are thus called pseudomales. Pseudomale tongue sole can reach sexual maturity but produce only Z-type sperm, and the Z sperm carries paternal epigenetic information. Whether phosphorylation plays a role in the sperm abnormality of pseudomales is unknown. In this study, a phosphoproteomic analysis was performed to compare protein phosphorylation profiles between pseudomale and male testes. Altogether, we identified 14,253 phosphopeptides matching with 4843 proteins, with 1329 differentially phosphorylated peptides corresponding to 1045 differentially phosphorylated proteins (DPPs). Phosphorylation at 781 sites was upregulated and at 548 sites was downregulated. Four motifs were identified among differentially phosphorylated peptides, which were “SP”, “SD”, “RxxS”, and “TP”. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that the cell cycle and DNA/RNA processing were significantly enriched with the genes encoding DPPs. To analyze DPP function in depth, a protein-protein interaction network was constructed, and Ran-binding protein 2 was found to play a central role in spermatogenesis by regulating several processes such as the cell cycle, eukaryotic translation, ubiquitination, and minichromosome maintenance. In kinase-associated network analyses, two “mitogen-activated protein kinase (Mapk)-centered” clusters were identified that may account for abnormal spermatogenesis in pseudomales. One cluster was centered on Mapk6, which predominantly regulated the cell cycle by interacting with several cyclin-dependent kinases, and the other was centered on the “testis-expressed kinase 1-like (Tesk1l)/Pim1l-Mapk4l- testis-expressed 14 (Tex14)” kinase cascade, which might contribute to spermatogenesis by regulating β-catenin. Taken together, these data suggested the new candidates involved in pseudomale sperm abnormalities and provided clues to discover the phosphorylated regulatory mechanism underlying tongue sole spermatogenesis.

Chinese tongue sole (Cynoglossus semilaevis) has a ZZ/ZW sex determination system, but the genotypic female (ZW) can be sex-reversed into phenotypic males, namely, pseudomales. Pseudomale fish can produce only Z-type sperm but not W sperm. However, the molecular mechanism is unclear. To screen the key genes involved in pseudomale sperm abnormalities, we analysed the transcriptomic profiles of pseudomale and male sperm. In comparison to male sperm, 592 differentially expressed genes (DEGs) were identified in pseudomale sperm, including 499 upregulated and 93 downregulated genes. KEGG analysis indicated that the FoxO signalling pathway, especially the foxo3a and foxo6-like genes, may play an important role in spermatogenesis. The DEGs were mainly distributed on sex chromosomes, with 158 downregulated genes on the Z chromosome and 41 upregulated genes on the W chromosome. A specific area (14–15 M) on the Z chromosome was identified, which enriched eight DEGs inside the ~1 M region. In addition, there were five gene alleles on the sex chromosomes, which showed the opposite transcription pattern (upregulated for the W allele, downregulated for the Z allele). This study has provided valuable data for screening candidate genes involved in the pseudomale sperm abnormality.

Fishes of the genus Seriola are widely farmed and highly valued in global aquaculture production. To further understand their economically important traits and help improve aquaculture product quality and sustainability, we performed a chromosome‐level genome construction for Seriola aureovittata. Combining two technologies, PacBio and BGISEQ‐500, we assembled 649.86 Mb S. aureovittata genome sequences with a contig N50 of 22.21 Mb, and 98% of BUSCO genes were detected in total. The initial assembly was then further scaffolded into 24 pseudochromosomes using Hi‐C data, indicating the high quality of the genome. Genome evolution analysis showed that many genes related to fatty acid metabolism and oxygen binding, or transport were expanded, which provided insights into the metabolic characteristics of fatty acids and efficient oxygen transport. Based on the genome data, we confirmed the evolutionary relationship of S. aureovittata, S. dorsalis and S. lalandi and identified chr12 as the putative sex chromosome of S. aureovittata. Our chromosome‐level genome assembly provides a genetic foundation for the phylogenetic and taxonomic investigation of different Seriola species. Moreover, the genome will provide an important genomic resource for further biological and aquaculture studies of S. aureovittata.

The complete mitochondrial DNA sequence of Triplophysa venusta was determined using a PCR-based method in our present study. The genome is totally 16 574 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, and 1 non-coding control region. The overall base composition of T. venusta is A 27.8%, T 26.9%, C 26.9%, and G 18.4%, with an A + T bias of 54.7%. This complete mitogenome of T. venusta provides a basic data for studies on species identification, molecular systematics, and conservation genetics. The phylogenetic trees consistently showed that the Family Cobitidae was divided into three major clades: the subfamily Botiidae, the subfamily Nemaeheilidae, and the subfamily Cobitinae. Cobitinae and Nomaeheilidae formed a main Loach clade, with Botiidae clustered at the basal.

Interactions between the co-stimulatory molecule programmed death 1 (PD-1) and its ligands, PD-L1 and PD-L2, constrain T-cell responses and help maintain peripheral tolerance. Glomerulonephritis can result from a variety of antigens, both self and foreign, and from humoural and cellular effector responses. These studies aimed to define the role of PD1 and its ligands in circulating immune complex glomerulonephritis induced by immunity to a foreign antigen. Immune complex glomerulonephritis was initiated by injecting BALB/c mice with horse spleen apoferritin intraperitoneally daily for 14 days. Inhibitory anti-mouse PD-1, anti-PD-L1 or anti-PD-L2 antibodies were administered every other day. Renal disease and immune responses were studied. Daily injection of horse spleen apoferritin-induced proliferative immune complex glomerulonephritis in control antibody-treated mice, but inhibiting PD-1 did not augment renal injury. Specifically, blocking PD-1 did not increase serum antigen-specific antibodies or increase glomerular immunoglobulin G deposition, the hallmark of injury in this model. Furthermore, C3 deposition was unaffected and glomerular macrophages were reduced after anti-PD-1 antibodies. However, anti-PD-1 administration did increase splenocyte proliferation and cytokine production including interferon-γ, interleukin (IL)-4, and IL-17, but not IL-10. Neutralizing either PD-L1 or PD-L2 alone did not result in major alterations in renal injury. The endogenous PD-1/PD-L pathway does not limit acute experimental foreign antigen-induced circulating immune complex glomerulonephritis.