To understand the molecular mechanisms and adaptive strategies of holocentrid fish, we sequenced the mitogenome of eight species within the family Holocentridae and compared them with six other holocentrid species. The mitogenomes were found to be 16,507–16,639 bp in length and to encode 37 typical mitochondrial genes, including 13 PCGs, two ribosomal RNAs, and 22 transfer RNA genes. Structurally, the gene arrangement, base composition, codon usage, tRNA size, and putative secondary structures were comparable between species. Of the 13 PCGs, nad6 was the most specific gene that exhibited negative AT-skews and positive GC-skews. Most of the genes begin with the standard codon ATG, except cox1, which begins with the codon GTG. By examining their phylogeny, Sargocentron and Neoniphon were verified to be closely related and to belong to the same subfamily Holocentrinae, while Myripristis and Ostichthys belong to the other subfamily Myripristinae. The subfamilies were clearly distinguished by high-confidence-supported clades, which provide evidence to explain the differences in morphology and feeding habits between the two subfamilies. Selection pressure analysis indicated that all PCGs were subject to purifying selection. Overall, our study provides valuable insight into the habiting behavior, evolution, and ecological roles of these important marine fish.

Background: Egg quality is a major concern in fish reproduction and development. An effective evaluation of egg quality prior to fertilization is helpful in improving the fertilization rate and survival rate of the larva. In this study, we aim to identify quality instructors from the combination study of fertilization rate, hatching rate, embryo malformation rate and gene expression profile. Results: Eggs from 25 female fish were fertilized with sperm from the same fish. The egg quality was determined by the fertilization rates, hatching rate and embryo malformation rate and divided into three categories, low-quality (< 35%), medium-quality (35 to 75%), and high-quality (> 75%). Due to the distinct difference in fertilization, hatching and embryo malformation rate between low-quality eggs and high-quality eggs, these two groups were considered for the identification of quality markers. Then RNA-seq was performed for the originally preserved eggs from the low-quality group and high-quality group. We profiled the differentially expressed genes and identified a group of RNA-binding proteins (RBPs) as potential regulators. Gene function analysis indicated that most of these genes were enriched in RNA-regulated pathways including RNA processing. The RBPs were more related to egg quality from the PLS-DA analysis. Finally, gene expression was validated by qRT-PCR. Conclusions: We found a cluster of RBP genes including igf2bp3, zar1, elavl1, rbm25b and related regulatory factors including yy1, sirt1, anp32e, btg4 as novel biomarkers of egg quality.

Paternal factors play an important role in embryonic morphogenesis and contribute to sexual dimorphism in development. To assess the effect of paternal DNA on sexual dimorphism of embryonic genome activation, we compared X and Y sperm and different sexes of embryos before sex determination. Through transcriptome sequencing (RNA-seq) and whole-genome bisulfite sequencing (WGBS) of X and Y sperm, we found a big proportion of upregulated genes in Y sperm, supported by the observation that genome-wide DNA methylation level is slightly lower than in X sperm. Cytokine–cytokine receptor interaction, TGF-beta, and toll-like receptor pathways play important roles in spermatogenesis. Through whole-genome re-sequencing (WGRS) of parental fish and RNA-seq of five early embryonic stages, we found the low-blastocyst time point is a key to maternal transcriptome degradation and zygotic genome activation. Generally, sexual differences emerged from the bud stage. Moreover, through integrated analysis of paternal SNPs and gene expression, we evaluated the influence of paternal inheritance on sexual dimorphism of genome activation. Besides, we screened out gata6 and ddx5 as potential instructors for early sex determination and gonad development in yellow catfish. This work is meaningful for revealing the molecular mechanisms of sex determination and sexual dimorphism of fish species.

