Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献

Benzo[a]pyrene (BaP), a polycyclic aromatic hydrocarbon from incomplete combustion, builds up in coastal regions through river runoff, atmospheric deposition, and coastal activities. BaP's lipophilicity and stability lead to persistent environmental impacts due to its resistance to degradation. The economically valuable golden cuttlefish, Sepia esculenta, often spawns and hatches in shallow waters, making it prone to BaP exposure. This study employs transcriptomic analysis to initially investigate juvenile golden cuttlefish's response to BaP. The results indicate that BaP exposure significantly affects various physiological and molecular functions of the juveniles, particularly affecting pathways related to immune and inflammatory responses, metabolic regulation, and nervous system functions. Functional enrichment and PPI network analyses identified key genes such as HSGALT-like, ASAH1-like, and GTL-like in the BaP response. These genes exhibited a suppressive trend during short-term exposure, indicating that BaP exposure may influence lipid metabolism, energy conversion, and digestive functions at the genetic level, which could further disrupt the overall physiological state and developmental processes of juvenile golden cuttlefish. The study offers novel insights into BaP's effects on juvenile golden cuttlefish and marine life, aiding marine ecosystem and biodiversity conservation.

With the ongoing intensification of global warming, thermal stress poses significant challenges to tilapia aquaculture. However, the molecular mechanisms underlying the cardiac response of tilapia to high temperatures remain largely unexplored. To address this knowledge gap, we investigated the effects of high-temperature stress on the transcriptomic landscape of the tilapia heart. RNA sequencing was performed on the hearts of Oreochromis aureus (AR), Oreochromis niloticus (NL), and hybrids (O. niloticus ♀ × O. aureus ♂, AN) under treatments of 28 °C, 36 °C, and 39 °C. Using a multi-method approach, including Differentially Expressed Genes analysis, Weighted Gene Co-expression Network Analysis, Fuzzy C-Means, Self-Organizing Map, and Support Vector Machine-Recursive Feature Elimination, we identified six marker genes at 39 °C (AR: ptges3, tuba1a; NL: ran, tcima; AN: slc16a1, fam184b). These genes exhibited strong positive correlations and increased expression under high-temperature conditions. Gene Set Enrichment Analysis and GENIE3 revealed that these marker genes closely regulate three cardiovascular-related pathways: adrenergic signaling in cardiomyocytes, vascular smooth muscle contraction, and cardiac muscle contraction. We hypothesize that the synergistic inhibition of these pathways by marker genes leads to the deterioration of cardiovascular function. In summary, thermal stress activates marker genes, which in turn inhibit cardiovascular pathways, impairing cardiac performance. We propose that these marker genes could serve as dynamic thermal indicators of cardiac performance in tilapia. Additionally, our findings provide theoretical support for improving the management of tilapia farming under high-temperature stress.

Sea cucumbers, marine benthic invertebrates, play crucial roles in maintaining the stability of marine ecosystems and hold key evolutionary positions. However, information regarding their genomes remains limited. Here, we conducted genome survey analyses on seven species from four orders. Results indicated that Colochirus anceps, Colochirus quadrangularis, and Pseudocolochirus violaceus within the order Dendrochirotida have significantly larger genomes (2238–3754 Mbp) compared to conventional sea cucumber genomes, accompanied by a very high proportion of repeat sequences (69.39–72.52 %). While Holothuria edulis and Holothuria atra exhibited similar genome sizes comparable to those of other species within the order Holothuriida, heterozygosity and repeat content varied among all the six species in this order. The representative species Apostichopus californicus of the order Synallactida possesses the smallest genome size (573.45Mbp) within its order, but its heterozygosity (2.24 %) is significantly higher than that of other species. The representative species Synapta maculata of the order Apodida exhibited a normal genome size (900.97 Mbp), lower proportion of repeat sequences (42.19 %), and lower heterozygosity (0.84 %), making it the species with the least challenges for genome sequencing and assembly in the future among all surveyed species. Subsequently, we compiled genomic information from a total of 19 sea cucumber genomes, both newly sequenced and previously reported, revealing a significant linear relationship (P = 0.0001) between genome size and the proportion of repeat sequences in sea cucumbers. Additionally, phylogenetic and comparative analysis of mitochondrial genomes among them indicated extensive rearrangements within the order Apodida, leading to significant discrepancies between mitochondrial and nuclear genome phylogenies.