Transcriptome analysis of ovarian maturation in a chondrostei Chinese sturgeon Acipenser sinensis

Effect of larval rearing temperature on steroidogenesis pathway development in winter flounder (Pseudopleuronectes americanus) early life history

Winter flounder (Pseudopleuronectes americanus) is a North Atlantic flatfish that inhabits cold-water environments already affected by global warming. Flatfishes are particularly sensitive during their juvenile stage to a phenomenon known as temperature-dependent sex determination (TSD). In this study, we hypothesized that many genes involved in the steroidogenesis pathway are already expressed at the larval stage in winter flounder and that temperature conditions may influence this pathway prior to the juvenile stage, which is usually considered the TSD-sensitive period. We also hypothesized that temperature effects on the steroidogenesis pathway may carry over from the larval to the juvenile stage. We surveyed three cohorts issued from three different spawning events during spring. Rearing temperature and salinity conditions followed seasonal conditions in the St. Lawrence Estuary (Québec, Canada). As a result, cohorts were exposed to different temperature regimes during egg and larval development. Once metamorphosis occurred, all juveniles were held at a stable temperature of 10.1 ± 0.8 °C. Larvae were sampled at 20, 30, and, 40 days post-hatching and juveniles at one and two months post-metamorphosis. RNA was extracted from these individuals and then sequenced. Transcriptome analysis showed clear differentiation between larvae and juveniles. Gene expression patterns showed that the steroidogenesis pathway, including genes involved in gonadal differentiation, was influenced by temperature during larval development, which indicates that sexual determination at the cellular level is an early process in winter flounder development. Carry-over effects of larval rearing temperature conditions were present at the juvenile stage, with an increased number of genes involved in the steroidogenesis pathway being affected. Altogether, our study highlights the important role of larval development and temperature exposure on the transcriptome of winter flounder.

Transcript annotation of Chinese sturgeon (Acipenser sinensis) using Iso-seq and RNA-seq data

Chinese sturgeon (Acipenser sinensis) is a critically endangered fish inhabiting the Yangtze River and Chinese coastal waters. Numerous research projects and conservation efforts have focused on artificial propagation and release to restore this endangered species. However, genomic and full-length transcriptomic sequencing of Chinese sturgeon has rarely been reported. In this study, a total of 10 Chinese sturgeon tissues were used for PacBio Iso-seq and RNA-seq analyses. A total of 19,538 full-length transcripts were obtained with sizes from 51 bp to 7,033 bp. Moreover, cluster analysis of gene families and phylogenetic analysis of 14 species were performed. Furthermore, lncRNAs and coding sequence (CDS) were identified in all Chinese sturgeon tissues. Finally, gene expression profiles and differentially expressed genes (DEGs) were analyzed among 10 tissues in Chinese sturgeon. Taken together, full-length transcripts and the gene expression profile from Chinese sturgeon tissues will provide gene sequences and expression information for future functional genomic study and be very helpful for comprehensive understanding of the genetic mechanism of endangerment in Chinese sturgeon.

Transcriptome Analysis Provides Insights into Copulation, Fertilization, and Gestation in Sebastes schlegelii

Among the viviparous marine teleosts of China, the black rockfish (Sebastes schlegelii Hilgendorf) is one of the most economically important. In addition to copulation and internal fertilization, it features lengthy sperm storage in the female ovary as well as a high rate of abortion. A network of gene regulation is necessary for these processes. To elucidate the mechanisms of copulation, fertilization, and gestation, it is essential to determine the genetic basis of viviparous teleost oogenesis and embryogenesis. In this study, we analyzed the transcriptome of the ovary during different developmental phases to investigate the dynamic changes that occur. We constructed 24 ovary transcriptomes. In order to investigate the regulation of embryogenesis, differentially expressed genes (DEGs) with specific expression patterns were subjected to gene ontology annotation, pathway analyses, and weighted gene co-expression network analysis (WGCNA). The up-regulated genes were significantly enriched in focal adhesion, regulation of the actin cytoskeleton, Wnt, and ECM-receptor interaction signaling pathways. As a result of our study, we provide omics evidence for copulation, fertilization, and gestation in viviparous marine teleosts. Decoding the S. schlegelii gene regulation network, as well as providing new insights into embryogenesis, is highly valuable to researchers in the marine teleost reproduction sciences.