TET2 is a member of the ten-eleven translocation (Tet) family of DNA dioxygenases that regulate gene expression by promoting DNA demethylation (enzymatic activity) and partnering with chromatin regulatory complexes (nonenzymatic functions). TET2 is highly expressed in the hematopoietic lineage where its molecular functions are subject of continuous investigations due to the prevalence of TET2 mutations in hematologic malignancies. Previously, we have implicated Tet2 catalytic and noncatalytic functions in regulation of the myeloid and lymphoid lineages, respectively. However, the impact of these functions of Tet2 on hematopoiesis as the bone marrow ages remains unclear. Here, we conducted comparative transplantations and transcriptomic analyses of 3-, 6-, 9-, and 12-month-old Tet2 catalytic mutant (Mut) and knockout (KO) bone marrow. Tet2 Mut bone marrow of all ages exclusively caused hematopoietic disorders of the myeloid lineage. In contrast, young Tet2 KO bone marrow developed both lymphoid and myeloid diseases, while older Tet2 KO bone marrow predominantly elicited myeloid disorders with shorter latency than age-matched Tet2 Mut bone marrow. We identified robust gene dysregulation in Tet2 KO Lin^- cells at 6 months that involved lymphoma and myelodysplastic syndrome and/or leukemia-causing genes, many of which were hypermethylated early in life. There was a shift from lymphoid to myeloid gene deregulation in Tet2 KO Lin^- cells with age, underpinning the higher incidence of myeloid diseases. These findings expand on the dynamic regulation of bone marrow by Tet2 and show that its catalytic dependent and independent roles have distinct impacts on myeloid and lymphoid lineages with age.

The maternal-to-zygotic transition (MZT) is a fundamental process in vertebrate embryogenesis, involving the clearance of maternal mRNA and activation of the zygotic genome. Orchestration of maternal mRNA stability ensures early embryogenesis. Recently, some germ plasm (GP) factors have been demonstrated to regulate the stability of maternal mRNA. Bucky ball (Buc) functions as a zebrafish GP organizer. However, it remains unclear whether Buc also protects maternal mRNAs from widespread decay in early embryos. Here, we report that overexpression of buc results in delayed maternal mRNA degradation and a concomitant delay in embryonic development, whereas buc knockout leads to accelerated maternal mRNA degradation and severe developmental defects, suggesting that both gain and loss of buc perturb early developmental programs. Mechanistically, this regulatory mechanism of Buc on maternal mRNA is mediated through the expression of RNA-binding protein Igf2bp3. Together, our findings suggest that the GP organizer Buc may stabilize maternal mRNAs in coordination with Igf2bp3, thereby contributing to the maintenance of maternal mRNA required for proper embryonic development during the MZT. This study expands the functional scope of Buc beyond GP assembly and reveals its critical role in safeguarding maternal mRNA integrity to ensure proper embryo development.

Over the past decade, the continuous and rapid advances in bioinformatics have led to an increasingly common use of molecular sequence comparison for phylogenetic analysis. However, the use of multi-software and cross-platform strategies has increased the complexity of phylogenetic tree estimation. Therefore, the development and application of streamlined phylogenetic analysis tools are growing in significance in the field of biology. Particularly for genomes with relatively short sequences, there is a lack of simple and integrative tools for phylogenetic analysis. In this study, we present CamlTree (Concatenated alignments maximum-likelihood tree), a user-friendly desktop software designed to simplify phylogenetic analysis for viral and mitochondrial genomes, ultimately facilitating related research. CamlTree provides a workflow including gene concatenation (or coalescence), sequence alignment, alignment optimization, and the estimation of phylogenetic trees using both maximum-likelihood (ML) and Bayesian inference (BI) methods. CamlTree was written in TypeScript and developed using the Electron framework. It offers a primarily user-friendly interface based on the React framework. CamlTree software has been released for the Windows OS. It integrates several popular analysis tools to optimize and simplify the process of estimating polygenic phylogenetic trees. The establishment of software can assist researchers in reducing their workload and enhancing data processing efficiency, enabling them to expedite their research progress. The software, along with a detailed user manual, is available at https://github.com/BioCrossCoder/camltree .